NAMD Papers and Citations
A list of papers citing NAMD is included below.
How to Cite NAMD
The NAMD License Agreement specifies that any reports or published results obtained with NAMD shall acknowledge its use and credit the developers as:
"NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."
Any published work which utilizes NAMD shall include the following reference:
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal
Electronic documents shall include a direct link to the official NAMD page:
Proper citation is essential to continued NIH funding for NAMD development, as it is a primary way in which we demonstrate the value of our software to the scientific community. Thank you for your attention to these details.
Papers About NAMD
Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kale, James C.Phillips, and Chris Harrison.
Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime.
In Proceedings of the 2011 ACM/IEEE Conference on Supercomputing (SC11), 2011.
abstract,
conference
Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell, Jr., Klaus Schulten, and Benoit Roux.
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD.
J. Phys. Chem. Lett., Vol. 2, pp. 87-92, 2011.
abstract,
journal
Abhinav Bhatele, Laxmikant V. Kale and Sameer Kumar.
Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications.
In Proceedings of 23rd ACM International Conference on Supercomputing (ICS), 2009.
abstract
James C. Phillips, John E. Stone, and Klaus Schulten.
Adapting a message-driven parallel application to GPU-accelerated clusters.
In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC08), 2008.
abstract,
conference
Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale.
Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms.
In Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008.
abstract
John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten.
Accelerating molecular modeling applications with graphics processors.
Journal of Computational Chemistry, 28:2618-2640, 2007.
abstract, journal
Klaus Schulten, James C. Phillips, Laxmikant V. Kale, Abhinav Bhatele.
Biomolecular modeling in the era of petascale computing.
In Petascale Computing: Algorithms and Applications, pp. 165-181, D. Bader, Ed., Chapman & Hall / CRC Press, New York, 2008.
abstract
Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, and Laxmikant V. Kale.
Scalable Molecular Dynamics with NAMD on Blue Gene/L.
IBM Journal of Research and Development, Volume 52, No. 1/2, 2007.
abstract
K.Y. Sanbonmatsu and C.-S. Tung.
High performance computing in biology: Multimillion atom simulations of nanoscale systems.
Journal of Structural Biology, 157:470-480, 2007.
journal
Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus Schulten.
Managing biomolecular simulations in a grid environment with NAMD-G.
Proceedings of the 2006 TeraGrid Conference, 2006. In Press.
abstract
Sameer Kumar, Chao Huang, Gheorghe Almasi, and Laxmikant V. Kale.
Achieving Strong Scaling with NAMD on Blue Gene/L.
Proceedings of IEEE International Parallel & Distributed Processing Symposium 2006, 2006.
abstract
Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng.
Biomolecular modeling using parallel supercomputers.
In S. Aluru, editor, Handbook of computational molecular biology, pp. 34.1-34.43. Taylor and Francis, 2005.
abstract
James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten.
Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry, 26:1781-1802, 2005.
abstract,
journal
Joachim Hein, Fiona Reid, Lorna Smith, Ian Bush, Martyn Guest, and Paul Sherwood.
On the performance of molecular dynamics applications on current high-end systems.
Phil. Trans. R. Soc. A, 363:1987-1998, 2005.
journal
James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kalé.
NAMD: Biomolecular Simulation on Thousands of Processors.
Proceedings of the IEEE/ACM SC2002 Conference. IEEE Press, 2002.
Technical Paper 277.
abstract,
pdf
Robert K. Brunner, James C. Phillips, Laxmikant V. Kalé.
Scalable Molecular Dynamics for Large Biomolecular Systems.
Proceedings of the IEEE/ACM SC2000 Conference. IEEE Press, 2000.
Technical Paper 271.
abstract,
pdf
R. Sharma, M. Zeller, V. I. Pavlovic, T. S. Huang, Z. Lo, S. Chu, Y. Zhao,
J. Phillips, and K. Schulten.
Speech/Gesture Interface to a Visual Computing Environment.
IEEE Computer Graphics and Applications, March/April 2000, 29-37.
abstract,
Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten.
NAMD2: Greater scalability for parallel molecular dynamics.
Journal of Computational Physics, 151:283-312, 1999.
abstract
Robert Brunner, Laxmikant Kalé, and James Phillips.
Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code.
In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.
James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten.
Avoiding algorithmic obfuscation in a message-driven parallel MD code.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, 4:472-482, 1999. Springer-Verlag.
abstract
L. V. Kalé, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki.
NAMD: A Case Study in Multilingual Parallel Programming.
In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag.
abstract
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert D. Skeel, and Klaus Schulten.
NAMD-A parallel, object-oriented molecular dynamics program.
International Journal of Supercomputer Applications
and High Performance Computing, 10:251-268, 1996.
abstract
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
Computational Physics Communications, 91:111-134, 1995.
abstract
Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé,
Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
In S.N. Atluri, G. Yagawa, and T.A.
Cruse, editors, Computational Mechanics 95, volume 1, pages 476-481, 1995.
abstract
Papers Citing NAMD
The "full text" links lead to Google Scholar searches for the article. We do not provide copies of these articles ourselves. Articles by TCBG members are available in the TCBG Publications Database.
3032 citations found April 16, 2012.
Long, F., Su, C.C., Lei, H.T., Bolla, J.R., Do, S.V., Yu, E.W.
Structure and mechanism of the tripartite CusCBA heavy-metal efflux complex
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 367:1047-1058, APR 19 2012
abstract,
full text
Zhang, L., Yan, F., Zhang, S.L., Lei, D.S., Charles, M.A., Cavigiolio, G., Oda, M., Krauss, R.M., Weisgraber, K.H., Rye, K.A., Pownall, H.J., Qiu, X.Y., Ren, G.
Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein
NATURE CHEMICAL BIOLOGY, 8:342-349, APR 2012
abstract,
full text
Li, Y., Hao, M., Ren, H., Zhang, S.W., Wang, X., Ma, M., Li, G.H., Yang, L.
Exploring the structure requirement for KC theta inhibitory activity of pyridinecarbonitrile derivatives: an in silico analysis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 34:76-88, APR 2012
abstract,
full text
Bukovnik, U., Gao, J., Cook, G.A., Shank, L.P., Seabra, M.B., Schultz, B.D., Iwamoto, T., Chen, J., Tomich, J.M.
Structural and biophysical properties of a synthetic channel-forming peptide: Designing a clinically relevant anion selective pore
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1039-1048, APR 2012
abstract,
full text
Calligari, P.A., Salgado, G.F., Pelupessy, P., Lopes, P., Ouazzani, J., Bodenhausen, G., Abergel, D.
Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1196-1210, APR 2012
abstract,
full text
Asses, Y., Venkatraman, V., Leroux, V., Ritchie, D.W., Maigret, B.
Exploring c-Met kinase flexibility by sampling and clustering its conformational space
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1227-1238, APR 2012
abstract,
full text
Gonnet, P.
A short note on the fast evaluation of dihedral angle potentials and their derivatives
JOURNAL OF COMPUTATIONAL PHYSICS, 231:2691-2694, APR 1 2012
full text
Wereszczynski, J., McCammon, J.A.
Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates
PROTEIN SCIENCE, 21:475-486, APR 2012
abstract,
full text
Priyadarzini, T.R.K., Subashini, B., Selvin, J.F.A., Veluraja, K.
Molecular dynamics simulation and quantum mechanical calculations on alpha-D-N-acetylneuraminic acid
CARBOHYDRATE RESEARCH, 351:93-97, APR 1 2012
abstract,
full text
Zhao, Y., De Nicola, A., Kawakatsu, T., Milano, G.
Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:868-880, MAR 30 2012
abstract,
full text
Giussani, L., Tabacchi, G., Gianotti, E., Coluccia, S., Fois, E.
Disentangling protein-silica interactions
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 370:1463-1477, MAR 28 2012
abstract,
full text
McCullagh, M., Franco, I., Ratner, M.A., Schatz, G.C.
Defects in DNA: Lessons from Molecular Motor Design
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:689-693, MAR 15 2012
abstract,
full text
Zobnina, V.G., Kosevich, M.V., Chagovets, V.V., Boryak, O.A., Vekey, K., Gomory, A., Kulyk, A.N.
Interactions of oligomers of organic polyethers with histidine amino acid
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 26:532-540, MAR 15 2012
abstract,
full text
Ngo, V.A.
Parallel-pulling protocol for free-energy evaluation
PHYSICAL REVIEW E, 85: Art. No. 036702, MAR 13 2012
abstract,
full text
Sanford, B., Cao, B., Johnson, J.M., Zimmerman, K., Strom, A.M., Mueller, R.M., Bhattacharyya, S., Musier-Forsyth, K., Hati, S.
Role of Coupled Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases
BIOCHEMISTRY, 51:2146-2156, MAR 13 2012
abstract,
full text
Du, J., Dong, H., Zhou, H.X.
Gating mechanism of a P2X4 receptor developed from normal mode analysis and molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:4140-4145, MAR 13 2012
abstract,
full text
Diaz, N., Suarez, D.
Alternative Interdomain Configurations of the Full-Length MMP-2 Enzyme Explored by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2677-2686, MAR 8 2012
abstract,
full text
Rodriguez, J., Elola, M.D., Laria, D.
Ionic Liquid Aqueous Solutions under Nanoconfinement
JOURNAL OF PHYSICAL CHEMISTRY C, 116:5394-5400, MAR 8 2012
abstract,
full text
Chen, R., Chung, S.H.
Engineering a Potent and Specific Blocker of Voltage-Gated Potassium Channel Kv1.3, a Target for Autoimmune Diseases
BIOCHEMISTRY, 51:1976-1982, MAR 6 2012
abstract,
full text
Gautieri, A., Vesentini, S., Redaelli, A., Buehler, M.J.
Viscoelastic properties of model segments of collagen molecules
MATRIX BIOLOGY, 31:141-149, MAR 2012
abstract,
full text
Li, L., Li, S.L., Jones, M.K., Segrest, J.P.
Rotational and hinge dynamics of discoidal high density lipoproteins probed by interchain disulfide bond formation
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 1821:481-489, MAR 2012
abstract,
full text
Morozov, D., Khrenova, M., Andrijchenko, N., Grigorenko, B., Nemukhin, A.
Minimum energy reaction profiles for the hydrolysis reaction of the cyclic guanosine monophosphate in water: Comparison of the results of two QM/MM approaches
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 983:88-94, MAR 1 2012
abstract,
full text
Yanagita, H., Yamamoto, N., Fuji, H., Liu, X.L., Ogata, M., Yokota, M., Takaku, H., Hasegawa, H., Odagiri, T., Tashiro, M., Hoshino, T.
Mechanism of Drug Resistance of Hemagglutinin of Influenza Virus and Potent Scaffolds Inhibiting Its Function
ACS CHEMICAL BIOLOGY, 7:552-562, MAR 2012
abstract,
full text
Willis, C.D., Oashi, T., Busby, B., Mackerell, A.D., Bloch, R.J.
Hydrophobic residues in small ankyrin 1 participate in binding to obscurin
MOLECULAR MEMBRANE BIOLOGY, 29:36-51, MAR 2012
abstract,
full text
Jana, S., Dalapati, S., Ghosh, S., Guchhait, N.
Binding interaction between plasma protein bovine serum albumin and flexible charge transfer fluorophore: A spectroscopic study in combination with molecular docking and molecular dynamics simulation
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY, 231:19-27, MAR 1 2012
abstract,
full text
Stober, S.T., Abrams, C.F.
Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors
PROTEIN SCIENCE, 21:307-317, MAR 2012
abstract,
full text
Perez-Siles, G., Nunez, E., Morreale, A., Jimenez, E., Leo-Macias, A., Pita, G., Cherubino, F., Sangaletti, R., Bossi, E., Ortiz, A.R., Aragon, C., Lopez-Corcuera, B.
An aspartate residue in the external vestibule of GLYT2 (glycine transporter 2) controls cation access and transport coupling
BIOCHEMICAL JOURNAL, 442:323-334, MAR 1 2012
abstract,
full text
Kuttel, M., Ravenscroft, N., Foschiatti, M., Cescutti, P., Rizzo, R.
Conformational properties of two exopolysaccharides produced by Inquilinus limosus, a cystic fibrosis lung pathogen
CARBOHYDRATE RESEARCH, 350:40-48, MAR 1 2012
abstract,
full text
Sergelius, C., Niinivehmas, S., Maula, T., Kurita, M., Yamaguchi, S., Yamamoto, T., Katsumura, S., Pentikainen, O.T., Slotte, J.P.
Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:474-480, MAR 2012
abstract,
full text
Cui, T.X., Mowrey, D., Bondarenko, V., Tillman, T., Ma, D.J., Landrum, E., Perez-Aguilar, J.M., He, J., Wang, W., Saven, J.G., Eckenhoff, R.G., Tang, P., Xu, Y.
NMR structure and dynamics of a designed water-soluble transmembrane domain of nicotinic acetylcholine receptor
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:617-626, MAR 2012
abstract,
full text
Sun, C.B., Tang, T., Uludag, H.
Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2405-2413, MAR 1 2012
abstract,
full text
Wedberg, R., Abildskov, J., Peters, G.H.
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2575-2585, MAR 1 2012
abstract,
full text
Domene, C., Illingworth, C.J.R.
Effects of point mutations in pVHL on the binding of HIF-1 alpha
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:733-746, MAR 2012
abstract,
full text
Noinaj, N., Easley, N.C., Oke, M., Mizuno, N., Gumbart, J., Boura, E., Steere, A.N., Zak, O., Aisen, P., Tajkhorshid, E., Evans, R.W., Gorringe, A.R., Mason, A.B., Steven, A.C., Buchanan, S.K.
Structural basis for iron piracy by pathogenic Neisseria
NATURE, 483:53-U92, MAR 1 2012
abstract,
full text
Vanni, S., Rothlisberger, U.
A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations
CURRENT MEDICINAL CHEMISTRY, 19:1135-1145, MAR 2012
abstract,
full text
Girolami, A., Scarparo, P., Bonamigo, E., Santarossa, L., Cristiani, A., Moro, S., Lombardi, A.M.
A cluster of factor XI-deficient patients due to a new mutation (Ile 436 Lys) in northeastern Italy
EUROPEAN JOURNAL OF HAEMATOLOGY, 88:229-236, MAR 2012
abstract,
full text
Enlow, M.A.
Binding of TNT to amplifying fluorescent polymers: An ab initio and molecular dynamics study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 33:12-18, MAR 2012
abstract,
full text
Norris, S.E., Landstrom, J., Weintraub, A., Bull, T.E., Widmalm, G., Freedberg, D.I.
Transient hydrogen bonding in uniformly 13C,15N-Labeled Carbohydrates in Water
BIOPOLYMERS, 97:145-154, MAR 2012
abstract,
full text
Ramya, L., Gautham, N.
Conformational space exploration of met- and Leu-enkephalin using the mols method, molecular dynamics, and Monte Carlo simulation-a comparative study
BIOPOLYMERS, 97:165-176, MAR 2012
abstract,
full text
Domene, C., Furini, S.
Molecular Dynamics Simulations of the TrkH Membrane Protein
BIOCHEMISTRY, 51:1559-1565, FEB 28 2012
abstract,
full text
Ishikawa, T., Krzysko, K.A., Kowalska-Loth, B., Skrajna, A.M., Czubaty, A., Girstun, A., Cieplak, M.K., Lesyng, B., Staron, K.
Activities of Topoisomerase I in Its Complex with SRSF1
BIOCHEMISTRY, 51:1803-1816, FEB 28 2012
abstract,
full text
Wang, H.L., Cheng, X.L., Sine, S.M.
Intramembrane Proton Binding Site Linked to Activation of Bacterial Pentameric Ion Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:6482-6489, FEB 24 2012
abstract,
full text
Zhou, K., Gao, Y., Hoy, J.A., Mann, F.M., Honzatko, R.B., Peters, R.J.
Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:6840-6850, FEB 24 2012
abstract,
full text
Avila-Salas, F., Sandoval, C., Caballero, J., Guinez-Molinos, S., Santos, L.S., Cachau, R.E., Gonzalez-Nilo, F.D.
Study of Interaction Energies between the PAMAM Dendrimer and Nonsteroidal Anti-Inflammatory Drug Using a Distributed Computational Strategy and Experimental Analysis by ESI-MS/MS
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2031-2039, FEB 23 2012
abstract,
full text
Sgrignani, J., Magistrato, A.
The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2259-2268, FEB 23 2012
abstract,
full text
Hilder, T.A., Yang, R., Gordon, D., Rendell, A.P., Chung, S.H.
Silicon Carbide Nanotube as a Chloride-Selective Channel
JOURNAL OF PHYSICAL CHEMISTRY C, 116:4465-4470, FEB 23 2012
abstract,
full text
Liu, P., Chipot, C., Shao, X.G., Cai, W.S.
Solvent-Controlled Shuttling in a Molecular Switch
JOURNAL OF PHYSICAL CHEMISTRY C, 116:4471-4476, FEB 23 2012
abstract,
full text
Becker, T., Franckenberg, S., Wickles, S., Shoemaker, C.J., Anger, A.M., Armache, J.P., Sieber, H., Ungewickell, C., Berninghausen, O., Daberkow, I., Karcher, A., Thomm, M., Hopfner, K.P., Green, R., Beckmann, R.
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea
NATURE, 482:501-U221, FEB 23 2012
abstract,
full text
Gumbart, J., Roux, B.
Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 102:795-801, FEB 22 2012
abstract,
full text
Nong, E.X., DeVience, S.J., Herschbach, D.
Minimalist Model for Force-Dependent DNA Replication
BIOPHYSICAL JOURNAL, 102:810-818, FEB 22 2012
abstract,
full text
Smith, N.E., Vrielink, A., Attwood, P.V., Corry, B.
Biological Channeling of a Reactive Intermediate in the Bifunctional Enzyme DmpFG
BIOPHYSICAL JOURNAL, 102:868-877, FEB 22 2012
abstract,
full text
Qiu, H., Guo, W.L.
Detecting ssDNA at single-nucleotide resolution by sub-2-nanometer pore in monoatomic graphene: A molecular dynamics study
APPLIED PHYSICS LETTERS, 100: Art. No. 083106, FEB 20 2012
abstract,
full text
Das, R.K., Crick, S.L., Pappu, R.V.
N-Terminal Segments Modulate the alpha-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins
JOURNAL OF MOLECULAR BIOLOGY, 416:287-299, FEB 17 2012
abstract,
full text
Tipmanee, V., Blumberger, J.
Kinetics of the Terminal Electron Transfer Step in Cytochrome c Oxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1876-1883, FEB 16 2012
abstract,
full text
Ravi, H.K., Simona, F., Hulliger, J., Cascella, M.
Molecular Origin of Piezo- and Pyroelectric Properties in Collagen Investigated by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1901-1907, FEB 16 2012
abstract,
full text
Gordon, D., Chen, R., Ho, J.M., Coote, M.L., Chung, S.H.
Rigid Body Brownian Dynamics as a Tool for Studying Ion Channel Blockers
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1933-1941, FEB 16 2012
abstract,
full text
da Silva, L.P., da Silva, J.C.G.E.
TD-DFT/Molecular Mechanics Study of the Photinus pyralis Bioluminescence System
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2008-2013, FEB 16 2012
abstract,
full text
Gao, C., Pan, M.M., Lei, Y.J., Tian, L.Q., Jiang, H.Y., Li, X.L., Shi, Q., Tian, C., Yuan, Y.K., Fan, G.X., Dong, X.P.
A point mutation in the DNA-binding domain of HPV-2 E2 protein increases its DNA-binding capacity and reverses its transcriptional regulatory activity on the viral early promoter
BMC MOLECULAR BIOLOGY, 13: Art. No. 5, FEB 15 2012
abstract,
full text
Gonzalez, W., Riedelsberger, J., Morales-Navarro, S.E., Caballero, J., Alzate-Morales, J.H., Gonzalez-Nilo, F.D., Dreyer, I.
The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids
BIOCHEMICAL JOURNAL, 442:57-63, FEB 15 2012
abstract,
full text
Rao, F., Spichty, M.
Thermodynamics and kinetics of large-time-step molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:475-483, FEB 15 2012
abstract,
full text
Huggins, D.J.
Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 064518, FEB 14 2012
abstract,
full text
Pfaendtner, J., Volkmann, N., Hanein, D., Dalhaimer, P., Pollard, T.D., Voth, G.A.
Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation
JOURNAL OF MOLECULAR BIOLOGY, 416:148-161, FEB 10 2012
abstract,
full text
Potoyan, D.A., Zhuravlev, P.I., Papoian, G.A.
Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase Using All Atom Explicit Solvent Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1709-1715, FEB 9 2012
abstract,
full text
Connelly, L., Jang, H., Arce, F.T., Capone, R., Kotler, S.A., Ramachandran, S., Kagan, B.L., Nussinov, R., Lal, R.
Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's beta-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1728-1735, FEB 9 2012
abstract,
full text
Comer, J., Aksimentiey, A.
Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 116:3376-3393, FEB 9 2012
abstract,
full text
Cheung, L.S.L., Kanwar, M., Ostermeier, M., Konstantopoulos, K.
A Hot-Spot Motif Characterizes the Interface between a Designed Ankyrin-Repeat Protein and Its Target Ligand
BIOPHYSICAL JOURNAL, 102:407-416, FEB 8 2012
abstract,
full text
Chen, R., Chung, S.H.
Binding Modes of mu-Conotoxin to the Bacterial Sodium Channel (Na(v)Ab)
BIOPHYSICAL JOURNAL, 102:483-488, FEB 8 2012
abstract,
full text
Ndlovu, H., Ashcroft, A.E., Radford, S.E., Harris, S.A.
Effect of Sequence Variation on the Mechanical Response of Amyloid Fibrils Probed by Steered Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 102:587-596, FEB 8 2012
abstract,
full text
Selvaratnam, R., VanSchouwen, B., Fogolari, F., Mazhab-Jafari, M.T., Das, R., Melacini, G.
The Projection Analysis of NMR Chemical Shifts Reveals Extended EPAC Autoinhibition Determinants
BIOPHYSICAL JOURNAL, 102:630-639, FEB 8 2012
abstract,
full text
Basilio, N., Garcia-Rio, L., Martin-Pastor, M.
Calixarene-Based Surfactants: Evidence of Structural Reorganization upon Micellization
LANGMUIR, 28:2404-2414, FEB 7 2012
abstract,
full text
Russell, J.T., Wang, B.Y., Kral, P.
Nanodroplet Transport on Vibrated Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:353-357, FEB 2 2012
abstract,
full text
Kalyaanamoorthy, S., Chen, Y.P.P.
Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:589-603, FEB 2012
abstract,
full text
Best, R.B.
Atomistic molecular simulations of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 22:52-61, FEB 2012
abstract,
full text
Merino, F., Rivas-Pardo, J.A., Caniuguir, A., Garcia, I., Guixe, V.
Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea
BIOCHIMIE, 94:516-524, FEB 2012
abstract,
full text
Prakash, P., Sayyed-Ahmad, A., Gorfe, A.A.
The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002394, FEB 2012
abstract,
full text
Kowalczyk, S.W., Wells, D.B., Aksimentiev, A., Dekker, C.
Slowing down DNA Translocation through a Nanopore in Lithium Chloride
NANO LETTERS, 12:1038-1044, FEB 2012
abstract,
full text
Do, T.N., Ippoliti, E., Carloni, P., Varani, G., Parrinello, M.
Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:688-694, FEB 2012
abstract,
full text
Mallajosyula, S.S., Guvench, O., Hatcher, E., MacKerell, A.D.
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:759-776, FEB 2012
abstract,
full text
Drakulic, B.J., Marinkovic, A.D., Juranic, I.O.
On the choice of optimal conformation in linear free-energy relationships. Reactivity of 2-[(carboxymethyl)sulfanyl]-4-oxo-4-arylbutanoic acids with diphenyldiazomethane
TETRAHEDRON LETTERS, 53:553-556, FEB 1 2012
abstract,
full text
Fleming, P.J., Freites, J.A., Moon, C.P., Tobias, D.J., Fleming, K.G.
Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:126-134, FEB 2012
abstract,
full text
Li, J., Tajkhorshid, E.
A gate-free pathway for substrate release from the inward-facing state of the Na+-galactose transporter
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:263-271, FEB 2012
abstract,
full text
Wood, M.L., Schow, E.V., Freites, J.A., White, S.H., Tombola, F., Tobias, D.J.
Water wires in atomistic models of the Hvl proton channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:286-293, FEB 2012
abstract,
full text
Gumbart, J., Khalili-Araghi, F., Sotomayor, M., Roux, B.
Constant electric field simulations of the membrane potential illustrated with simple systems
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:294-302, FEB 2012
abstract,
full text
Receveur-Brechot, V., Durand, D.
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective
CURRENT PROTEIN & PEPTIDE SCIENCE, 13:55-75, FEB 2012
abstract,
full text
Ihle, N.T., Byers, L.A., Kim, E.S., Saintigny, P., Lee, J.J., Blumenschein, G.R., Tsao, A., Liu, S.Y., Larsen, J.E., Wang, J., Diao, L.X., Coombes, K.R., Chen, L., Zhang, S.X., Abdelmelek, M.F., Tang, X.M., Papadimitrakopoulou, V., Minna, J.D., Lippman, S.M., Hong, W.K., Herbst, R.S., Wistuba, I.I., Heymach, J.V., Powis, G.
Effect of KRAS Oncogene Substitutions on Protein Behavior: Implications for Signaling and Clinical Outcome
JOURNAL OF THE NATIONAL CANCER INSTITUTE, 104:228-239, FEB 2012
abstract,
full text
Liu, L., Gronenborn, A.M., Bahar, I.
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:616-625, FEB 2012
abstract,
full text
Negureanu, L., Salsbury, F.R.
Insights into Protein - DNA Interactions, Stability and Allosteric Communications: A Computational Study of Muts alpha-DNA Recognition Complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:757-776, FEB 2012
abstract,
full text
Uchida, M., Morris, D.S., Kang, S., Jolley, C.C., Lucon, J., Liepold, L.O., LaFrance, B., Prevelige, P.E., Douglas, T.
Site-Directed Coordination Chemistry with P22 Virus-like Particles
LANGMUIR, 28:1998-2006, JAN 31 2012
abstract,
full text
Limongelli, V., Marinelli, L., Cosconati, S., La Motta, C., Sartini, S., Mugnaini, L., Da Settimo, F., Novellino, E., Parrinello, M.
Sampling protein motion and solvent effect during ligand binding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:1467-1472, JAN 31 2012
abstract,
full text
Lettieri, S., Zuckerman, D.M.
Accelerating molecular monte carlo simulations using distance and orientation-dependent energy tables: Tuning from atomistic accuracy to smoothed "coarse-grained" models
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:268-275, JAN 30 2012
abstract,
full text
Mori, T., Ogushi, F., Sugita, Y.
Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:286-293, JAN 30 2012
abstract,
full text
Kamath, G., Ketko, M., Baker, G.A., Potoff, J.J.
Monte Carlo predictions of phase equilibria and structure for dimethyl ether plus sulfur dioxide and dimethyl ether plus carbon dioxide
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 044514, JAN 28 2012
abstract,
full text
Jiao, W.T., Hutton, R.D., Cross, P.J., Jameson, G.B., Parker, E.J.
Dynamic Cross-Talk among Remote Binding Sites: The Molecular Basis for Unusual Synergistic Allostery
JOURNAL OF MOLECULAR BIOLOGY, 415:716-726, JAN 27 2012
abstract,
full text
Taylor, C.B., Talib, M.F., McCabe, C., Bu, L.T., Adney, W.S., Himmel, M.E., Crowley, M.F., Beckham, G.T.
Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-binding Module
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:3147-3155, JAN 27 2012
abstract,
full text
Hernandez-Rodriguez, E.W., Sanchez-Garcia, E., Crespo-Otero, R., Montero-Alejo, A.L., Montero, L.A., Thiel, W.
Understanding Rhodopsin Mutations Linked to the Retinitis pigmentosa Disease: a QM/MM and DFT/MRCI Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1060-1076, JAN 26 2012
abstract,
full text
Jing, Y.Y., Zheng, R.H., Li, H.X., Shi, Q.
Theoretical Study of the Electronic-Vibrational Coupling in the Q(y) States of the Photosynthetic Reaction Center in Purple Bacteria
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1164-1171, JAN 26 2012
abstract,
full text
Naveed, H., Xu, Y., Jackups, R., Liang, J.
Predicting Three-Dimensional Structures of Transmembrane Domains of beta-Barrel Membrane Proteins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:1775-1781, JAN 25 2012
abstract,
full text
Corry, B., Thomas, M.
Mechanism of Ion Permeation and Selectivity in a Voltage Gated Sodium Channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:1840-1846, JAN 25 2012
abstract,
full text
Volkov, S.N., Paramonova, E.V., Yakubovich, A.V., Solov'yov, A.V.
Micromechanics of base pair unzipping in the DNA duplex
JOURNAL OF PHYSICS-CONDENSED MATTER, 24: Art. No. 035104, JAN 25 2012
abstract,
full text
Capone, R., Jang, H., Kotler, S.A., Kagan, B.L., Nussinov, R., Lal, R.
Probing Structural Features of Alzheimer's Amyloid-beta Pores in Bilayers Using Site-Specific Amino Acid Substitutions
BIOCHEMISTRY, 51:776-785, JAN 24 2012
abstract,
full text
Qi, Y., Nam, K., Spong, M.C., Banerjee, A., Sung, R.J., Zhang, M., Karplus, M., Verdine, G.L.
Strandwise translocation of a DNA glycosylase on undamaged DNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:1086-1091, JAN 24 2012
abstract,
full text
Spudich, E.N., Ozorowski, G., Schow, E.V., Tobias, D.J., Spudich, J.L., Luecke, H.
A Transporter Converted into a Sensor, a Phototaxis Signaling Mutant of Bacteriorhodopsin at 3.0 angstrom
JOURNAL OF MOLECULAR BIOLOGY, 415:455-463, JAN 20 2012
abstract,
full text
Musgaard, M., Thogersen, L., Schiott, B., Tajkhorshid, E.
Tracing Cytoplasmic Ca(2+) Ion and Water Access Points in the Ca(2+)-ATPase
BIOPHYSICAL JOURNAL, 102:268-277, JAN 18 2012
abstract,
full text
Stadler, A.M., Pellegrini, E., Johnson, M., Fitter, J., Zaccai, G.
Dynamics-Stability Relationships in Apo- and Holomyoglobin: A Combined Neutron Scattering and Molecular Dynamics Simulations Study
BIOPHYSICAL JOURNAL, 102:351-359, JAN 18 2012
abstract,
full text
Tarus, B., Chevalier, C., Richard, C.A., Delmas, B., Di Primo, C., Slama-Schwok, A.
Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding
PLOS ONE, 7: Art. No. e30038, JAN 17 2012
abstract,
full text
Weng, J.W., Fan, K.N., Wang, W.N.
The Conformational Transition Pathways of ATP-Binding Cassette Transporter BtuCD Revealed by Targeted Molecular Dynamics Simulation
PLOS ONE, 7: Art. No. e30465, JAN 17 2012
abstract,
full text
Kuttner, Y.Y., Engel, S.
Protein Hot Spots: The Islands of Stability
JOURNAL OF MOLECULAR BIOLOGY, 415:419-428, JAN 13 2012
abstract,
full text
Zheng, B., Sant, M., Demontis, P., Suffritti, G.B.
Force Field for Molecular Dynamics Computations in Flexible ZIF-8 Framework
JOURNAL OF PHYSICAL CHEMISTRY C, 116:933-938, JAN 12 2012
abstract,
full text
Lim, J.B., Rogaski, B., Klauda, J.B.
Update of the Cholesterol Force Field Parameters in CHARMM
JOURNAL OF PHYSICAL CHEMISTRY B, 116:203-210, JAN 12 2012
abstract,
full text
Kucerka, N., Holland, B.W., Gray, C.G., Tomberli, B., Katsaras, J.
Scattering Density Profile Model of POPG Bilayers As Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-ray Scattering Experiments
JOURNAL OF PHYSICAL CHEMISTRY B, 116:232-239, JAN 12 2012
abstract,
full text
Huang, B., Liu, F.F., Dong, X.Y., Sun, Y.
Molecular Mechanism of the Effects of Salt and pH on the Affinity between Protein A and Human lmmunoglobulin G1 Revealed by Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:424-433, JAN 12 2012
abstract,
full text
Lee, H.J., Hota, P.K., Chugha, P., Guo, H., Miao, H., Zhang, L.Q., Kim, S.J., Stetzik, L., Wang, B.C., Buck, M.
NMR Structure of a Heterodimeric SAM:SAM Complex: Characterization and Manipulation of EphA2 Binding Reveal New Cellular Functions of SHIP2
STRUCTURE, 20:41-55, JAN 11 2012
abstract,
full text
Satpati, P., Simonson, T.
Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways
BIOCHEMISTRY, 51:353-361, JAN 10 2012
abstract,
full text
Makiya, M., Dolan, M., Agulto, L., Purcell, R., Chen, Z.C.
Structural basis of anthrax edema factor neutralization by a neutralizing antibody
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 417:324-329, JAN 6 2012
abstract,
full text
Mastrangelo, E., Bolognesi, M., Milani, M.
Flaviviral helicase: Insights into the mechanism of action of a motor protein
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 417:84-87, JAN 6 2012
abstract,
full text
Barnard, T.J., Gumbart, J., Peterson, J.H., Noinaj, N., Easley, N.C., Dautin, N., Kuszak, A.J., Tajkhorshid, E., Bernstein, H.D., Buchanan, S.K.
Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter
JOURNAL OF MOLECULAR BIOLOGY, 415:128-142, JAN 6 2012
abstract,
full text
Gonnet, P.
Pairwise Verlet Lists: Combining Cell Lists and Verlet Lists to Improve Memory Locality and Parallelism
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:76-81, JAN 5 2012
abstract,
full text
Kang, Y.Y., Lu, S.Q., Ren, P., Huo, B., Long, M.
Molecular Dynamics Simulation of Shear- and Stretch-Induced Dissociation of P-Selectin/PSGL-1 Complex
BIOPHYSICAL JOURNAL, 102:112-120, JAN 4 2012
abstract,
full text
Zhang, J.F., He, Z.Q., Wang, Q.G., Barz, B., Kosztin, I., Shang, Y., Xu, D.
Prediction of Protein Tertiary Structures Using MUFOLD
FUNCTIONAL GENOMICS: METHODS AND PROTOCOLS, SECOND EDITION, 815:3-13, 2012
abstract,
full text
Chen, C., Li, W.Z., Song, Y.C., Weng, L.D., Zhang, N.
Concentration dependence of water self-diffusion coefficients in dilute glycerol-water binary and glycerol-water-sodium chloride ternary solutions and the insights from hydrogen bonds
MOLECULAR PHYSICS, 110:283-291, 2012
abstract,
full text
Cheng, C.L., Zhao, G.J.
Steered molecular dynamics simulation study on dynamic self-assembly of single-stranded DNA with double-walled carbon nanotube and graphene
NANOSCALE, 4:2301-2305, 2012
abstract,
full text
Kamath, G., Bhatnagar, N., Baker, G.A., Baker, S.N., Potoff, J.J.
Computational prediction of ionic liquid 1-octanol/water partition coefficients
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:4339-4342, 2012
abstract,
full text
Anand, R., Ottani, S., Manoli, F., Manet, I., Monti, S.
A close-up on doxorubicin binding to gamma-cyclodextrin: an elucidating spectroscopic, photophysical and conformational study
RSC ADVANCES, 2:2346-2357, 2012
abstract,
full text
Anandarajah, A., Amarasinghe, P.M.
Microstructural Investigation of Soil Suction and Hysteresis of Fine-Grained Soils
JOURNAL OF GEOTECHNICAL AND GEOENVIRONMENTAL ENGINEERING, 138:38-46, JAN 2012
abstract,
full text
Fogolari, F., Corazza, A., Toppo, S., Tosatto, S.C.E., Viglino, P., Ursini, F., Esposito, G.
Studying Interactions by Molecular Dynamics Simulations at High Concentration
JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, Art. No. 303190, 2012
abstract,
full text
Chen, X., Chen, X.L., Wu, T., Wang, Q.
Simulation of steered molecular dynamics on the exploration of the dynamic structure of HIV-1 protease
MOLECULAR SIMULATION, 38:293-299, 2012
abstract,
full text
Lawrenz, M., Baron, R., Wang, Y., McCammon, J.A.
Independent-Trajectory Thermodynamic Integration: A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:469-486, 2012
abstract,
full text
Besker, N., Gervasio, F.L.
Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:501-513, 2012
abstract,
full text
Amaro, R.E., Li, W.W.
Molecular-Level Simulation of Pandemic Influenza Glycoproteins
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:575-594, 2012
abstract,
full text
Chang, C.E.A., Ai, R.Z., Gutierrez, M., Marsella, M.J.
Homology Modeling of Cannabinoid Receptors: Discovery of Cannabinoid Analogues for Therapeutic Use
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:595-613, 2012
abstract,
full text
Xu, X., Li, R.B., Ma, M., Wang, X., Wang, Y.H., Zou, H.F.
Multidrug resistance protein P-glycoprotein does not recognize nanoparticle C-60: experiment and modeling
SOFT MATTER, 8:2915-2923, 2012
abstract,
full text
Liu, J., Fan, J.F.
Relationship between the Permeation-Diffusion Parameters of a Single-File Channel
CHINESE PHYSICS LETTERS, 29: Art. No. 010502, JAN 2012
abstract,
full text
Saiz-Poseu, J., Alcon, I., Alibes, R., Busque, F., Faraudo, J., Ruiz-Molina, D.
Self-assembly of alkylcatechols on HOPG investigated by scanning tunneling microscopy and molecular dynamics simulations
CRYSTENGCOMM, 14:264-271, 2012
abstract,
full text
Czajkowsky, D.M., Li, L., Sun, J.L., Hu, J., Shao, Z.F.
Heteroepitaxial Streptavidin Nanocrystals Reveal Critical Role of Proton "Fingers" and Subsurface Atoms in Determining Adsorbed Protein Orientation
ACS NANO, 6:190-198, JAN 2012
abstract,
full text
Orts, J., Bartoschek, S., Griesinger, C., Monecke, P., Carlomagno, T.
An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude
JOURNAL OF BIOMOLECULAR NMR, 52:23-30, JAN 2012
abstract,
full text
Luan, B.Q., Stolovitzky, G., Martyna, G.
Slowing and controlling the translocation of DNA in a solid-state nanopore
NANOSCALE, 4:1068-1077, 2012
abstract,
full text
Schmid, M., Nogueira, E.S., Monnard, F.W., Ward, T.R., Meuwly, M.
Arylsulfonamides as inhibitors for carbonic anhydrase: prediction & validation
CHEMICAL SCIENCE, 3:690-700, 2012
abstract,
full text
Feng, R., Xenos, M., Girdhar, G., Kang, W., Davenport, J.W., Deng, Y.F., Bluestein, D.
Viscous flow simulation in a stenosis model using discrete particle dynamics: a comparison between DPD and CFD
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 11:119-129, JAN 2012
abstract,
full text
Jana, S., Ghosh, S., Dalapati, S., Guchhait, N.
Exploring structural change of protein bovine serum albumin by external perturbation using extrinsic fluorescence probe: spectroscopic measurement, molecular docking and molecular dynamics simulation
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 11:323-332, 2012
abstract,
full text
Munz, M., Biggin, P.C.
JGromacs: A Java Package for Analyzing Protein Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:255-259, JAN 2012
abstract,
full text
Giannozzi, P., Jansen, K., La Penna, G., Minicozzi, V., Morante, S., Rossi, G., Stellato, F.
Zn induced structural aggregation patterns of beta-amyloid peptides by first-principle simulations and XAS measurements
METALLOMICS, 4:156-165, 2012
abstract,
full text
Barr, D., van der Vaart, A.
The natural DNA bending angle in the lac repressor headpiece-O1 operator complex is determined by protein-DNA contacts and water release
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:2070-2077, 2012
abstract,
full text
Lauer, T.M., Agrawal, N.J., Chennamsetty, N., Egodage, K., Helk, B., Trout, B.L.
Developability index: A rapid in silico tool for the screening of antibody aggregation propensity
JOURNAL OF PHARMACEUTICAL SCIENCES, 101:102-115, JAN 2012
abstract,
full text
Sinha, S.K., Bandyopadhyay, S.
Local heterogeneous dynamics of water around lysozyme: a computer simulation study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:899-913, 2012
abstract,
full text
Fjell, C.D., Hiss, J.A., Hancock, R.E.W., Schneider, G.
Designing antimicrobial peptides: form follows function
NATURE REVIEWS DRUG DISCOVERY, 11:37-51, JAN 2012
abstract,
full text
Sanderson, J.P., Waldburger-Hauri, K., Garzon, D., Matulis, G., Mansour, S., Pumphrey, N.J., Lissin, N., Villiger, P.M., Jakobsen, B., Faraldo-Gomez, J.D., Gadola, S.D.
Natural variations at position 93 of the invariant Va24-Ja18 a chain of human iNKT-cell TCRs strongly impact on CD1d binding
EUROPEAN JOURNAL OF IMMUNOLOGY, 42:248-255, JAN 2012
abstract,
full text
Fedoseyenko, D., Raghuraman, A., Ko, E., Burgess, K.
Omegatides: constrained analogs of peptide primary sequence
ORGANIC & BIOMOLECULAR CHEMISTRY, 10:921-924, 2012
full text
Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L., MacKerell, A.D.
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:348-362, JAN 2012
abstract,
full text
Agnew, C.R.J., Warrilow, A.G.S., Burton, N.M., Lamb, D.C., Kelly, S.L., Brady, R.L.
An Enlarged, Adaptable Active Site in CYP164 Family P450 Enzymes, the Sole P450 in Mycobacterium leprae
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 56:391-402, JAN 2012
abstract,
full text
Pizzirusso, A., Berardi, R., Muccioli, L., Ricci, M., Zannoni, C.
Predicting surface anchoring: molecular organization across a thin film of 5CB liquid crystal on silicon
CHEMICAL SCIENCE, 3:573-579, 2012
abstract,
full text
Zhu, X., Lopes, P.E.M., MacKerell, A.D.
Recent developments and applications of the CHARMM force fields
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2:167-185, JAN-FEB 2012
abstract,
full text
Figueras, L., Faraudo, J.
Competition between hydrogen bonding and electric field in single-file transport of water in carbon nanotubes
MOLECULAR SIMULATION, 38:23-25, 2012
abstract,
full text
Gorny, K., Dendzik, Z., Raczynski, P., Gburski, Z.
Dynamic properties of propylene glycol confined in ZSM-5 zeolite matrix-A computer simulation study
SOLID STATE COMMUNICATIONS, 152:8-12, JAN 2012
abstract,
full text
Fu, J., Bottegoni, G., Sasso, O., Bertorelli, R., Rocchia, W., Masetti, M., Guijarro, A., Lodola, A., Armirotti, A., Garau, G., Bandiera, T., Reggiani, A., Mor, M., Cavalli, A., Piomelli, D.
A catalytically silent FAAH-1 variant drives anandamide transport in neurons
NATURE NEUROSCIENCE, 15:64-U82, JAN 2012
abstract,
full text
Zhang, Y.B., Cui, Y.B., Chen, L.Y.
Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel
BIOPHYSICAL CHEMISTRY, 160:69-74, JAN 2012
abstract,
full text
Espinoza-Fonseca, L.M.
Aromatic residues link binding and function of intrinsically disordered proteins
MOLECULAR BIOSYSTEMS, 8:237-246, 2012
abstract,
full text
Muszala, S.P., Alaghband, G., Hack, J., Connors, D.
Natural Load Indices (NLI) for scientific simulation
JOURNAL OF SUPERCOMPUTING, 59:392-413, JAN 2012
abstract,
full text
Sapay, N., Cabannes, E., Petitou, M., Imberty, A.
Molecular Model of Human Heparanase with Proposed Binding Mode of a Heparan Sulfate Oligosaccharide and Catalytic Amino Acids
BIOPOLYMERS, 97:21-34, JAN 2012
abstract,
full text
Golebiowska, M., Roth, M., Firlej, L., Kuchta, B., Wexler, C.
The reversibility of the adsorption of methane-methyl mercaptan mixtures in nanoporous carbon
CARBON, 50:225-234, JAN 2012
abstract,
full text
Georgoulia, P.S., Glykos, N.M.
Using J-Coupling Constants for Force Field Validation: Application to Hepta-alanine
JOURNAL OF PHYSICAL CHEMISTRY B, 115:15221-15227, DEC 29 2011
abstract,
full text
Faro, T.M.C., Skaf, M.S., Coluci, V.R.
Mechanisms of the rotational dynamics of C(70) in C(70)-cubane heteromolecular crystals
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 244510, DEC 28 2011
abstract,
full text
Sinha, S.K., Bandyopadhyay, S.
Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 245104, DEC 28 2011
abstract,
full text
Musgaard, M., Thogersen, L., Schiott, B.
Protonation States of Important Acidic Residues in the Central Ca(2+) Ion Binding Sites of the Ca(2+)-ATPase: A Molecular Modeling Study
BIOCHEMISTRY, 50:11109-11120, DEC 27 2011
abstract,
full text
Jones, P.M., Robinson, M.W., Dalton, J.P., George, A.M.
The Plasmodium falciparum Malaria M1 Alanyl Aminopeptidase (PfA-M1): Insights of Catalytic Mechanism and Function from MD Simulations
PLOS ONE, 6: Art. No. e28589, DEC 21 2011
abstract,
full text
Krueger, S., Shin, J.H., Raghunandan, S., Curtis, J.E., Kelman, Z.
Atomistic Ensemble Modeling and Small-Angle Neutron Scattering of Intrinsically Disordered Protein Complexes: Applied to Minichromosome Maintenance Protein
BIOPHYSICAL JOURNAL, 101:2999-3007, DEC 21 2011
abstract,
full text
Zhao, J., Wang, Q., Liang, G., Zheng, J.
Molecular Dynamics Simulations of Low-Ordered Alzheimer beta-Amyloid Oligomers from Dimer to Hexamer on Self-Assembled Monolayers
LANGMUIR, 27:14876-14887, DEC 20 2011
abstract,
full text
Puri, A., Jang, H., Yavlovich, A., Masood, M.A., Veenstra, T.D., Luna, C., Aranda-Espinoza, H., Nussinov, R., Blumenthal, R.
Material Properties of Matrix Lipids Determine the Conformation and Intermolecular Reactivity of Diacetylenic Phosphatidylcholine in the Lipid Bilayer
LANGMUIR, 27:15120-15128, DEC 20 2011
abstract,
full text
Gannon, G., O'Dwyer, C., Larsson, J.A., Thompson, D.
Interdigitating Organic Bilayers Direct the Short Inter layer Spacing in Hybrid Organic-Inorganic Layered Vanadium Oxide Nanostructures
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14518-14525, DEC 15 2011
abstract,
full text
Vivcharuk, V., Kaznessis, Y.N.
Thermodynamic Analysis of Protegrin-1 Insertion and Permeation through a Lipid Bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14704-14712, DEC 15 2011
abstract,
full text
Matysiak, S., Debenedetti, P.G., Rossky, P.J.
Dissecting the Energetics of Hydrophobic Hydration of Polypeptides
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14859-14865, DEC 15 2011
abstract,
full text
Christelle, B., Eduardo, B.D.O., Latifa, C., Elaine-Rose, M., Bernard, M., Evelyne, R.H., Mohamed, G., Jean-Marc, E., Catherine, H.
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation
JOURNAL OF BIOTECHNOLOGY, 156:203-210, DEC 10 2011
abstract,
full text
Vargas, E., Bezanilla, F., Roux, B.
In Search of a Consensus Model of the Resting State of a Voltage-Sensing Domain
NEURON, 72:713-720, DEC 8 2011
abstract,
full text
Rudzinski, J.F., Noid, W.G.
Coarse-graining entropy, forces, and structures
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 214101, DEC 7 2011
abstract,
full text
Chen, R., Robinson, A., Gordon, D., Chung, S.H.
Modeling the Binding of Three Toxins to the Voltage-Gated Potassium Channel (Kv1.3)
BIOPHYSICAL JOURNAL, 101:2652-2660, DEC 7 2011
abstract,
full text
Gordon, D., Chung, S.H.
Permeation and Block of the Kv1.2 Channel Examined Using Brownian and Molecular Dynamics
BIOPHYSICAL JOURNAL, 101:2671-2678, DEC 7 2011
abstract,
full text
Bucher, D., Grant, B.J., McCammon, J.A.
Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein
BIOCHEMISTRY, 50:10530-10539, DEC 6 2011
abstract,
full text
Marinelli, F., Kuhlmann, S.I., Grell, E., Kunte, H.J., Ziegler, C., Faraldo-Gomez, J.D.
Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:E1285-E1292, DEC 6 2011
abstract,
full text
Lin, Y.W., Nie, C.M., Liao, L.F.
Insights into Uranyl Ion Binding to Ubiquitin from Molecular Modeling and Dynamics Simulations
CHEMISTRY LETTERS, 40:1330-1331, DEC 5 2011
abstract,
full text
Castro-Nallar, E., Martin, M.C.S., Mascayano, C., Molina, C., Crandall, K.A.
Molecular Phylodynamics and Protein Modeling of Infectious Salmon Anemia Virus (ISAV)
BMC EVOLUTIONARY BIOLOGY, 11: Art. No. 349, DEC 2 2011
abstract,
full text
Krammer, E.M., Homble, F., Prevost, M.
Concentration Dependent Ion Selectivity in VDAC: A Molecular Dynamics Simulation Study
PLOS ONE, 6: Art. No. e27994, DEC 2 2011
abstract,
full text
Biswas, M., Voltz, K., Smith, J.C., Langowski, J.
Role of Histone Tails in Structural Stability of the Nucleosome
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002279, DEC 2011
abstract,
full text
Ruiz, L., Keten, S.
ATOMISTIC MODELING AND MECHANICS OF SELF-ASSEMBLED ORGANIC NANOTUBES
INTERNATIONAL JOURNAL OF APPLIED MECHANICS, 3:667-684, DEC 2011
abstract,
full text
Tordesillas, L., Gamboa, P., Sanz, M.L., Palacin, A., Gomez-Casado, C., Cuesta-Herranz, J., Pacios, L.F., Salcedo, G., Diaz-Perales, A.
A mutant of the major melon allergen, Cuc m 2, with reduced IgE binding capacity is a good candidate for specific immunotherapy
MOLECULAR IMMUNOLOGY, 49:504-511, DEC 2011
abstract,
full text
Wanunu, M., Bhattacharya, S., Xie, Y., Tor, Y., Aksimentiev, A., Drndic, M.
Nanopore Analysis of Individual RNA/Antibiotic Complexes
ACS NANO, 5:9345-9353, DEC 2011
abstract,
full text
Mrinal, N., Tomar, A., Nagaraju, J.
Role of sequence encoded kappa B DNA geometry in gene regulation by Dorsal
NUCLEIC ACIDS RESEARCH, 39:9574-9591, DEC 2011
abstract,
full text
Kurkcuoglu, Z., Ural, G., Akten, E.D., Doruker, P.
Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human
MOLECULAR INFORMATICS, 30:986-995, DEC 2011
abstract,
full text
Zobnina, V.G., Kosevich, M.V., Chagovets, V.V., Boryak, O.A., Kulik, A.N., Gomory, A.
Stable associates of polyether oligomers with chlorine anion as revealed by the data of electrospray mass spectrometry and molecular dynamics
JOURNAL OF ANALYTICAL CHEMISTRY, 66:1341-1347, DEC 2011
abstract,
full text
Wang, X.L., Kumar, S., Singh, S.K.
Disulfide Scrambling in IgG2 Monoclonal Antibodies: Insights from Molecular Dynamics Simulations
PHARMACEUTICAL RESEARCH, 28:3128-3144, DEC 2011
abstract,
full text
Sanli, D., Keskin, O., Gursoy, A., Erman, B.
Structural cooperativity in histone H3 tail modifications
PROTEIN SCIENCE, 20:1982-1990, DEC 2011
abstract,
full text
Melillo, M., Zhu, F.Q., Snyder, M.A., Mittal, J.
Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2978-2983, DEC 1 2011
abstract,
full text
Colpitts, C.C., Kim, S.S., Posehn, S.E., Jepson, C., Kim, S.Y., Wiedemann, G., Reski, R., Wee, A.G.H., Douglas, C.J., Suh, D.Y.
PpASCL, a moss ortholog of anther-specific chalcone synthase-like enzymes, is a hydroxyalkylpyrone synthase involved in an evolutionarily conserved sporopollenin biosynthesis pathway
NEW PHYTOLOGIST, 192:855-868, DEC 2011
abstract,
full text
Matthai, C.C., March, N.H.
The application of condensed matter methods to the study of the conformation and elastic properties of biopolymers and the transport of DNA through cell membranes
THEORETICAL CHEMISTRY ACCOUNTS, 130:1155-1167, DEC 2011
abstract,
full text
Schmidtke, P., Bidon-Chanal, A., Luque, F.J., Barril, X.
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
BIOINFORMATICS, 27:3276-3285, DEC 1 2011
abstract,
full text
Ren, H., Jiang, J., Mukamel, S.
Deep UV Resonance Raman Spectroscopy of beta-Sheet Amyloid Fibrils: A QM/MM Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13955-13962, DEC 1 2011
abstract,
full text
Du, H.L., Li, J.Y., Zhang, J., Su, G., Li, X.Y., Zhao, Y.L.
Separation of Hydrogen and Nitrogen Gases with Porous Graphene Membrane
JOURNAL OF PHYSICAL CHEMISTRY C, 115:23261-23266, DEC 1 2011
abstract,
full text
Lin, Y.W., Liao, L.F.
Probing interactions between uranyl ions and lipid membrane by molecular dynamics simulation
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 976:130-134, DEC 1 2011
abstract,
full text
Skjaerven, L., Reuter, N., Martinez, A.
Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach
FUTURE MEDICINAL CHEMISTRY, 3:2079-2100, DEC 2011
abstract,
full text
Izanloo, C., Parsafar, G.A., Abroshan, H., Akbarzadeh, H.
Denaturation of Drew-Dickerson DNA in a High Salt Concentration Medium: Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3354-3361, DEC 2011
abstract,
full text
Bairagya, H.R., Mukhopadhyay, B.P., Bera, A.K.
Role of Salt Bridge Dynamics in Inter Domain Recognition of Human IMPDH Isoforms: An Insight to Inhibitor Topology for Isoform-II
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:441-462, DEC 2011
abstract,
full text
Renthal, R., Brancaleon, L., Pena, I., Silva, F., Chen, L.Y.
Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles
BIOPHYSICAL CHEMISTRY, 159:321-327, DEC 2011
abstract,
full text
Dawid, A., Gorny, K., Gburski, Z.
The structural studies of fullerenol C(60)(OH)(24) and nitric oxide mixture in water solvent - MD simulation
NITRIC OXIDE-BIOLOGY AND CHEMISTRY, 25:373-380, NOV 30 2011
abstract,
full text
Abdel-Azeim, S., Li, X., Chung, L.W., Morokuma, K.
Zinc-Homocysteine Binding in Cobalamin-Dependent Methionine Synthase and its Role in the Substrate Activation: DFT, ONIOM, and QM/MM Molecular Dynamics Studies
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3154-3167, NOV 30 2011
abstract,
full text
Bannerman, M.N., Sargant, R., Lue, L.
DynamO: A Free O(N) General Event-Driven Molecular Dynamics Simulator
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3329-3338, NOV 30 2011
abstract,
full text
Xiang, X., Lee, C.Y., Li, T., Chen, W., Lou, J.Z., Zhu, C.
Structural Basis and Kinetics of Force-Induced Conformational Changes of an alpha A Domain-Containing Integrin
PLOS ONE, 6: Art. No. e27946, NOV 28 2011
abstract,
full text
Joshi, H., Cheluvaraja, S., Somogyi, E., Brown, D.R., Ortoleva, P.
A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity
VACCINE, 29:9423-9430, NOV 28 2011
abstract,
full text
Fu, C.W., Lin, T.H.
Theoretical Study on the Alkaline Hydrolysis of Methyl Thioacetate in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY A, 115:13523-13533, NOV 24 2011
abstract,
full text
Gross, A.S., Bell, A.T., Chu, J.W.
Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13433-13440, NOV 24 2011
abstract,
full text
Priya, M.H., Ashbaugh, H.S., Paulaitis, M.E.
Cosolvent Preferential Molecular Interactions in Aqueous Solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13633-13642, NOV 24 2011
abstract,
full text
Yuzlenko, O., Lazandis, T.
Interactions between Ionizable Amino Acid Side Chains at a Lipid Bilayer-Water Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13674-13684, NOV 24 2011
abstract,
full text
Shukla, D., Schneider, C.P., Trout, B.L.
Complex Interactions between Molecular Ions in Solution and Their Effect on Protein Stability
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:18713-18718, NOV 23 2011
abstract,
full text
Nemkevich, A., Spackman, M.A., Corry, B.
Mechanism of Concerted Hydrogen Bond Reorientation in Clathrates of Dianin's Compound and Hydroquinone
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:18880-18888, NOV 23 2011
abstract,
full text
Yamaguchi, S., Watanabe, H., Mondal, S.K., Kundu, A., Tahara, T.
"Up" versus "down" alignment and hydration structures of solutes at the air/water interface revealed by heterodyne-detected electronic sum frequency generation with classical molecular dynamics simulation
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 194705, NOV 21 2011
abstract,
full text
Schneider, C.P., Shukla, D., Trout, B.L.
Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers
PLOS ONE, 6: Art. No. e27665, NOV 18 2011
abstract,
full text
da Silva, L.P., da Silva, J.C.G.E.
Study on the Effects of Intermolecular Interactions on Firefly Multicolor Bioluminescence
CHEMPHYSCHEM, 12:3002-3008, NOV 18 2011
abstract,
full text
Dai, Z.W., Wan, L.S., Huang, X.J., Ling, J., Xu, Z.K.
Selective Adsorption of Isopropyl Alcohol Aqueous Solution on Polypropylene Surfaces: A Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY C, 115:22415-22421, NOV 17 2011
abstract,
full text
Sun, S., Wong, J.T.Y., Zhang, T.Y.
Atomistic Simulations of Electroporation in Water Preembedded Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13355-13359, NOV 17 2011
abstract,
full text
Cho, S.S., Reddy, G., Straub, J.E., Thirumalai, D.
Entropic Stabilization of Proteins by TMAO
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13401-13407, NOV 17 2011
abstract,
full text
Heinzelmann, G., Bastug, T., Kuyucak, S.
Free Energy Simulations of Ligand Binding to the Aspartate Transporter Glt(Ph)
BIOPHYSICAL JOURNAL, 101:2380-2388, NOV 16 2011
abstract,
full text
Re, S., Miyashita, N., Yamaguchi, Y., Sugita, Y.
Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 101:L44-L46, NOV 16 2011
abstract,
full text
Shekhar, P., Nanda, H., Losche, M., Heinrich, F.
Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques
JOURNAL OF APPLIED PHYSICS, 110: Art. No. 102216, NOV 15 2011
abstract,
full text
Luo, Y., Harder, E., Faibish, R.S., Roux, B.
Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane
JOURNAL OF MEMBRANE SCIENCE, 384:1-9, NOV 15 2011
abstract,
full text
Lam, A.R., Jiang, J., Mukamel, S.
Distinguishing Amyloid Fibril Structures in Alzheimer's Disease (AD) by Two-Dimensional Ultraviolet (2DUV) Spectroscopy
BIOCHEMISTRY, 50:9809-9816, NOV 15 2011
abstract,
full text
Garate, J.A., English, N.J., Singh, A., Ryan, K.M., Mooney, D.A., MacElroy, J.M.D.
Electrophoretic Deposition of Poly(3-decylthiophene) onto Gold-Mounted Cadmium Selenide Nanorods
LANGMUIR, 27:13506-13513, NOV 15 2011
abstract,
full text
Ganesan, N., Bauer, B.A., Lucas, T.R., Patel, S., Taufer, M.
Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers From Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs)
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2958-2973, NOV 15 2011
abstract,
full text
Borstnik, U., Miller, B.T., Brooks, B.R., Janezic, D.
The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3005-3013, NOV 15 2011
abstract,
full text
Garcia-Risueno, P., Echenique, P., Alonso, J.L.
Exact and Efficient Calculation of Lagrange Multipliers in Biological Polymers with Constrained Bond Lengths and Bond Angles: Proteins and Nucleic Acids as Example Cases
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3039-3046, NOV 15 2011
abstract,
full text
Jo, S., Song, K.C., Desaire, H., MacKerell, A.D., Im, W.
Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3135-3141, NOV 15 2011
abstract,
full text
Weber, V., Merchant, S., Asthagiri, D.
Communication: Regularizing binding energy distributions and thermodynamics of hydration: Theory and application to water modeled with classical and ab initio simulations
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 181101, NOV 14 2011
abstract,
full text
Ferrer, T., Cordero-Morales, J.F., Arias, M., Ficker, E., Medovoy, D., Perozo, E., Tristani-Firouzi, M.
Molecular Coupling in the Human ether-a-go-go-related gene-1 (hERG1) K(+) Channel Inactivation Pathway
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:39091-39099, NOV 11 2011
abstract,
full text
Li, M.H., Zheng, W.J.
Probing the Structural and Energetic Basis of Kinesin-Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
BIOCHEMISTRY, 50:8645-8655, NOV 11 2011
abstract,
full text
Lim, K.H., Huang, H., Pralle, A., Park, S.
Engineered Streptavidin Monomer and Dimer with Improved Stability and Function
BIOCHEMISTRY, 50:8682-8691, NOV 11 2011
abstract,
full text
Elola, M.D., Rodriguez, J., Laria, D.
Liquid Methanol Confined within Functionalized Silica Nanopores. 2. Solvation Dynamics of Coumarin 153
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12859-12867, NOV 10 2011
abstract,
full text
D'Antonio, E.L., D'Antonio, J., de Serrano, V., Gracz, H., Thompson, M.K., Ghiladi, R.A., Bowden, E.F., Franzen, S.
Functional Consequences of the Creation of an Asp-His-Fe Triad in a 3/3 Globin
BIOCHEMISTRY, 50:9664-9680, NOV 8 2011
abstract,
full text
Calligari, P., Calandrini, V., Kneller, G.R., Abergel, D.
From NMR Relaxation to Fractional Brownian Dynamics in Proteins: Results from a Virtual Experiment
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12370-12379, NOV 3 2011
abstract,
full text
Mondal, S., Khelashvili, G., Shan, J.F., Andersen, O.S., Weinstein, H.
Quantitative Modeling of Membrane Deformations by Multihelical Membrane Proteins: Application to G-Protein Coupled Receptors
BIOPHYSICAL JOURNAL, 101:2092-2101, NOV 2 2011
abstract,
full text
Luan, B.Q., Martyna, G., Stolovitzky, G.
Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore
BIOPHYSICAL JOURNAL, 101:2214-2222, NOV 2 2011
abstract,
full text
Anisimov, V.M., Ziemys, A., Kizhake, S., Yuan, Z.Y., Natarajan, A., Cavasotto, C.N.
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:1071-1084, NOV 2011
abstract,
full text
Gao, X., Zhang, N., Wei, T.D., Su, H.N., Xie, B.B., Dong, C.C., Zhang, X.Y., Chen, X.L., Zhou, B.C., Wang, Z.X., Wu, J.W., Zhang, Y.Z.
Crystal structure of the N-terminal domain of linker L(R) and the assembly of cyanobacterial phycobilisome rods
MOLECULAR MICROBIOLOGY, 82:698-705, NOV 2011
abstract,
full text
Elder, R.M., Emrick, T., Jayaraman, A.
Understanding the Effect of Polylysine Architecture on DNA Binding Using Molecular Dynamics Simulations
BIOMACROMOLECULES, 12:3870-3879, NOV 2011
abstract,
full text
Kraszewski, S., Tarek, M., Ramseyer, C.
Uptake and Translocation Mechanisms of Cationic Amino Derivatives Functionalized on Pristine C(60) by Lipid Membranes: A Molecular Dynamics Simulation Study
ACS NANO, 5:8571-8578, NOV 2011
abstract,
full text
Sathe, C., Zou, X.Q., Leburton, J.P., Schulten, K.
Computational Investigation of DNA Detection Using Graphene Nanopores
ACS NANO, 5:8842-8851, NOV 2011
abstract,
full text,
TCBG publications
Huggins, D.J., Marsh, M., Payne, M.C.
Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3514-3522, NOV 2011
abstract,
full text
Tanner, D.E., Chan, K.Y., Phillips, J.C., Schulten, K.
Parallel Generalized Born Implicit Solvent Calculations with NAMD
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3635-3642, NOV 2011
abstract,
full text,
TCBG publications
Gilman-Politi, R., Harries, D.
Unraveling the Molecular Mechanism of Enthalpy Driven Peptide Folding by Polyol Osmolytes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3816-3828, NOV 2011
abstract,
full text
Durrant, J.D., McCammon, J.A.
HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 31:5-9, NOV 2011
abstract,
full text
Du, X.N., Zhang, X., Qi, J.L., An, H.L., Li, J.W., Wan, Y.M., Fu, Y., Gao, H.X., Gao, Z.B., Zhan, Y., Zhang, H.L.
Characteristics and molecular basis of celecoxib modulation on K(v)7 potassium channels
BRITISH JOURNAL OF PHARMACOLOGY, 164:1722-1737, NOV 2011
abstract,
full text
Kwon, T., Harris, A.L., Rossi, A., Bargiello, T.A.
Molecular dynamics simulations of the Cx26 hemichannel: Evaluation of structural models with Brownian dynamics
JOURNAL OF GENERAL PHYSIOLOGY, 138:475-493, NOV 2011
abstract,
full text
Feldmann, E.A., Ni, S., Sahu, I.D., Mishler, C.H., Risser, D.D., Murakami, J.L., Tom, S.K., McCarrick, R.M., Lorigan, G.A., Tolbert, B.S., Callahan, S.M., Kennedy, M.A.
Evidence for Direct Binding between HetR from Anabaena sp PCC 7120 and PatS-5
BIOCHEMISTRY, 50:9212-9224, NOV 1 2011
abstract,
full text
Mishra, S., Caflisch, A.
Dynamics in the Active Site of beta-Secretase: A Network Analysis of Atomistic Simulations
BIOCHEMISTRY, 50:9328-9339, NOV 1 2011
abstract,
full text
Utesch, T., Daminelli, G., Mroginski, M.A.
Molecular Dynamics Simulations of the Adsorption of Bone Morphogenetic Protein-2 on Surfaces with Medical Relevance
LANGMUIR, 27:13144-13153, NOV 1 2011
abstract,
full text
Valley, C.C., Perlmutter, J.D., Braun, A.R., Sachs, J.N.
NaCl Interactions with Phosphatidylcholine Bilayers Do Not Alter Membrane Structure but Induce Long-Range Ordering of Ions and Water
JOURNAL OF MEMBRANE BIOLOGY, 244:35-42, NOV 2011
abstract,
full text
Severin, P.M.D., Zou, X.Q., Gaub, H.E., Schulten, K.
Cytosine methylation alters DNA mechanical properties
NUCLEIC ACIDS RESEARCH, 39:8740-8751, NOV 2011
abstract,
full text,
TCBG publications
Barata, T.S., Brocchini, S., Teo, I., Shaunak, S., Zloh, M.
From sequence to 3D structure of hyperbranched molecules: application to surface modified PAMAM dendrimers
JOURNAL OF MOLECULAR MODELING, 17:2741-2749, NOV 2011
abstract,
full text
Sadasivan, V.D., Narpala, S.R., Budil, D.E., Sacco, A., Carrier, R.L.
Modeling the human intestinal Mucin (MUC2) C-terminal cystine knot dimer
JOURNAL OF MOLECULAR MODELING, 17:2953-2963, NOV 2011
abstract,
full text
Contreras-Torres, F.F., Martinez-Loran, E.
DNA insertion in and wrapping around carbon nanotubes
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:902-919, NOV-DEC 2011
abstract,
full text
Caulfield, T., Medina-Franco, J.L.
Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A
JOURNAL OF STRUCTURAL BIOLOGY, 176:185-191, NOV 2011
abstract,
full text
Sammond, D.W., Joce, C., Takeshita, R., McQuate, S.E., Ghosh, N., Martin, J.M., Yin, H.
Transmembrane Peptides Used to Investigate the Homo-Oligomeric Interface and Binding Hotspot of Latent Membrane Protein 1
BIOPOLYMERS, 95:772-784, NOV 2011
abstract,
full text
Durrant, J.D., McCammon, J.A.
Molecular dynamics simulations and drug discovery
BMC BIOLOGY, 9: Art. No. 71, OCT 28 2011
abstract,
full text
Espinoza-Fonseca, L.M., Thomas, D.D.
Atomic-Level Characterization of the Activation Mechanism of SERCA by Calcium
PLOS ONE, 6: Art. No. e26936, OCT 27 2011
abstract,
full text
Tsutakawa, S.E., Van Wynsberghe, A.W., Freudenthal, B.D., Weinacht, C.P., Gakhar, L., Washington, M.T., Zhuang, Z.H., Tainer, J.A., Ivanov, I.
Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:17672-17677, OCT 25 2011
abstract,
full text
Nam, K.Y., Chang, B.H., No, K.T.
Conformational Study of N-terminal Prion Peptides by Molecular Dynamics Simulations
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 32:3553-3554, OCT 20 2011
full text
Teh, A.H., Saito, J.A., Baharuddin, A., Tuckerman, J.R., Newhouse, J.S., Kanbe, M., Newhouse, E.I., Rahim, R.A., Favier, F., Didierjean, C., Sousa, E.H.S., Stott, M.B., Dunfield, P.F., Gonzalez, G., Gilles-Gonzalez, M.A., Najimudin, N., Alam, M.
Hell's Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin
FEBS LETTERS, 585:3250-3258, OCT 20 2011
abstract,
full text
Lee, T.S., Giambasu, G.M., Harris, M.E., York, D.M.
Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2538-2543, OCT 20 2011
abstract,
full text
Shukla, D., Trout, B.L.
Understanding the Synergistic Effect of Arginine and Glutamic Acid Mixtures on Protein Solubility
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11831-11839, OCT 20 2011
abstract,
full text
Lin, Y.C., Silvestre-Ryan, J., Himmel, M.E., Crowley, M.F., Beckham, G.T., Chu, J.W.
Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:16617-16624, OCT 19 2011
abstract,
full text
Willenbring, D., Liu, L.T., Mowrey, D., Xu, Y., Tang, P.
Isoflurane Alters the Structure and Dynamics of GLIC
BIOPHYSICAL JOURNAL, 101:1905-1912, OCT 19 2011
abstract,
full text
Ettig, R., Kepper, N., Stehr, R., Wedemann, G., Rippe, K.
Dissecting DNA-Histone Interactions in the Nucleosome by Molecular Dynamics Simulations of DNA Unwrapping
BIOPHYSICAL JOURNAL, 101:1999-2008, OCT 19 2011
abstract,
full text
Virtanen, J.J., Makowski, L., Sosnick, T.R., Freed, K.F.
Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering
BIOPHYSICAL JOURNAL, 101:2061-2069, OCT 19 2011
abstract,
full text
Mekhaiel, D.N.A., Czajkowsky, D.M., Andersen, J.T., Shi, J.G., El-Faham, M., Doenhoff, M., McIntosh, R.S., Sandlie, I., He, J.F., Hu, J., Shao, Z.F., Pleass, R.J.
Polymeric human Fc-fusion proteins with modified effector functions
SCIENTIFIC REPORTS, 1: Art. No. 124, OCT 19 2011
abstract,
full text
Ma, C.W., Xiu, Z.L., Zeng, A.P.
A New Concept to Reveal Protein Dynamics Based on Energy Dissipation
PLOS ONE, 6: Art. No. e26453, OCT 17 2011
abstract,
full text
Jackson, P.L., Noerager, B.D., Jablonsky, M.J., Hardison, M.T., Cox, B.D., Patterson, J.C., Dhanapal, B., Blalock, J.E., Muccio, D.D.
A CXCL8 receptor antagonist based on the structure of N-acetyl-proline-glycine-proline
EUROPEAN JOURNAL OF PHARMACOLOGY, 668:435-442, OCT 15 2011
abstract,
full text
Saunders, M.G., Voth, G.A.
Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis
JOURNAL OF MOLECULAR BIOLOGY, 413:279-291, OCT 14 2011
abstract,
full text
Pedretti, A., Labozzetta, A., Lo Monte, M., Beccari, A.R., Moriconi, A., Vistoli, G.
Exploring the activation mechanism of TRPM8 channel by targeted MD simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 414:14-19, OCT 14 2011
abstract,
full text
Palermo, G., Branduardi, D., Masetti, M., Lodoa, A., Mor, M., Piomelli, D., Cavalli, A., De Vivo, M.
Covalent Inhibitors of Fatty Acid Amide Hydrolase: A Rationale for the Activity of Piperidine and Piperazine Aryl Ureas
JOURNAL OF MEDICINAL CHEMISTRY, 54:6612-6623, OCT 13 2011
abstract,
full text
Dlugosz, M., Trylska, J.
Secondary Structures of Native and Pathogenic Huntingtin N-Terminal Fragments
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11597-11608, OCT 13 2011
abstract,
full text
Souza, P.C.T., Barra, G.B., Velasco, L.F.R., Ribeiro, I.C.J., Simeoni, L.A., Togashi, M., Webb, P., Neves, F.A.R., Skaf, M.S., Martinez, L., Polikarpov, I.
Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants
JOURNAL OF MOLECULAR BIOLOGY, 412:882-893, OCT 7 2011
abstract,
full text
Duff, N., Peters, B.
Polymorph specific RMSD local order parameters for molecular crystals and nuclei: alpha-, beta-, and gamma-glycine
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 134101, OCT 7 2011
abstract,
full text
Sinha, S.K., Bandyopadhyay, S.
Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 135101, OCT 7 2011
abstract,
full text
Sorensen, J., Periole, X., Skeby, K.K., Marrink, S.J., Schiott, B.
Protofibrillar Assembly Toward the Formation of Amyloid Fibrils
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2385-2390, OCT 6 2011
abstract,
full text
Carnevale, V., Treptow, W., Klein, M.L.
Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2504-2508, OCT 6 2011
abstract,
full text
Dixit, A., Verkhivker, G.M.
The Energy Landscape Analysis of Cancer Mutations in Protein Kinases
PLOS ONE, 6: Art. No. e26071, OCT 6 2011
abstract,
full text
Goldsmith, J., Hinds, B.J.
Simulation of Steady-State Methanol Flux through a Model Carbon Nanotube Catalyst Support
JOURNAL OF PHYSICAL CHEMISTRY C, 115:19158-19164, OCT 6 2011
abstract,
full text
Giangreco, I., Lattanzi, G., Nicolotti, O., Catto, M., Laghezza, A., Leonetti, F., Stefanachi, A., Carotti, A.
Insights into the Complex Formed by Matrix Metalloproteinase-2 and Alloxan Inhibitors: Molecular Dynamics Simulations and Free Energy Calculations
PLOS ONE, 6: Art. No. e25597, OCT 5 2011
abstract,
full text
Furini, S., Domene, C.
Gating at the Selectivity Filter of Ion Channels that Conduct Na(+) and K(+) Ions
BIOPHYSICAL JOURNAL, 101:1623-1631, OCT 5 2011
abstract,
full text
Sarkar, A., Zhou, C., Meklemburg, R., Wintrode, P.L.
Local Conformational Flexibility Provides a Basis for Facile Polymer Formation in Human Neuroserpin
BIOPHYSICAL JOURNAL, 101:1758-1765, OCT 5 2011
abstract,
full text
Patapati, K.K., Glykos, N.M.
Three Force Fields' Views of the 3(10) Helix
BIOPHYSICAL JOURNAL, 101:1766-1771, OCT 5 2011
abstract,
full text
Bisson, M., Bernaschi, M., Melchionna, S.
Parallel Molecular Dynamics with Irregular Domain Decomposition
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 10:1071-1088, OCT 2011
abstract,
full text
Demir, O., Baronio, R., Salehi, F., Wassman, C.D., Hall, L., Hatfield, G.W., Chamberlin, R., Kaiser, P., Lathrop, R.H., Amaro, R.E.
Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002238, OCT 2011
abstract,
full text
Dixit, A., Verkhivker, G.M.
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002179, OCT 2011
abstract,
full text
Koldso, H., Noer, P., Grouleff, J., Autzen, H.E., Sinning, S., Schiott, B.
Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na(+) Ion Release
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002246, OCT 2011
abstract,
full text
Sethi, A., Goldstein, B., Gnanakaran, S.
Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002192, OCT 2011
abstract,
full text
Atkinson, J., Kapralov, A.A., Yanamala, N., Tyurina, Y.Y., Amoscato, A.A., Pearce, L., Peterson, J., Huang, Z.T., Jiang, J.F., Samhan-Arias, A.K., Maeda, A., Feng, W.H., Wasserloos, K., Belikova, N.A., Tyurin, V.A., Wang, H., Fletcher, J., Wang, Y.S., Vlasova, I.I., Klein-Seetharaman, J., Stoyanovsky, D.A., Bayir, H., Pitt, B.R., Epperly, M.W., Greenberger, J.S., Kagan, V.E.
A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death
NATURE COMMUNICATIONS, 2: Art. No. 497, OCT 2011
abstract,
full text
Skillman, K.M., Diraviyam, K., Khan, A., Tang, K.L., Sept, D., Sibley, L.D.
Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites
PLOS PATHOGENS, 7: Art. No. e1002280, OCT 2011
abstract,
full text
Ahmed, A.A., Goldsmith, J., Fokt, I., Le, X.F., Krzysko, K.A., Lesyng, B., Bast, R.C., Priebe, W.
A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer
CANCER CHEMOTHERAPY AND PHARMACOLOGY, 68:1033-1044, OCT 2011
abstract,
full text
Han, C., Wang, J.P.
Temperature-Dependence of the Amide-I Frequency Map for Peptides Proteins
CHINESE JOURNAL OF CHEMICAL PHYSICS, 24:529-537, OCT 2011
abstract,
full text
Lindbo, D., Tornberg, A.K.
Spectral accuracy in fast Ewald-based methods for particle simulations
JOURNAL OF COMPUTATIONAL PHYSICS, 230:8744-8761, OCT 1 2011
abstract,
full text
Vaitheeswaran, S., Chen, J., Thirumalai, D.
Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins
JOURNAL OF STATISTICAL PHYSICS, 145:276-292, OCT 2011
abstract,
full text
Joshi, H., Singharoy, A., Sereda, Y.V., Cheluvaraja, S.C., Ortoleva, P.J.
Multiscale simulation of microbe structure and dynamics
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 107:200-217, OCT 2011
abstract,
full text
Vassiliev, S., Mahboob, A., Bruce, D.
Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes
PHOTOSYNTHESIS RESEARCH, 110:25-38, OCT 2011
abstract,
full text
Guvench, O., Mallajosyula, S.S., Raman, E.P., Hatcher, E., Vanommeslaeghe, K., Foster, T.J., Jamison, F.W., MacKerell, A.D.
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate-Protein Modeling
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3162-3180, OCT 2011
abstract,
full text
Wang, Y., Markwick, P.R.L., de Oliveira, C.A.F., McCammon, J.A.
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3199-3207, OCT 2011
abstract,
full text
Nayar, D., Agarwal, M., Chakravarty, C.
Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3354-3367, OCT 2011
abstract,
full text
Patel, J.S., Branduardi, D., Masetti, M., Rocchia, W., Cavalli, A.
Insights into Ligand-Protein Binding from Local Mechanical Response
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3368-3378, OCT 2011
abstract,
full text
Eichenberger, A.P., Allison, J.R., Dolenc, J., Geerke, D.P., Horta, B.A.C., Meier, K., Oostenbrink, C., Schmid, N., Steiner, D., Wang, D.Q., van Gunsteren, W.F.
GROMOS plus plus Software for the Analysis of Biomolecular Simulation Trajectories
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3379-3390, OCT 2011
abstract,
full text
Volzing, K., Biliouris, K., Kaznessis, Y.N.
proTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression
ACS CHEMICAL BIOLOGY, 6:1107-1116, OCT 2011
abstract,
full text
Durrant, J.D., Friedman, A.J., McCammon, J.A.
CrystalDock: A Novel Approach to Fragment-Based Drug Design
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2573-2580, OCT 2011
abstract,
full text
Wright, D.W., Coveney, P.V.
Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2636-2649, OCT 2011
abstract,
full text
Muixi, L., Gay, M., Munoz-Torres, P.M., Guitart, C., Cedano, J., Abian, J., Alvarez, I., Jaraquemada, D.
The peptide-binding motif of HLA-DR8 shares important structural features with other type 1 diabetes-associated alleles
GENES AND IMMUNITY, 12:504-512, OCT 2011
abstract,
full text
Soriano-Ursua, M.A., Correa-Basurto, J., Trujillo-Ferrara, J.G., Kaumann, A.J.
Homology model and docking studies on porcine beta(2) adrenoceptor: description of two binding sites
JOURNAL OF MOLECULAR MODELING, 17:2525-2538, OCT 2011
abstract,
full text
Spangberg, D., Larsson, D.S.D., van der Spoel, D.
Trajectory NG: portable, compressed, general molecular dynamics trajectories
JOURNAL OF MOLECULAR MODELING, 17:2669-2685, OCT 2011
abstract,
full text
Sun, C.B., T'ang, T., Uludag, H.
Molecular Dynamics Simulations of PEI Mediated DNA Aggregation
BIOMACROMOLECULES, 12:3698-3707, OCT 2011
abstract,
full text
Blasco, B., Stenta, M., Alonso-Sarduy, L., Dietler, G., Dal Peraro, M., Cole, S.T., Pojer, F.
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
MOLECULAR MICROBIOLOGY, 82:251-264, OCT 2011
abstract,
full text
Korchowiec, B., Korchowiec, J., Hato, M., Rogalska, E.
Glycolipid-cholesterol monolayers: Towards a better understanding of the interaction between the membrane components
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2466-2476, OCT 2011
abstract,
full text
Warshaviak, D.T., Muellner, M.J., Chachisvilis, M.
Effect of membrane tension on the electric field and dipole potential of lipid bilayer membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2608-2617, OCT 2011
abstract,
full text
Li, P., Liu, M., Tan, J.J., Zhang, X.Y., Chen, W.Z., Wang, C.X.
Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:311-323, OCT 2011
abstract,
full text
Liu, Y.Z., Chipot, C., Shao, X.G., Cai, W.S.
The effects of 7-dehydrocholesterol on the structural properties of membranes
PHYSICAL BIOLOGY, 8: Art. No. 056005, OCT 2011
abstract,
full text
Lucas, M.F., Rousseau, D.L., Guallar, V.
Electron transfer pathways in cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:1305-1313, OCT 2011
abstract,
full text
Wan, S.Z., Coveney, P.V.
Molecular Dynamics Simulation Reveals Structural and Thermodynamic Features of Kinase Activation by Cancer Mutations Within the Epidermal Growth Factor Receptor
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2843-2852, OCT 2011
abstract,
full text
Ma, B.Y., Nussinov, R.
Polymorphic Triple beta-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid beta 42 Peptide
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:34244-34253, SEP 30 2011
abstract,
full text
Lee, K.H., Miller, C.R., Nagel, A.C., Wichman, H.A., Joyce, P., Ytreberg, F.M.
First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus
PLOS ONE, 6: Art. No. e25640, SEP 29 2011
abstract,
full text
Slade, D., Dunstan, M.S., Barkauskaite, E., Weston, R., Lafite, P., Dixon, N., Ahel, M., Leys, D., Ahel, I.
The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase
NATURE, 477:616-U150, SEP 29 2011
abstract,
full text
Mallajosyula, S.S., MacKerell, A.D.
Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11215-11229, SEP 29 2011
abstract,
full text
Bardhan, J.P., Knepley, M.G.
Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 124107, SEP 28 2011
abstract,
full text
Calero, C., Faraudo, J., Bastos-Gonzalez, D.
Interaction of Monovalent Ions with Hydrophobic and Hydrophilic Colloids: Charge Inversion and Ionic Specificity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:15025-15035, SEP 28 2011
abstract,
full text
Torres, R., Swift, R.V., Chim, N., Wheatley, N., Lan, B.S., Atwood, B.R., Pujol, C., Sankaran, B., Bliska, J.B., Amaro, R.E., Goulding, C.W.
Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis
PLOS ONE, 6: Art. No. e25084, SEP 26 2011
abstract,
full text
Monajjemi, M., Sabaghzadeh, R., Ilkhani, A.R., Mollaamin, F.
Nano-modeling of insulin-like growth factor 1 (IGF-1) by computational methods
AFRICAN JOURNAL OF MICROBIOLOGY RESEARCH, 5:2895-2905, SEP 23 2011
abstract,
full text
Favia, A.D., Masetti, M., Recanatini, M., Cavalli, A.
Substrate Binding Process and Mechanistic Functioning of Type 1 11 beta-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods
PLOS ONE, 6: Art. No. e25375, SEP 23 2011
abstract,
full text
Shim, J.Y., Bertalovitz, A.C., Kendall, D.A.
Identification of Essential Cannabinoid-binding Domains STRUCTURAL INSIGHTS INTO EARLY DYNAMIC EVENTS IN RECEPTOR ACTIVATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:33422-33435, SEP 23 2011
abstract,
full text
Kim, S.N., Kuang, Z.F., Slocik, J.M., Jones, S.E., Cui, Y., Farmer, B.L., McAlpine, M.C., Naik, R.R.
Preferential Binding of Peptides to Graphene Edges and Planes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14480-14483, SEP 21 2011
abstract,
full text
Miao, Y.L., Baudry, J.
Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process
BIOPHYSICAL JOURNAL, 101:1493-1503, SEP 21 2011
abstract,
full text
King, D.T., Warren, D.B., Pouton, C.W., Chalmers, D.K.
Using Molecular Dynamics to Study Liquid Phase Behavior: Simulations of the Ternary Sodium Laurate/Sodium Oleate/Water System
LANGMUIR, 27:11381-11393, SEP 20 2011
abstract,
full text
Barr, D., Oashi, T., Burkhard, K., Lucius, S., Samadani, R., Zhang, J., Shapiro, P., MacKerell, A.D., van der Vaart, A.
Importance of Domain Closure for the Autoactivation of ERK2
BIOCHEMISTRY, 50:8038-8048, SEP 20 2011
abstract,
full text
Modi, N., Singh, P.R., Mahendran, K.R., Schulz, R., Winterhalter, M., Kleinekathofer, U.
Probing the Transport of Ionic Liquids in Aqueous Solution through Nanopores
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2331-2336, SEP 15 2011
abstract,
full text
Naidu, M.D., Agarwal, R., Pena, L.A., Cunha, L., Mezei, M., Shen, M., Wilson, D.M., Liu, Y., Sanchez, Z., Chaudhary, P., Wilson, S.H., Waring, M.J.
Lucanthone and Its Derivative Hycanthone Inhibit Apurinic Endonuclease-1 (APE1) by Direct Protein Binding
PLOS ONE, 6: Art. No. e23679, SEP 15 2011
abstract,
full text
Singleton, B.K., Lau, W., Fairweather, V.S.S., Burton, N.M., Wilson, M.C., Parsons, S.F., Richardson, B.M., Trakarnsanga, K., Brady, R.L., Anstee, D.J., Frayne, J.
Mutations in the second zinc finger of human EKLF reduce promoter affinity but give rise to benign and disease phenotypes
BLOOD, 118:3137-3145, SEP 15 2011
abstract,
full text
Matyushov, D.V.
Nanosecond Stokes Shift Dynamics, Dynamical Transition, and Gigantic Reorganization Energy of Hydrated Heme Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10715-10724, SEP 15 2011
abstract,
full text
Videla, P.E., Sala, J., Marti, J., Guardia, E., Laria, D.
Aqueous electrolytes confined within functionalized silica nanopores
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 104503, SEP 14 2011
abstract,
full text
Ulucan, O., Keskin, O., Erman, B., Gursoy, A.
A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A
PLOS ONE, 6: Art. No. e24664, SEP 13 2011
abstract,
full text
Cui, Y.B., Bastien, D.A.
Water transport in human aquaporin-4: Molecular dynamics (MD) simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 412:654-659, SEP 9 2011
abstract,
full text
Lawrence, S.A., Hackett, J.C., Moran, R.G.
Tetrahydrofolate Recognition by the Mitochondrial Folate Transporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:31480-31489, SEP 9 2011
abstract,
full text
Shah, M., Santiso, E.E., Trout, B.L.
Computer Simulations of Homogeneous Nucleation of Benzene from the Melt
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10400-10412, SEP 8 2011
abstract,
full text
Cho, H.M., Gross, A.S., Chu, J.W.
Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14033-14041, SEP 7 2011
abstract,
full text
Hsin, J., LaPointe, L.M., Kazy, A., Chipot, C., Senes, A., Schulten, K.
Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14071-14081, SEP 7 2011
abstract,
full text,
TCBG publications
Gonzalez, A., Perez-Acle, T., Pardo, L., Deupi, X.
Molecular Basis of Ligand Dissociation in beta-Adrenergic Receptors
PLOS ONE, 6: Art. No. e23815, SEP 7 2011
abstract,
full text
Chan, K.Y., Gumbart, J., McGreevy, R., Watermeyer, J.M., Sewell, B.T., Schulten, K.
Symmetry-Restrained Flexible Fitting for Symmetric EM Maps
STRUCTURE, 19:1211-1218, SEP 7 2011
abstract,
full text,
TCBG publications
McParland, V., Varsano, G., Li, X., Thornton, J., Baby, J., Aravind, A., Meyer, C., Pavic, K., Rios, P., Kohn, M.
The Metastasis-Promoting Phosphatase PRL-3 Shows Activity toward Phosphoinositides
BIOCHEMISTRY, 50:7579-7590, SEP 6 2011
abstract,
full text
Perlmutter, J.D., Drasler, W.J., Xie, W.S., Gao, J.L., Popot, J.L., Sachs, J.N.
All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer
LANGMUIR, 27:10523-10537, SEP 6 2011
abstract,
full text
Gentilucci, L., Tolomelli, A., De Marco, R., Spampinato, S., Bedini, A., Artali, R.
The Inverse Type II beta-Turn on D-Trp-Phe, a Pharmacophoric Motif for MOR Agonists
CHEMMEDCHEM, 6:1640-1653, SEP 5 2011
abstract,
full text
Henry, L.K., Iwamoto, H., Field, J.R., Kaufmann, K., Dawson, E.S., Jacobs, M.T., Adams, C., Felts, B., Zdravkovic, I., Armstrong, V., Combs, S., Solis, E., Rudnick, G., Noskov, S.Y., DeFelice, L.J., Meiler, J., Blakely, R.D.
A Conserved Asparagine Residue in Transmembrane Segment 1 (TM1) of Serotonin Transporter Dictates Chloride-coupled Neurotransmitter Transport
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:30823-30836, SEP 2 2011
abstract,
full text
Long, M., Sato, M., Lim, C.T., Wu, J.H., Adachi, T., Inoue, Y.
Advances in Experiments and Modeling in Micro- and Nano-Biomechanics: A Mini Review
CELLULAR AND MOLECULAR BIOENGINEERING, 4:327-339, SEP 2011
abstract,
full text
Huang, Q.S., Lou, J.Z., Wu, J.H., Zhu, C.
Conformational Transition of Glycoprotein Ib alpha Mutants in Flow Molecular Dynamics Simulation
CELLULAR AND MOLECULAR BIOENGINEERING, 4:495-504, SEP 2011
abstract,
full text
Barducci, A., Bonomi, M., Parrinello, M.
Metadynamics
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:826-843, SEP-OCT 2011
abstract,
full text
Heinrich, J.C., Tuukkanen, A., Schroeder, M., Fahrig, T., Fahrig, R.
RP101 (brivudine) binds to heat shock protein HSP27 (HSPB1) and enhances survival in animals and pancreatic cancer patients
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY, 137:1349-1361, SEP 2011
abstract,
full text
Meredith, J.S., Roth, P.C., Spafford, K.L., Vetter, J.S.
PERFORMANCE IMPLICATIONS OF NONUNIFORM DEVICE TOPOLOGIES IN SCALABLE HETEROGENEOUS ARCHITECTURES
IEEE MICRO, 31:66-75, SEP-OCT 2011
full text
Wang, Y.T., Lee, W.J., Su, Z.Y., Chen, C.L.
Carbon-nanotube-based artificial peptide channel: Transportation of small peptide under external electric field force
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS, 42:724-726, SEP 2011
abstract,
full text
Necula, G., Mihai, M.E., Sbarcea, C.E., Dinu, S., Lupulescu, E., Ceausu, E., Streinu-Cercel, A., Mihailescu, D.F., Alexandrescu, V.I.
Overview of influenza virus antiviral resistance in Romania in the last four epidemic seasons - phenotyping, genotyping and molecular analysis study
REVISTA ROMANA DE MEDICINA DE LABORATOR, 19:227-240, SEP 2011
abstract,
full text
Phatak, M., Adamczak, R., Cao, B.Q., Wagner, M., Meller, J.
Solvent and Lipid Accessibility Prediction as a Basis for Model Quality Assessment in Soluble and Membrane Proteins
CURRENT PROTEIN & PEPTIDE SCIENCE, 12:563-573, SEP 2011
abstract,
full text
Styrcz, A., Mrozek, J., Mazur, G.
A NEURAL-NETWORK CONTROLLED DYNAMIC EVOLUTIONARY SCHEME FOR GLOBAL MOLECULAR GEOMETRY OPTIMIZATION
INTERNATIONAL JOURNAL OF APPLIED MATHEMATICS AND COMPUTER SCIENCE, 21:559-566, SEP 2011
abstract,
full text
Izanloo, C., Parsafar, G.A., Abroshan, H., Akbarzade, H.
Calculation of Melting Temperature and Transition Curve for Dickerson DNA Dodecamer on the Basis of Configurational Entropy, Hydrogen Bonding Energy, and Heat Capacity: A Molecular Dynamics Simulation Study
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 8:708-716, SEP 2011
abstract,
full text
Moldovan, C., Thompson, D.
Molecular dynamics of the "hydrophobic patch" that immobilizes hydrophobin protein HFBII on silicon
JOURNAL OF MOLECULAR MODELING, 17:2227-2235, SEP 2011
abstract,
full text
Mikulska, K., Peplowski, L., Nowak, W.
Nanomechanics of Ig-like domains of human contactin (BIG-2)
JOURNAL OF MOLECULAR MODELING, 17:2313-2323, SEP 2011
abstract,
full text
Robinson, D., Besley, N.A., O'Shea, P., Hirst, J.D.
Water Order Profiles on Phospholipid/Cholesterol Membrane Bilayer Surfaces
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2613-2618, SEP 2011
abstract,
full text
Pietropaolo, A., Branduardi, D., Bonomi, M., Parrinello, M.
A Chirality-Based Metrics for Free-Energy Calculations in Biomolecular Systems
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2627-2637, SEP 2011
abstract,
full text
Da Silva, L.P., Da Silva, J.C.G.E.
Theoretical Modulation of the Color of Light Emitted by Firefly Oxyluciferin
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2654-2663, SEP 2011
abstract,
full text
Vazquez, N., Schmeisser, H., Dolan, M.A., Bekisz, J., Zoon, K.C., Wahl, S.M.
Structural variants of IFN alpha preferentially promote antiviral functions
BLOOD, 118:2567-2577, SEP 1 2011
abstract,
full text
Vetter, J.S., Glassbrook, R., Dongarra, J., Schwan, K., Loftis, B., McNally, S., Meredith, J., Rogers, J., Roth, P., Spafford, K., Yalamanchili, S.
KEENELAND: BRINGING HETEROGENEOUS GPU COMPUTING TO THE COMPUTATIONAL SCIENCE COMMUNITY
COMPUTING IN SCIENCE & ENGINEERING, 13:90-95, SEP-OCT 2011
full text
Balaeff, A., Craig, S.L., Beratan, D.N.
B-DNA to Zip-DNA: Simulating a DNA Transition to a Novel Structure with Enhanced Charge-Transport Characteristics
JOURNAL OF PHYSICAL CHEMISTRY A, 115:9377-9391, SEP 1 2011
abstract,
full text
Oteri, F., Falconi, M., Chillemi, G., Andersen, F.F., Oliveira, C.L.P., Pedersen, J.S., Knudsen, B.R., Desideri, A.
Simulative Analysis of a Truncated Octahedral DNA Nanocage Family Indicates the Single-Stranded Thymidine Linkers as the Major Player for the Conformational Variability
JOURNAL OF PHYSICAL CHEMISTRY C, 115:16819-16827, SEP 1 2011
abstract,
full text
Kostyuchenko, V.A., Jakana, J., Liu, X.A., Haddow, A.D., Aung, M., Weaver, S.C., Chiu, W., Lok, S.M.
The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions
JOURNAL OF VIROLOGY, 85:9327-9333, SEP 2011
abstract,
full text
Pittala, V., Siracusa, M.A., Modica, M.N., Salerno, L., Pedretti, A., Vistoli, G., Cagnotto, A., Mennini, T., Romeo, G.
Synthesis and molecular modeling of 1H-pyrrolopyrimidine-2,4-dione derivatives as ligands for the alpha(1)-adrenoceptors
BIOORGANIC & MEDICINAL CHEMISTRY, 19:5260-5276, SEP 1 2011
abstract,
full text
Sapay, N., Cabannes, E., Petitou, M., Imberty, A.
Molecular modeling of the interaction between heparan sulfate and cellular growth factors: Bringing pieces together
GLYCOBIOLOGY, 21:1181-1193, SEP 2011
abstract,
full text
Morozov, I.V., Valuev, I.A.
Automatic distributed workflow generation with GridMD library
COMPUTER PHYSICS COMMUNICATIONS, 182:2052-2058, SEP 2011
abstract,
full text
Rezende, M.C., Mascayano, C., Briones, L., Aliaga, C.
Sensing different micellar microenvironments with solvatochromic dyes of variable lipophilicity
DYES AND PIGMENTS, 90:219-224, SEP 2011
abstract,
full text
Vukovic, L., Khatib, F.A., Drake, S.P., Madriaga, A., Brandenburg, K.S., Kral, P., Onyuksel, H.
Structure and Dynamics of Highly PEG-ylated Sterically Stabilized Micelles in Aqueous Media
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13481-13488, AUG 31 2011
abstract,
full text
Nishima, W., Kanamaru, S., Arisaka, F., Kitao, A.
Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13571-13576, AUG 31 2011
abstract,
full text
Mao, D.B., Lu, S.Q., Li, N., Zhang, Y., Long, M.
Conformational Stability Analyses of Alpha Subunit I Domain of LFA-1 and Mac-1
PLOS ONE, 6: Art. No. e24188, AUG 31 2011
abstract,
full text
Wedberg, R., O'Connell, J.P., Peters, G.H., Abildskov, J.
Pair correlation function integrals: Computation and use
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 084113, AUG 28 2011
abstract,
full text
Thota, A., Luckow, A., Jha, S.
Efficient large-scale replica-exchange simulations on production infrastructure
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369:3318-3335, AUG 28 2011
abstract,
full text
Zasada, S.J., Haidar, A.N., Coveney, P.V.
On the usability of grid middleware and security mechanisms
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369:3413-3428, AUG 28 2011
abstract,
full text
Morishita, M., di Luccio, E.
Structural insights into the regulation and the recognition of histone marks by the SET domain of NSD1
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 412:214-219, AUG 26 2011
abstract,
full text
Legrand, B., Giudice, E., Nicolas, A., Delalande, O., Le Rumeur, E.
Computational Study of the Human Dystrophin Repeats: Interaction Properties and Molecular Dynamics
PLOS ONE, 6: Art. No. e23819, AUG 25 2011
abstract,
full text
van Hoof, B., Markvoort, A.J., van Santen, R.A., Hilbers, P.A.J.
The CUMULUS Coarse Graining Method: Transferable Potentials for Water and Solutes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10001-10012, AUG 25 2011
abstract,
full text
Anzini, M., Valenti, S., Braile, C., Cappelli, A., Vomero, S., Acaro, S., Ortuso, F., Marinelli, L., Limongelli, V., Novellino, E., Betti, L., Giannaccini, G., Lucacchini, A., Daniele, S., Martini, C., Ghelardini, C., Mannelli, L.D., Giorgi, G., Mascia, M.P., Biggio, G.
New Insight into the Central Benzodiazepine Receptor-Ligand Interactions: Design, Synthesis, Biological Evaluation, and Molecular Modeling of 3-Substituted 6-Phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and Related Compounds
JOURNAL OF MEDICINAL CHEMISTRY, 54:5694-5711, AUG 25 2011
abstract,
full text
Centrone, A., Santiso, E.E., Hatton, T.A.
Separation of Chemical Reaction Intermediates by Metal-Organic Frameworks
SMALL, 7:2356-2364, AUG 22 2011
abstract,
full text
Bellesia, G., Chundawat, S.P.S., Langan, P., Dale, B.E., Gnanakaran, S.
Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9782-9788, AUG 18 2011
abstract,
full text
Raghuraman, A., Ko, E., Perez, L.M., Ioerger, T.R., Burgess, K.
Pyrrolinone-Pyrrolidine Oligomers as Universal Peptidomimetics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12350-12353, AUG 17 2011
abstract,
full text
Wang, J., Ma, C.L., Fiorin, G., Carnevale, V., Wang, T., Hu, F.H., Lamb, R.A., Pinto, L.H., Hong, M., Kein, M.L., DeGrado, W.F.
Molecular Dynamics Simulation Directed Rational Design of Inhibitors Targeting Drug-Resistant Mutants of Influenza A Virus M2
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12834-12841, AUG 17 2011
abstract,
full text
Lee, T.S., Kantarjian, H., Ma, W.L., Yeh, C.H., Giles, F., Albitar, M.
Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling
PLOS ONE, 6: Art. No. e23396, AUG 17 2011
abstract,
full text
ElSawy, K.M., Caves, L.S.D., Twarock, R.
On the Origin of Order in the Genome Organization of ssRNA Viruses
BIOPHYSICAL JOURNAL, 101:774-780, AUG 17 2011
abstract,
full text
Grasso, G.I., Arena, G., Bellia, F., Maccarrone, G., Parrinello, M., Pietropaolo, A., Vecchio, G., Rizzarelli, E.
Intramolecular Weak Interactions in the Thermodynamic Stereoselectivity of Copper(II) Complexes with Carnosine-Trehalose Conjugates
CHEMISTRY-A EUROPEAN JOURNAL, 17:9448-9455, AUG 16 2011
abstract,
full text
Liu, L.P., Ghosh, N., Slivka, P.F., Fiorini, Z., Hutchinson, M.R., Watkins, L.R., Yin, H.
An MD2 Hot-Spot-Mimicking Peptide that Suppresses TLR4-Mediated Inflammatory Response in vitro and in vivo
CHEMBIOCHEM, 12:1827-1831, AUG 16 2011
full text
Chen, M.H., Sandberg, D.J., Babu, K.R., Bubis, J., Surya, A., Ramos, L.S., Zapata, H.J., Galan, J.F., Sandberg, M.N., Birge, R.R., Knox, B.E.
Conserved Residues in the Extracellular Loops of Short-Wavelength Cone Visual Pigments
BIOCHEMISTRY, 50:6763-6773, AUG 16 2011
abstract,
full text
Wan, S.Z., Coveney, P.V.
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 8:1114-1127, AUG 7 2011
abstract,
full text
Louet, M., Perahia, D., Martinez, J., Floquet, N.
A Concerted Mechanism for Opening the GDP Binding Pocket and Release of the Nucleotide in Hetero-Trimeric G-Proteins
JOURNAL OF MOLECULAR BIOLOGY, 411:298-312, AUG 5 2011
abstract,
full text
Manji, S.S.M., Miller, K.A., Williams, L.H., Andreasen, L., Siboe, M., Rose, E., Bahlo, M., Kuiper, M., Dahl, H.H.M.
An ENU-Induced Mutation of Cdh23 Causes Congenital Hearing Loss, but No Vestibular Dysfunction, in Mice
AMERICAN JOURNAL OF PATHOLOGY, 179:903-914, AUG 2011
abstract,
full text
Watanabe, H., Suzuki, M., Ito, N.
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
PROGRESS OF THEORETICAL PHYSICS, 126:203-235, AUG 2011
abstract,
full text
Pietra, F.
On the Egress of Carbon Monoxide from Myoglobin
CHEMISTRY & BIODIVERSITY, 8:1410-1421, AUG 2011
abstract,
full text
Maeda, S., Morokuma, K.
Finding Reaction Pathways of Type A+B -> X: Toward Systematic Prediction of Reaction Mechanisms
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2335-2345, AUG 2011
abstract,
full text
Romo, T.D., Grossfield, A.
Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2464-2472, AUG 2011
abstract,
full text
Srinivas, G., Cheng, X.L., Smith, J.C.
A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2539-2548, AUG 2011
abstract,
full text
Cojocaru, V., Balali-Mood, K., Sansom, M.S.P., Wade, R.C.
Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002152, AUG 2011
abstract,
full text
Matts, R.L., Dixit, A., Peterson, L.B., Sun, L., Voruganti, S., Kalyanaraman, P., Hartson, S.D., Verkhivker, G.M., Blagg, B.S.J.
Elucidation of the Hsp90 C-Terminal Inhibitor Binding Site
ACS CHEMICAL BIOLOGY, 6:800-807, AUG 2011
abstract,
full text
Papadopoulos, P.M.
Extending clusters to Amazon EC2 using the Rocks toolkit
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 25:317-327, AUG 2011
abstract,
full text
Glykos, N.M.
On the application of structure-specific bulk-solvent models
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 67:739-741, AUG 2011
abstract,
full text
Du, H.B., Qian, X.H.
Molecular Dynamics Simulations of PNIPAM-co-PEGMA Copolymer Hydrophilic to Hydrophobic Transition in NaCl Solution
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 49:1112-1122, AUG 1 2011
abstract,
full text
Knapp, B., Frantal, S., Cibena, M., Schreiner, W., Bauer, P.
Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?
JOURNAL OF COMPUTATIONAL BIOLOGY, 18:997-1005, AUG 2011
abstract,
full text
Lin, T.L., Song, G.
Efficient mapping of ligand migration channel networks in dynamic proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2475-2490, AUG 2011
abstract,
full text
Pedretti, A., De Luca, L., Marconi, C., Regazzoni, L., Aldini, G., Vistoli, G.
Fragmental modeling of hPepT2 and analysis of its binding features by docking studies and pharmacophore mapping
BIOORGANIC & MEDICINAL CHEMISTRY, 19:4544-4551, AUG 2011
abstract,
full text
Caulfield, T.R.
Inter-ring rotation of apolipoprotein A-I protein monomers for the double-belt model using biased molecular dynamics
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:1006-1014, AUG 2011
abstract,
full text
Venkatesan, B.M., Polans, J., Comer, J., Sridhar, S., Wendell, D., Aksimentiev, A., Bashir, R.
Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore
BIOMEDICAL MICRODEVICES, 13:671-682, AUG 2011
abstract,
full text
McGeagh, J.D., Ranaghan, K.E., Mulholland, A.J.
Protein dynamics and enzyme catalysis: Insights from simulations
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:1077-1092, AUG 2011
abstract,
full text
Klenin, K., Strode, B., Wales, D.J., Wenzel, W.
Modelling proteins: Conformational sampling and reconstruction of folding kinetics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:977-1000, AUG 2011
abstract,
full text
Guerry, P., Herrmann, T.
Advances in automated NMR protein structure determination
QUARTERLY REVIEWS OF BIOPHYSICS, 44:257-309, AUG 2011
abstract,
full text
Romo, T.D., Bradney, L.A., Greathouse, D.V., Grossfield, A.
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2019-2030, AUG 2011
abstract,
full text
Boresch, S., Bruckner, S.
Avoiding the van der Waals Endpoint Problem Using Serial Atomic Insertion
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2449-2458, AUG 2011
abstract,
full text
Makowski, L., Gore, D., Mandava, S., Minh, D., Park, S., Rodi, D.J., Fischetti, R.F.
X-ray Solution Scattering Studies of the Structural Diversity Intrinsic to Protein Ensembles
BIOPOLYMERS, 95:531-542, AUG 2011
abstract,
full text
Shintani, M., Yoshida, K., Sakuraba, S., Nakahara, M., Matubayasi, N.
NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9106-9115, JUL 28 2011
abstract,
full text
Karachevtsev, M.V., Karachevtsev, V.A.
Peculiarities of Homooligonucleotides Wrapping around Carbon Nanotubes: Molecular Dynamics Modeling
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9271-9279, JUL 28 2011
abstract,
full text
Chundawat, S.P.S., Bellesia, G., Uppugundla, N., Sousa, L.D., Gao, D.H., Cheh, A.M., Agarwal, U.P., Bianchetti, C.M., Phillips, G.N., Langan, P., Balan, V., Gnanakaran, S., Dale, B.E.
Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:11163-11174, JUL 27 2011
abstract,
full text
Rivalta, I., Amin, M., Luber, S., Vassiliev, S., Pokhrel, R., Umena, Y., Kawakami, K., Shen, J.R., Kamiya, N., Bruce, D., Brudvig, G.W., Gunner, M.R., Batista, V.S.
Structural-Functional Role of Chloride in Photosystem II
BIOCHEMISTRY, 50:6312-6315, JUL 26 2011
abstract,
full text
He, Y.H., Scheicher, R.H., Grigoriev, A., Ahuja, R., Long, S.B., Huo, Z.L., Liu, M.
Enhanced DNA Sequencing Performance Through Edge-Hydrogenation of Graphene Electrodes
ADVANCED FUNCTIONAL MATERIALS, 21:2674-2679, JUL 22 2011
abstract,
full text
Bond, P.J., Faraldo-Gomez, J.D.
Molecular Mechanism of Selective Recruitment of Syk Kinases by the Membrane Antigen-Receptor Complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:25872-25881, JUL 22 2011
abstract,
full text
Ufimtsev, I.S., Luehr, N., Martinez, T.J.
Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1789-1793, JUL 21 2011
abstract,
full text
Carr, R., Comer, J., Ginsberg, M.D., Aksimentiev, A.
Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1804-1807, JUL 21 2011
abstract,
full text
Zanuy, D., Hamley, I.W., Aleman, C.
Modeling the Tetraphenylalanine-PEG Hybrid Amphiphile: From DFT Calculations on the Peptide to Molecular Dynamics Simulations on the Conjugate
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8937-8946, JUL 21 2011
abstract,
full text
Watt, E.D., Rivalta, I., Whittier, S.K., Batista, V.S., Loria, J.P.
Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid
BIOPHYSICAL JOURNAL, 101:411-420, JUL 20 2011
abstract,
full text
Liu, J.J., Stockton, R.A., Gingras, A.R., Ablooglu, A.J., Han, J., Bobkov, A.A., Ginsberg, M.H.
A mechanism of Rap1-induced stabilization of endothelial cell-cell junctions
MOLECULAR BIOLOGY OF THE CELL, 22:2509-2519, JUL 15 2011
abstract,
full text
Beretta, G., Artali, R., Facino, R.M., Gelmini, F.
An analytical and theoretical approach for the profiling of the antioxidant activity of essential oils: The case of Rosmarinus officinalis L.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 55:1255-1264, JUL 15 2011
abstract,
full text
Denning, E.J., Priyakumar, U.D., Nilsson, L., Mackerell, A.D.
Impact of 2 '-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1929-1943, JUL 15 2011
abstract,
full text
Andersson, M., Freites, J.A., Tobias, D.J., White, S.H.
Structural Dynamics of the S4 Voltage-Sensor Helix in Lipid Bilayers Lacking Phosphate Groups
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8732-8738, JUL 14 2011
abstract,
full text
Banerjee, R., Reynolds, N.M., Yadavalli, S.S., Rice, C., Roy, H., Banerjee, P., Alexander, R.W., Ibba, M.
Mitochondrial Aminoacyl-tRNA Synthetase Single-Nucleotide Polymorphisms That Lead to Defects in Refolding but Not Aminoacylation
JOURNAL OF MOLECULAR BIOLOGY, 410:280-293, JUL 8 2011
abstract,
full text
Rommel, J.B., Kastner, J.
The Fragmentation-Recombination Mechanism of the Enzyme Glutamate Mutase Studied by QM/MM Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:10195-10203, JUL 6 2011
abstract,
full text
Hamaneh, M.B., Zhang, L.Q., Buck, M.
A Direct Coupling between Global and Internal Motions in a Single Domain Protein? MD Investigation of Extreme Scenarios
BIOPHYSICAL JOURNAL, 101:196-204, JUL 6 2011
abstract,
full text
Gamini, R., Sotomayor, M., Chipot, C., Schulten, K.
Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance
BIOPHYSICAL JOURNAL, 101:80-89, JUL 6 2011
abstract,
full text,
TCBG publications
Cristiani, A., Costa, G., Cozza, G., Meggio, F., Scapozza, L., Moro, S.
The Role of the N-Terminal Domain in the Regulation of the "Constitutively Active" Conformation of Protein Kinase CK2 alpha: Insight from a Molecular Dynamics Investigation
CHEMMEDCHEM, 6:1207-1216, JUL 4 2011
abstract,
full text
Bettinelli, I., Graziani, D., Marconi, C., Pedretti, A., Vistoli, G.
The Approach of Conformational Chimeras to Model the Role of Proline-Containing Helices on GPCR Mobility: the Fertile Case of Cys-LTR1
CHEMMEDCHEM, 6:1217-1227, JUL 4 2011
abstract,
full text
Kralikova, S., Budesinsky, M., Barvik, I., Masojidkova, M., Tocik, Z., Rosenberg, I.
SYNTHESIS AND PROPERTIES OF ApA ANALOGUES WITH SHORTENED PHOSPHONATE INTERNUCLEOTIDE LINKAGE
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 30:524-543, JUL-SEP 2011
abstract,
full text
Amarasinghe, P.M., Anandarajah, A.
Influence of fabric variables on clay-water-air capillary meniscus
CANADIAN GEOTECHNICAL JOURNAL, 48:987-995, JUL 2011
abstract,
full text
Wang, L.Z., Chen, D., Deng, Z., Huang, F.
Large scale distributed visualization on computational Grids: A review
COMPUTERS & ELECTRICAL ENGINEERING, 37:403-416, JUL 2011
abstract,
full text
Romanowska, J., McCammon, J.A., Trylska, J.
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002099, JUL 2011
abstract,
full text
Parker, L.J., Italiano, L.C., Morton, C.J., Hancock, N.C., Ascher, D.B., Aitken, J.B., Harris, H.H., Campomanes, P., Rothlisberger, U., De Luca, A., Lo Bello, M., Ang, W.H., Dyson, P.J., Parker, M.W.
Studies of Glutathione Transferase P1-1 Bound to a Platinum(IV)-Based Anticancer Compound Reveal the Molecular Basis of Its Activation
CHEMISTRY-A EUROPEAN JOURNAL, 17:7806-7816, JUL 2011
abstract,
full text
Iacovache, I., Degiacomi, M.T., Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M., van der Goot, F.G.
Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLOS PATHOGENS, 7: Art. No. e1002135, JUL 2011
abstract,
full text
Splettstoesser, T., Holmes, K.C., Noe, F., Smith, J.C.
Structural modeling and molecular dynamics simulation of the actin filament
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2033-2043, JUL 2011
abstract,
full text
Janosi, L., Keer, H., Cogdell, R.J., Ritz, T., Kosztin, I.
In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2306-2315, JUL 2011
abstract,
full text
Soriano-Ursua, M.A., Ocampo-Lopez, J.O., Ocampo-Mendoza, K., Trujillo-Ferrara, J.G., Correa-Basurto, J.
Theoretical study of 3-D molecular similarity and ligand binding modes of orthologous human and rat D(2) dopamine receptors
COMPUTERS IN BIOLOGY AND MEDICINE, 41:537-545, JUL 2011
abstract,
full text
Kim, S.K., Huh, J., Kim, S.Y., Byun, Y., Lee, D.Y., Moon, H.T.
Physicochemical Conjugation with Deoxycholic Acid and Dimethylsulfoxide for Heparin Oral Delivery
BIOCONJUGATE CHEMISTRY, 22:1451-1458, JUL 2011
abstract,
full text
Lawrenz, M., Baron, R., Wang, Y., McCammon, J.A.
Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2224-2232, JUL 2011
abstract,
full text
Perez-Siles, G., Morreale, A., Leo-Macias, A., Pita, G., Ortiz, A.R., Aragon, C., Lopez-Corcuera, B.
Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2
JOURNAL OF NEUROCHEMISTRY, 118:195-204, JUL 2011
abstract,
full text
Hubner, M., Dixit, A., Mou, T.C., Lushington, G.H., Pinto, C., Gille, A., Geduhn, J., Konig, B., Sprang, S.R., Seifert, R.
Structural Basis for the High-Affinity Inhibition of Mammalian Membranous Adenylyl Cyclase by 2 ',3 '-O-(N-Methylanthraniloyl)-Inosine 5 '-Triphosphate
MOLECULAR PHARMACOLOGY, 80:87-96, JUL 2011
abstract,
full text
Savol, A.J., Burger, V.M., Agarwal, P.K., Ramanathan, A., Chennubhotla, C.S.
QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
BIOINFORMATICS, 27:I52-I60, JUL 1 2011
abstract,
full text
Jevnikar, Z., Obermajer, N., Doljak, B., Turk, S., Gobec, S., Svajger, U., Hailfinger, S., Thome, M., Kos, J.
Cathepsin X cleavage of the beta(2) integrin regulates talin-binding and LFA-1 affinity in T cells
JOURNAL OF LEUKOCYTE BIOLOGY, 90:99-109, JUL 2011
abstract,
full text
Strunk, T., Hamacher, K., Hoffgaard, F., Engelhardt, H., Zillig, M.D., Faist, K., Wenzel, W., Pfeifer, F.
Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo
MOLECULAR MICROBIOLOGY, 81:56-68, JUL 2011
abstract,
full text
Palmai, Z., Perahia, D., Lionne, C., Fidy, J., Balog, E., Chaloin, L.
Ligand chirality effects on the dynamics of human 3-phosphoglycerate kinase: Comparison between D- and L-nucleotides
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 511:88-100, JUL 2011
abstract,
full text
Tavoosi, N., Davis-Harrison, R.L., Pogorelov, T.V., Ohkubo, Y.Z., Arcario, M.J., Clay, M.C., Rienstra, C.M., Tajkhorshid, E., Morrissey, J.H.
Molecular Determinants of Phospholipid Synergy in Blood Clotting
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:23247-23253, JUL 1 2011
abstract,
full text
Mayo, D., Zhou, A., Sahu, I., McCarrick, R., Walton, P., Ring, A., Troxel, K., Coey, A., Hawn, J., Emwas, A.H., Lorigan, G.A.
Probing the structure of membrane proteins with electron spin echo envelope modulation spectroscopy
PROTEIN SCIENCE, 20:1100-1104, JUL 2011
abstract,
full text
Beassoni, P.R., Otero, L.H., Boetsch, C., Domenech, C.E., Gonzalez-Nilo, F.D., Lisa, A.T.
Site-directed mutations and kinetic studies show key residues involved in alkylammonium interactions and reveal two sites for phosphorylcholine in Pseudomonas aeruginosa phosphorylcholine phosphatase
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:858-863, JUL 2011
abstract,
full text
Sokkar, P., Mohandass, S., Ramachandran, M.
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking
JOURNAL OF MOLECULAR MODELING, 17:1565-1577, JUL 2011
abstract,
full text
Khrenova, M., Domratcheva, T., Grigorenko, B., Nemukhin, A.
Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1
JOURNAL OF MOLECULAR MODELING, 17:1579-1586, JUL 2011
abstract,
full text
Raliou, M., Grauso, M., Hoffmann, B., Schlegel-Le-Poupon, C., Nespoulous, C., Debat, H., Belloir, C., Wiencis, A., Sigoillot, M., Bano, S.P., Trotier, D., Pernollet, J.C., Montmayeur, J.P., Faurion, A., Briand, L.
Human Genetic Polymorphisms in T1R1 and T1R3 Taste Receptor Subunits Affect Their Function
CHEMICAL SENSES, 36:527-537, JUL 2011
abstract,
full text
Narayanan, S.S., Sokkar, P., Ramachandran, M., Nampoothiri, K.M.
Glycine in the conserved motif III modulates the thermostability and oxidative stress resistance of peptide deformylase in Mycobacterium tuberculosis
FEMS MICROBIOLOGY LETTERS, 320:40-47, JUL 2011
abstract,
full text
Wu, B.J., Xin, B., Jin, M., Wei, T.D., Bai, Z.L.
Comparative and phylogenetic analyses of three TIR domain-containing adaptors in metazoans: Implications for evolution of TLR signaling pathways
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY, 35:764-773, JUL 2011
abstract,
full text
Kleinekathofer, U., Isralewitz, B., Dittrich, M., Schulten, K.
Domain Motion of Individual F(1)-ATPase beta-Subunits during Unbiased Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 115:7267-7274, JUN 30 2011
abstract,
full text,
TCBG publications
Schulz, R., Vargiu, A.V., Ruggerone, P., Kleinekathofer, U.
Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8278-8287, JUN 30 2011
abstract,
full text
Bravaya, K.B., Khrenova, M.G., Grigorenko, B.L., Nemukhin, A.V., Krylov, A.I.
Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8296-8303, JUN 30 2011
abstract,
full text
White, K.H., Orzechowski, M., Fourmy, D., Visscher, K.
Mechanical Unfolding of the Beet Western Yellow Virus-1 Frameshift Signal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9775-9782, JUN 29 2011
abstract,
full text
Kotsikorou, E., Madrigal, K.E., Hurst, D.P., Sharir, H., Lynch, D.L., Heynen-Genel, S., Milan, L.B., Chung, T.D.Y., Setzman, H.H., Bai, Y.S., Caron, M.G., Barak, L., Abood, M.E., Reggio, P.H.
Identification of the GPR55 Agonist Binding Site Using a Novel Set of High-Potency GPR55 Selective Ligands
BIOCHEMISTRY, 50:5633-5647, JUN 28 2011
abstract,
full text
Lee, W., Luckner, S.R., Kisker, C., Tonge, P.J., Engels, B.
Elucidation of the Protonation States of the Catalytic Residues in mtKasA: Implications for Inhibitor Design
BIOCHEMISTRY, 50:5743-5756, JUN 28 2011
abstract,
full text
Truong, K., Su, Y., Song, J., Chen, Y.
Entropy-Driven Mechanism of an E3 Ligase
BIOCHEMISTRY, 50:5757-5766, JUN 28 2011
abstract,
full text
Furini, S., Domene, C.
Selectivity and Permeation of Alkali Metal Ions in K(+)-channels
JOURNAL OF MOLECULAR BIOLOGY, 409:867-878, JUN 24 2011
abstract,
full text
Bleicher, L., Prates, E.T., Gomes, T.C.F., Silveira, R.L., Nascimento, A.S., Rojas, A.L., Golubev, A., Martinez, L., Skaf, M.S., Polikarpov, I.
Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7940-7949, JUN 23 2011
abstract,
full text
Frauer, C., Hoffmann, T., Bultmann, S., Casa, V., Cardoso, M.C., Antes, I., Leonhardt, H.
Recognition of 5-Hydroxymethylcytosine by the Uhrf1 SRA Domain
PLOS ONE, 6: Art. No. e21306, JUN 22 2011
abstract,
full text
Liu, Y.X., Hsin, J., Kim, H., Selvin, P.R., Schulten, K.
Extension of a Three-Helix Bundle Domain of Myosin VI and Key Role of Calmodulins
BIOPHYSICAL JOURNAL, 100:2964-2973, JUN 22 2011
abstract,
full text,
TCBG publications
Jones, P.M., George, A.M.
Molecular-Dynamics Simulations of the ATP/apo State of a Multidrug ATP-Binding Cassette Transporter Provide a Structural and Mechanistic Basis for the Asymmetric Occluded State
BIOPHYSICAL JOURNAL, 100:3025-3034, JUN 22 2011
abstract,
full text
Buch, I., Giorgino, T., De Fabritiis, G.
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:10184-10189, JUN 21 2011
abstract,
full text
Ziemys, A., Kojic, M., Milosevic, M., Kojic, N., Hussain, F., Ferrari, M., Grattoni, A.
Hierarchical modeling of diffusive transport through nanochannels by coupling molecular dynamics with finite element method
JOURNAL OF COMPUTATIONAL PHYSICS, 230:5722-5731, JUN 20 2011
abstract,
full text
Pan, Z.Z., McCullagh, M., Schatz, G.C., Lewis, F.D.
Conformational Control of Thymine Photodimerization in Purine-Containing Trinucleotides
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1432-1438, JUN 16 2011
abstract,
full text
Rose, F., Hodak, M., Bernholc, J.
Mechanism of copper(II)-induced misfolding of Parkinson's disease protein
SCIENTIFIC REPORTS, 1: Art. No. 11, JUN 14 2011
abstract,
full text
Tian, J.H., Garcia, A.E.
Simulations of the confinement of ubiquitin in self-assembled reverse micelles
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 225101, JUN 14 2011
abstract,
full text
Miller, Y., Ma, B.Y., Nussinov, R.
Synergistic Interactions between Repeats in Tau Protein and A beta Amyloids May Be Responsible for Accelerated Aggregation via Polymorphic States
BIOCHEMISTRY, 50:5172-5181, JUN 14 2011
abstract,
full text
Dixit, P.D., Asthagiri, D.
An Elastic-Network-Based Local Molecular Field Analysis of Zinc Finger Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7374-7382, JUN 9 2011
abstract,
full text
Schneider, C.P., Shukla, D., Trout, B.L.
Arginine and the Hofmeister Series: The Role of Ion-Ion Interactions in Protein Aggregation Suppression
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7447-7458, JUN 9 2011
abstract,
full text
Serrano, A.L., Tucker, M.J., Gai, F.
Direct Assessment of the alpha-Helix Nucleation Time
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7472-7478, JUN 9 2011
abstract,
full text
Tanner, D.E., Ma, W., Chen, Z.Z., Schulten, K.
Theoretical and Computational Investigation of Flagellin Translocation and Bacterial Flagellum Growth
BIOPHYSICAL JOURNAL, 100:2548-2556, JUN 8 2011
abstract,
full text,
TCBG publications
Sun, C.B., Tang, T., Uludag, H., Cuervo, J.E.
Molecular Dynamics Simulations of DNA/PEI Complexes: Effect of PEI Branching and Protonation State
BIOPHYSICAL JOURNAL, 100:2754-2763, JUN 8 2011
abstract,
full text
Yu, X., Zheng, J.
Polymorphic Structures of Alzheimer's beta-Amyloid Globulomers
PLOS ONE, 6: Art. No. e20575, JUN 7 2011
abstract,
full text
Falvo, C., Meier, C.
A fluctuating quantum model of the CO vibration in carboxyhemoglobin
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 214106, JUN 7 2011
abstract,
full text
Matsushita, S., Inoue, Y., Hojo, M., Sokabe, M., Adachi, T.
Effect of tensile force on the mechanical behavior of actin filaments
JOURNAL OF BIOMECHANICS, 44:1776-1781, JUN 3 2011
abstract,
full text
Zomot, E., Bahar, I.
Protonation of Glutamate 208 Induces the Release of Agmatine in an Outward-facing Conformation of an Arginine/Agmatine Antiporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:19693-19701, JUN 3 2011
abstract,
full text
Dai, Z.W., Ling, J., Huang, X.J., Wan, L.S., Xu, Z.K.
Molecular Simulation on the Interactions of Water with Polypropylene Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 115:10702-10708, JUN 2 2011
abstract,
full text
Balog, E., Perahia, D., Smith, J.C., Merzel, F.
Vibrational Softening of a Protein on Ligand Binding
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6811-6817, JUN 2 2011
abstract,
full text
Madsen, J.J., Linderoth, L., Subramanian, A.K., Andresen, T.L., Peters, G.H.
Secretory Phospholipase A(2) Activity toward Diverse Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6853-6861, JUN 2 2011
abstract,
full text
Arcario, M.J., Ohkubo, Y.Z., Tajkhorshid, E.
Capturing Spontaneous Partitioning of Peripheral Proteins Using a Biphasic Membrane-Mimetic Model
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7029-7037, JUN 2 2011
abstract,
full text
Verde, A.V., Campen, R.K.
Disaccharide Topology Induces Slowdown in Local Water Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7069-7084, JUN 2 2011
abstract,
full text
Ivetac, A., McCammon, J.A.
Molecular Recognition in the Case of Flexible Targets
CURRENT PHARMACEUTICAL DESIGN, 17:1663-1671, JUN 2011
abstract,
full text
Li, C., Shen, J., Li, W.H., Lu, C.H., Liu, G.X., Tang, Y.
Possible ligand release pathway of dipeptidyl peptidase IV investigated by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1800-1809, JUN 2011
abstract,
full text
Kim, S.K., Riley, L., Abrol, R., Jacobson, K.A., Goddard, W.A.
Predicted structures of agonist and antagonist bound complexes of adenosine A(3) receptor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1878-1897, JUN 2011
abstract,
full text
Dong, H., Zhou, H.X.
Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor
NATURE COMMUNICATIONS, 2: Art. No. 354, JUN 2011
abstract,
full text
Liao, C.Z., Sitzmann, M., Pugliese, A., Nicklaus, M.C.
Software and resources for computational medicinal chemistry
FUTURE MEDICINAL CHEMISTRY, 3:1057-1085, JUN 2011
abstract,
full text
Cristiani, A., Brisotto, N., Cedrati, F.C., Floris, M., Scapozza, L., Moro, S.
ClickMD: an intuitive web-oriented molecular dynamics platform
FUTURE MEDICINAL CHEMISTRY, 3:923-931, JUN 2011
abstract,
full text
Bourne, J.W., Torzilli, P.A.
Molecular simulations predict novel collagen conformations during cross-link loading
MATRIX BIOLOGY, 30:356-360, JUN 2011
abstract,
full text
Baker, J.A., Hirst, J.D.
Molecular Dynamics Simulations Using Graphics Processing Units
MOLECULAR INFORMATICS, 30:498-504, JUN 2011
abstract,
full text
Skulachev, M.V., Antonenko, Y.N., Anisimov, V.N., Chernyak, B.V., Cherepanov, D.A., Chistyakov, V.A., Egorov, M.V., Kolosova, N.G., Korshunova, G.A., Lyamzaev, K.G., Plotnikov, E.Y., Roginsky, V.A., Savchenko, A.Y., Severina, I.I., Severin, F.F., Shkurat, T.P., Tashlitsky, V.N., Shidlovsky, K.M., Vyssokikh, M.Y., Zamyatnin, A.A., Zorov, D.B., Skulachev, V.P.
Mitochondrial-Targeted Plastoquinone Derivatives. Effect on Senescence and Acute Age-Related Pathologies
CURRENT DRUG TARGETS, 12:800-826, JUN 2011
abstract,
full text
Liu, L., Liu, X.F., Gong, J.Y., Jiang, H.L., Li, H.L.
Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1595-1603, JUN 2011
abstract,
full text
Grouleff, J., Jensen, F.
Searching Peptide Conformational Space
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1783-1790, JUN 2011
abstract,
full text
Moya-Garcia, A.A., Rodriguez-Agudo, D., Hayashi, H., Medina, M.A., Urdiales, J.L., Sanchez-Jimenez, F.
Analysis of Mammalian Histidine Decarboxylase Dimerization Interface Reveals an Electrostatic Hotspot Important for Catalytic Site Topology and Function
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1935-1942, JUN 2011
abstract,
full text
Giorgino, T., De Fabritiis, G.
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1943-1950, JUN 2011
abstract,
full text
Mangold, M., Rolland, L., Costanzo, F., Sprik, M., Sulpizi, M., Blumberger, J.
Absolute pK(a) Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1951-1961, JUN 2011
abstract,
full text
Kenzaki, H., Koga, N., Hori, N., Kanada, R., Li, W.F., Okazaki, K., Yao, X.Q., Takada, S.
CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1979-1989, JUN 2011
abstract,
full text
Shin, A.J., Telesco, S.E., Choi, S.H., Lemmon, M.A., Radhakrishnan, R.
Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases
BIOCHEMICAL JOURNAL, 436:241-251, JUN 1 2011
abstract,
full text
Hernandez-Ortega, A., Borrelli, K., Ferreira, P., Medina, M., Martinez, A.T., Guallar, V.
Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase
BIOCHEMICAL JOURNAL, 436:341-350, JUN 1 2011
abstract,
full text
Librando, V., Pappalardo, M.
Computational study on the interaction of a ring-hydroxylating dioxygenase from Sphingomonas CHY-1 with PAHs
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:915-919, JUN 2011
abstract,
full text
Chen, C., Li, W.Z., Song, Y.C., Weng, L.D.
Structure and Kinetics of Hydrogen Bonds in Aqueous Glucose Solutions
ACTA PHYSICO-CHIMICA SINICA, 27:1372-1378, JUN 2011
abstract,
full text
Dai, W.M., You, Z.L., Zhou, H., Zhang, J., Hu, Y.Q.
Structure-function relationships of the human bitter taste receptor hTAS2R1: insights from molecular modeling studies
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:229-240, JUN 2011
abstract,
full text
Pan, Y.P., Nussinov, R.
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-beta Enhanceosome Example
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002077, JUN 2011
abstract,
full text
Floquet, N., Hernandez, J.F., Boucher, J.L., Martinez, J.
L-Arginine Binding to Human Inducible Nitric Oxide Synthase: An Antisymmetric Funnel Route toward Isoform-Specific Inhibitors?
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1325-1335, JUN 2011
abstract,
full text
Yang, M.J., Zhang, X.
Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1774-1785, JUN 2011
abstract,
full text
Karthik, S., Senapati, S.
Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1830-1840, JUN 2011
abstract,
full text
Veldhuis, N.A., Kuiper, M.J., Dobson, R.C.J., Pearson, R.B., Camakaris, J.
In silico modeling of the Menkes copper-translocating P-type ATPase 3rd metal binding domain predicts that phosphorylation regulates copper-binding
BIOMETALS, 24:477-487, JUN 2011
abstract,
full text
Yokota, R., Bardhan, J.P., Knepley, M.G., Barba, L.A., Hamada, T.
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
COMPUTER PHYSICS COMMUNICATIONS, 182:1272-1283, JUN 2011
abstract,
full text
Kote-Jarai, Z., Al Olama, A.A., Leongamornlert, D., Tymrakiewicz, M., Saunders, E., Guy, M., Giles, G.G., Severi, G., Southey, M., Hopper, J.L., Sit, K.C., Harris, J.M., Batra, J., Spurdle, A.B., Clements, J.A., Hamdy, F., Neal, D., Donovan, J., Muir, K., Pharoah, P.D.P., Chanock, S.J., Brown, N., Benlloch, S., Castro, E., Mahmud, N., O'Brien, L., Hall, A., Sawyer, E., Wilkinson, R., Easton, D.F., Eeles, R.A.
Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript
HUMAN GENETICS, 129:687-694, JUN 2011
abstract,
full text
Poghosyan, A.H., Arsenyan, L.H., Gharabekyan, H.H., Falkenhagen, S., Koetz, J., Shahinyan, A.A.
Molecular dynamics simulations of inverse sodium dodecyl sulfate (SDS) micelles in a mixed toluene/pentanol solvent in the absence and presence of poly(diallyldimethylammonium chloride) (PDADMAC)
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 358:175-181, JUN 1 2011
abstract,
full text
Qu, Z.W., Zhu, H., May, V.
Vibrational Spectral Signatures of Peptide Secondary Structures: N-methylation and Side chain Hydrogen Bond in Cyclosporin A
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1500-1518, JUN 2011
abstract,
full text
Prates, E.T., Souza, P.C.T., Pickholz, M., Skaf, M.S.
CHARMM-Based Parameterization of Neutral Articaine-A Widely Used Local Anesthetic
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1339-1345, JUN-JUL 2011
abstract,
full text
Hansson, A., Souza, P.C.T., Silveira, R.L., Martinez, L., Skaf, M.S.
CHARMM Force Field Parameterization of Rosiglitazone
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1346-1354, JUN-JUL 2011
abstract,
full text
Riihimaki, T.A., Kukkurainen, S., Varjonen, S., Horha, J., Nyholm, T.K.M., Kulomaa, M.S., Hytonen, V.P.
Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins
PLOS ONE, 6: Art. No. e20535, MAY 31 2011
abstract,
full text
Timko, J., De Castro, A., Kuyucak, S.
Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 204510, MAY 28 2011
abstract,
full text
O'Connor, J.W., Klauda, J.B.
Lipid Membranes with a Majority of Cholesterol: Applications to the Ocular Lens and Aquaporin 0
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6455-6464, MAY 26 2011
abstract,
full text
Satpati, P., Clavaguera, C., Ohanessian, G., Simonson, T.
Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6749-6763, MAY 26 2011
abstract,
full text
Huang, Y.M.M., Chang, C.E.A.
Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics
BMC BIOPHYSICS, 4: Art. No. 12, MAY 25 2011
abstract,
full text
Kaye, M.D., Schmalzl, K., Nibali, V.C., Tarek, M., Rheinstadter, M.C.
Ethanol enhances collective dynamics of lipid membranes
PHYSICAL REVIEW E, 83: Art. No. 050907, MAY 25 2011
abstract,
full text
Sorensen, J., Palmer, D.S., Qvist, K.B., Schiott, B.
Initial Stage of Cheese Production: A Molecular Modeling Study of Bovine and Camel Chymosin Complexed with Peptides from the Chymosin-Sensitive Region of kappa-Casein
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 59:5636-5647, MAY 25 2011
abstract,
full text
Schreiner, E., Trabuco, L.G., Freddolino, P.L., Schulten, K.
Stereochemical errors and their implications for molecular dynamics simulations
BMC BIOINFORMATICS, 12: Art. No. 190, MAY 23 2011
abstract,
full text,
TCBG publications
Makowski, L., Bardhan, J., Gore, D., Lal, J., Mandava, S., Park, S., Rodi, D.J., Ho, N.T., Ho, C., Fischetti, R.F.
WAXS Studies of the Structural Diversity of Hemoglobin in Solution
JOURNAL OF MOLECULAR BIOLOGY, 408:909-921, MAY 20 2011
abstract,
full text
Stewart, M.D., Morgan, B., Massi, F., Igumenova, T.I.
Probing the Determinants of Diacylglycerol Binding Affinity in the C1B Domain of Protein Kinase C alpha
JOURNAL OF MOLECULAR BIOLOGY, 408:949-970, MAY 20 2011
abstract,
full text
Jiang, J., Mukamel, S.
Probing Amyloid Fibril Growth by Two-Dimensional Near-Ultraviolet Spectroscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6321-6328, MAY 19 2011
abstract,
full text
Bai, Q.F., Shen, Y.L., Yao, X.J., Wang, F., Du, Y.P., Wang, Q., Jin, N.Z., Hai, J., Hu, T.J., Yang, J.B.
Modeling a New Water Channel That Allows SET9 to Dimethylate p53
PLOS ONE, 6: Art. No. e19856, MAY 19 2011
abstract,
full text
Ramachandran, A., Guo, Q.J., Iqbal, S.M., Liu, Y.L.
Coarse-Grained Molecular Dynamics Simulation of DNA Trans location in Chemically Modified Nanopores
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6138-6148, MAY 19 2011
abstract,
full text
Gumbart, J., Chipot, C., Schulten, K.
Free Energy of Nascent-Chain Folding in the Translocon
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:7602-7607, MAY 18 2011
abstract,
full text,
TCBG publications
Wilson, M.A., Wei, C.Y., Bjelkmar, P., Wallace, B.A., Pohorille, A.
Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance
BIOPHYSICAL JOURNAL, 100:2394-2402, MAY 18 2011
abstract,
full text
Chen, P.C., Kuyucak, S.
Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints
BIOPHYSICAL JOURNAL, 100:2466-2474, MAY 18 2011
abstract,
full text
Verde, A.V., Beltramo, P.J., Maranas, J.K.
Adsorption of Homopolypeptides on Gold Investigated Using Atomistic Molecular Dynamics
LANGMUIR, 27:5918-5926, MAY 17 2011
abstract,
full text
Maekawa, H., Ballano, G., Toniolo, C., Ge, N.H.
Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains
JOURNAL OF PHYSICAL CHEMISTRY B, 115:5168-5182, MAY 12 2011
abstract,
full text
Weng, L.D., Chen, C., Zuo, J.G., Li, W.Z.
Molecular Dynamics Study of Effects of Temperature and Concentration on Hydrogen-Bond Abilities of Ethylene Glycol and Glycerol: Implications for Cryopreservation
JOURNAL OF PHYSICAL CHEMISTRY A, 115:4729-4737, MAY 12 2011
abstract,
full text
Ketko, M.H., Kamath, G., Potoff, J.J.
Development of an Optimized Intermolecular Potential for Sulfur Dioxide
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4949-4954, MAY 5 2011
abstract,
full text
Gonidec, M., Biagi, R., Corradini, V., Moro, F., De Renzi, V., del Pennino, U., Summa, D., Muccioli, L., Zannoni, C., Amabilino, D.B., Veciana, J.
Surface Supramolecular Organization of a Terbium(III) Double-Decker Complex on Graphite and its Single Molecule Magnet Behavior
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6603-6612, MAY 4 2011
abstract,
full text
Berryman, J.T., Radford, S.E., Harris, S.A.
Systematic Examination of Polymorphism in Amyloid Fibrils by Molecular-Dynamics Simulation
BIOPHYSICAL JOURNAL, 100:2234-2242, MAY 4 2011
abstract,
full text
Sonntag, Y., Musgaard, M., Olesen, C., Schiott, B., Moller, J.V., Nissen, P., Thogersen, L.
Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes
NATURE COMMUNICATIONS, 2: Art. No. 304, MAY 2011
abstract,
full text
Aprikian, P., Interlandi, G., Kidd, B.A., Le Trong, I., Tchesnokova, V., Yakovenko, O., Whitfield, M.J., Bullitt, E., Stenkamp, R.E., Thomas, W.E., Sokurenko, E.V.
The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor
PLOS BIOLOGY, 9: Art. No. e1000617, MAY 2011
abstract,
full text
Vemparala, S., Mehrotra, S., Balaram, H.
Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: A molecular dynamics and normal mode analysis study
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:630-637, MAY 2011
abstract,
full text
Postila, P.A., Ylilauri, M., Pentikainen, O.T.
Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1037-1047, MAY 2011
abstract,
full text
Camargo, H., Nusspaumer, G., Abia, D., Briceno, V., Remacha, M., Ballesta, J.P.G.
The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2
NUCLEIC ACIDS RESEARCH, 39:3735-3743, MAY 2011
abstract,
full text
Lin, Y.W., Ying, T.L., Liao, L.F.
Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b (5)
JOURNAL OF MOLECULAR MODELING, 17:971-978, MAY 2011
abstract,
full text
Kutzner, C., Czub, J., Grubmuller, H.
Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1381-1393, MAY 2011
abstract,
full text
Chew, T.H., Joyce-Tan, K.H., Akma, F., Shamsir, M.S.
birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics
BIOINFORMATICS, 27:1320-1321, MAY 1 2011
abstract,
full text
Zhao, J., Yu, X., Liang, G.Z., Zheng, J.
Heterogeneous Triangular Structures of Human Islet Amyloid Polypeptide (Amylin) with Internal Hydrophobic Cavity and External Wrapping Morphology Reveal the Polymorphic Nature of Amyloid Fibrils
BIOMACROMOLECULES, 12:1781-1794, MAY 2011
abstract,
full text
Schlick, T., Collepardo-Guevara, R., Halvorsen, L.A., Jung, S., Xiao, X.
Biomolecular modeling and simulation: a field coming of age
QUARTERLY REVIEWS OF BIOPHYSICS, 44:191-228, MAY 2011
abstract,
full text
Khrenova, M.G., Domratcheva, T., Schlichting, I., Grigorenko, B.L., Nemukhin, A.V.
Computational Characterization of Reaction Intermediates in the Photocycle of the Sensory Domain of the AppA Blue Light Photoreceptor
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 87:564-573, MAY-JUN 2011
abstract,
full text
Darian, E., Guvench, O., Yu, B., Qu, C.K., MacKerell, A.D.
Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1573-1588, MAY 2011
abstract,
full text
Martinez, L., Malliavin, T.E., Blondel, A.
Mechanism of reactant and product dissociation from the anthrax edema factor: A locally enhanced sampling and steered molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1649-1661, MAY 2011
abstract,
full text
Fezoua-Boubegtiten, Z., Desbat, B., Brisson, A., Gounou, C., Laguerre, M., Lecomte, S.
Effect of Mg(2+) versus Ca(2+) on the behavior of Annexin A5 in a membrane-bound state
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:641-649, MAY 2011
abstract,
full text
Bellesia, G., Jewett, A.I., Shea, J.E.
Relative stability of de novo four-helix bundle proteins: Insights from coarse grained molecular simulations
PROTEIN SCIENCE, 20:818-826, MAY 2011
abstract,
full text
Sapay, N., Tieleman, D.P.
Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1400-1410, MAY 2011
abstract,
full text
Konig, G., Boresch, S.
Non-Boltzmann Sampling and Bennett's Acceptance Ratio Method: How to Profit from Bending the Rules
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1082-1090, APR 30 2011
abstract,
full text
Lettieri, S., Mamonov, A.B., Zuckerman, D.M.
Extending Fragment-Based Free Energy Calculations with Library Monte Carlo Simulation: Annealing in Interaction Space
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1135-1143, APR 30 2011
abstract,
full text
Busby, B., Oashi, T., Willis, C.D., Ackermann, M.A., Kontrogianni-Konstantopoulos, A., MacKerell, A.D., Bloch, R.J.
Electrostatic Interactions Mediate Binding of Obscurin to Small Ankyrin 1: Biochemical and Molecular Modeling Studies
JOURNAL OF MOLECULAR BIOLOGY, 408:321-334, APR 29 2011
abstract,
full text
Conejo-Garcia, A., Pisani, L., Nunez, M.D.C., Catto, M., Nicolotti, O., Leonetti, F., Campos, J.M., Gallo, M.A., Espinosa, A., Carotti, A.
Homodimeric Bis-Quaternary Heterocyclic Ammonium Salts as Potent Acetyl- and Butyrylcholinesterase Inhibitors: A Systematic Investigation of the Influence of Linker and Cationic Heads over Affinity and Selectivity
JOURNAL OF MEDICINAL CHEMISTRY, 54:2627-2645, APR 28 2011
abstract,
full text
Patra, N., Kral, P.
Controlled Self-Assembly of Filled Micelles on Nanotubes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6146-6149, APR 27 2011
abstract,
full text
Swedberg, J.E., de Veer, S.J., Sit, K.C., Reboul, C.F., Buckle, A.M., Harris, J.M.
Mastering the Canonical Loop of Serine Protease Inhibitors: Enhancing Potency by Optimising the Internal Hydrogen Bond Network
PLOS ONE, 6: Art. No. e19302, APR 27 2011
abstract,
full text
Walch, S.P.
Effect of Solvation on the Oxygen Reduction Reaction on Pt Catalyst
JOURNAL OF PHYSICAL CHEMISTRY C, 115:7377-7391, APR 21 2011
abstract,
full text
Agirrezabala, X., Schreiner, E., Trabuco, L.G., Lei, J.L., Ortiz-Meoz, R.F., Schulten, K., Green, R., Frank, J.
Structural insights into cognate versus near-cognate discrimination during decoding
EMBO JOURNAL, 30:1497-1507, APR 20 2011
abstract,
full text,
TCBG publications
Reboul, C.F., Andrews, D.A., Nahar, M.F., Buckle, A.M., Roujeinikova, A.
Crystallographic and Molecular Dynamics Analysis of Loop Motions Unmasking the Peptidoglycan-Binding Site in Stator Protein MotB of Flagellar Motor
PLOS ONE, 6: Art. No. e18981, APR 20 2011
abstract,
full text
Sun, G., Lu, K.Q., Kun, F.
Percolation-induced conductor-insulator transition in a system of metal spheres in a dielectric fluid
PHYSICAL REVIEW E, 83: Art. No. 041405, APR 15 2011
abstract,
full text
Lian, P., Wei, D.Q., Wang, J.F., Chou, K.C.
An Allosteric Mechanism Inferred from Molecular Dynamics Simulations on Phospholamban Pentamer in Lipid Membranes
PLOS ONE, 6: Art. No. e18587, APR 15 2011
abstract,
full text
Nurminen, E.M., Pihlavisto, M., Lazar, L., Pentikainen, U., Fulop, F., Pentikainen, O.T.
Novel Hydrazine Molecules as Tools To Understand the Flexibility of Vascular Adhesion Protein-1 Ligand-Binding Site: Toward More Selective Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 54:2143-2154, APR 14 2011
abstract,
full text
Zhao, X.C.
Self-Assembly of DNA Segments on Graphene and Carbon Nanotube Arrays in Aqueous Solution: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 115:6181-6189, APR 14 2011
abstract,
full text
Delemotte, L., Tarek, M., Klein, M.L., Amaral, C., Treptow, W.
Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:6109-6114, APR 12 2011
abstract,
full text
Wei, C.Y., Pohorile, A.
Permeation of Nucleosides through Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 115:3681-3688, APR 7 2011
abstract,
full text
Suyetin, M.V., Vakhrushev, A.V.
Guided Carbon Nanocapsules for Hydrogen Storage
JOURNAL OF PHYSICAL CHEMISTRY C, 115:5485-5491, APR 7 2011
abstract,
full text
Narita, A., Oda, T., Maeda, Y.
Structural basis for the slow dynamics of the actin filament pointed end
EMBO JOURNAL, 30:1230-1237, APR 6 2011
abstract,
full text
Jang, H., Arce, F.T., Mustata, M., Ramachandran, S., Capone, R., Nussinov, R., Lal, R.
Antimicrobial Protegrin-1 Forms Amyloid-Like Fibrils with Rapid Kinetics Suggesting a Functional Link
BIOPHYSICAL JOURNAL, 100:1775-1783, APR 6 2011
abstract,
full text
Song, S.H., Freddolino, P.L., Nash, A.I., Carroll, E.C., Schulten, K., Gardner, K.H., Larsen, D.S.
Modulating LOV Domain Photodynamics with a Residue Alteration outside the Chromophore Binding Site
BIOCHEMISTRY, 50:2411-2423, APR 5 2011
abstract,
full text,
TCBG publications
Robinson, M.W., Corvo, I., Jones, P.M., George, A.M., Padula, M.P., To, J., Cancela, M., Rinaldi, G., Tort, J.F., Roche, L., Dalton, J.P.
Collagenolytic Activities of the Major Secreted Cathepsin L Peptidases Involved in the Virulence of the Helminth Pathogen, Fasciola hepatica
PLOS NEGLECTED TROPICAL DISEASES, 5: Art. No. e1012, APR 2011
abstract,
full text
Beckham, G.T., Bomble, Y.J., Bayer, E.A., Himmel, M.E., Crowley, M.F.
Applications of computational science for understanding enzymatic deconstruction of cellulose
CURRENT OPINION IN BIOTECHNOLOGY, 22:231-238, APR 2011
abstract,
full text
Cardinali, A., Tursi, N., Ligorio, A., Giuffrida, M.G., Napolitano, L., Caliandro, R., Sergio, L., Di Venere, D., Lattanzio, V., Sonnante, G.
Purification, biochemical characterization and cloning of a new cationic peroxidase isoenzyme from artichoke
PLANT PHYSIOLOGY AND BIOCHEMISTRY, 49:395-403, APR 2011
abstract,
full text
Bucher, D., Grant, B.J., Markwick, P.R., McCammon, J.A.
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002034, APR 2011
abstract,
full text
Wang, J., Wang, Y., Chu, X.K., Hagen, S.J., Han, W., Wang, E.K.
Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1001118, APR 2011
abstract,
full text
Xie, L., Evangelidis, T., Xie, L., Bourne, P.E.
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002037, APR 2011
abstract,
full text
Vorob'ev, Y.N.
Molecular dynamics method for proteins with ionization-conformation coupling and equilibrium titration
MOLECULAR BIOLOGY, 45:309-317, APR 2011
abstract,
full text
Chodera, J.D., Mobley, D.L., Shirts, M.R., Dixon, R.W., Branson, K., Pande, V.S.
Alchemical free energy methods for drug discovery: progress and challenges
CURRENT OPINION IN STRUCTURAL BIOLOGY, 21:150-160, APR 2011
abstract,
full text
Bahrami, M., Kalantarinejad, R., Aghaei, M.J., Azadi, N.
Simulation of the Interaction of Carbon Nanotubes and External Flow
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8:563-567, APR 2011
abstract,
full text
Roth, M.W., Balasubramanya, M.K., Bergmann, P., Karl, M., Connolly, M.J., Gray, P.A.
Predicted Anomalous Behavior of C(60) Fullerenes on Graphite at Low Temperature: A New Hindered Cooperative Rotational Transition
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8:795-799, APR 2011
abstract,
full text
Liang, H., Liu, T., Chen, F.J., Liu, Z.Q., Liu, S.J.
A full-length 3D structure for MAPK/ERK kinase 2 (MEK2)
SCIENCE CHINA-LIFE SCIENCES, 54:336-341, APR 2011
abstract,
full text
Andronico, A., Randall, A., Benz, R.W., Baldi, P.
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:760-776, APR 2011
abstract,
full text
Ghosh-Kumar, M., Alam, T.I., Draper, B., Stack, J.D., Rao, V.B.
Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4
NUCLEIC ACIDS RESEARCH, 39:2742-2755, APR 2011
abstract,
full text
Buch, I., Tsai, C.J., Wolfson, H.J., Nussinov, R.
Symmetry-Based Self-assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers
PROTEIN AND PEPTIDE LETTERS, 18:362-372, APR 2011
abstract,
full text
Staritzbichler, R., Anselmi, C., Forrest, L.R., Faraldo-Gomez, J.D.
GRIFFIN: A Versatile Methodology for Optimization of Protein-Lipid Interfaces for Membrane Protein Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1167-1176, APR 2011
abstract,
full text
Lee, J.H., Park, H., Park, S.J., Kim, H.J., Eom, S.H.
The structural flexibility of the shank1 PDZ domain is important for its binding to different ligands
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 407:207-212, APR 1 2011
abstract,
full text
Firlej, L., Kuchta, B., Roth, M.W., Wexler, C.
Molecular simulations of intermediate and long alkanes adsorbed on graphite: Tuning of non-bond interactions
JOURNAL OF MOLECULAR MODELING, 17:811-816, APR 2011
abstract,
full text
Preat, J., Zanuy, D., Perpete, E.A., Aleman, C.
Binding of Cationic Conjugated Polymers to DNA: Atomistic Simulations of Adducts Involving the Dickerson's Dodecamer
BIOMACROMOLECULES, 12:1298-1304, APR 2011
abstract,
full text
Vattulainen, I., Rog, T.
Lipid Simulations: A Perspective on Lipids in Action
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY, 3: Art. No. a004655, APR 2011
abstract,
full text
Moss, C.L., Chung, T.W., Wyer, J.A., Nielsen, S.B., Hvelplund, P., Turecek, F.
Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22:731-751, APR 2011
abstract,
full text
Wada, M., Nishiyama, Y., Bellesia, G., Forsyth, T., Gnanakaran, S., Langan, P.
Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during the treatment of cellulose with ammonia
CELLULOSE, 18:191-206, APR 2011
abstract,
full text
Olmez, E.O., Alakent, B.
Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:675-693, APR 2011
abstract,
full text
Strzelecki, J.W., Strzelecka, J., Mikulska, K., Tszydel, M., Balter, A., Nowak, W.
Nanomechanics of new materials - AFM and computer modelling studies of trichoptera silk
CENTRAL EUROPEAN JOURNAL OF PHYSICS, 9:482-491, APR 2011
abstract,
full text
Kosevich, M.V., Zobnina, V.G., Chagovets, V.V., Boryak, O.A.
Observation of poly(ethylene glycol) clusters with the chlorine anion in the gas phase under electrospray conditions
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 25:713-718, MAR 30 2011
abstract,
full text
Jones, M.K., Gu, F.F., Catte, A., Li, L., Segrest, J.P.
"Sticky" and "Promiscuous", the Yin and Yang of Apolipoprotein A-I Termini in Discoidal High-Density Lipoproteins: A Combined Computational-Experimental Approach
BIOCHEMISTRY, 50:2249-2263, MAR 29 2011
abstract,
full text
Boettcher, J.M., Davis-Harrison, R.L., Clay, M.C., Nieuwkoop, A.J., Ohkubo, Y.Z., Tajkhorshid, E., Morrissey, J.H., Rienstra, C.M.
Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers
BIOCHEMISTRY, 50:2264-2273, MAR 29 2011
abstract,
full text
Geppert, T., Hoy, B., Wessler, S., Schneider, G.
Context-Based Identification of Protein-Protein Interfaces and "Hot-Spot" Residues
CHEMISTRY & BIOLOGY, 18:344-353, MAR 25 2011
abstract,
full text
Ozboyaci, M., Gursoy, A., Erman, B., Keskin, O.
Molecular Recognition of H3/H4 Histone Tails by the Tudor Domains of JMJD2A: A Comparative Molecular Dynamics Simulations Study
PLOS ONE, 6: Art. No. e14765, MAR 25 2011
abstract,
full text
Shukla, D., Zamolo, L., Cavallotti, C., Trout, B.L.
Understanding the Role of Arginine as an Eluent in Affinity Chromatography via Molecular Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:2645-2654, MAR 24 2011
abstract,
full text
Dalosto, S.D., Tinte, S.
Fluctuation Effects of the Electric Field Induced by Water on a Graphene Dot Band Gap
JOURNAL OF PHYSICAL CHEMISTRY C, 115:4381-4386, MAR 24 2011
abstract,
full text
Zhao, C.F., Noskov, S.Y.
The Role of Local Hydration and Hydrogen-Bonding Dynamics in Ion and Solute Release from Ion-Coupled Secondary Transporters
BIOCHEMISTRY, 50:1848-1856, MAR 22 2011
abstract,
full text
Radadia, A.D., Stavis, C.J., Carr, R., Zeng, H.J., King, W.P., Carlisle, J.A., Aksimentiev, A., Hamers, R.J., Bashir, R.
Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces
ADVANCED FUNCTIONAL MATERIALS, 21:1040-1050, MAR 22 2011
abstract,
full text
Sinha, S.K., Bandyopadhyay, S.
Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 115101, MAR 21 2011
abstract,
full text
Bhattacharya, S., Muzard, J., Payet, L., Mathe, J., Bockelmann, U., Aksimentiev, A., Viasnoff, V.
Rectification of the Current in alpha-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments
JOURNAL OF PHYSICAL CHEMISTRY C, 115:4255-4264, MAR 17 2011
abstract,
full text
Mihailescu, M., Vaswani, R.G., Jardon-Valadez, E., Castro-Roman, F., Freites, J.A., Worcester, D.L., Chamberlin, A.R., Tobias, D.J., White, S.H.
Acyl-Chain Methyl Distributions of Liquid-Ordered and -Disordered Membranes
BIOPHYSICAL JOURNAL, 100:1455-1462, MAR 16 2011
abstract,
full text
Dixit, P.D., Asthagiri, D.
The Role of Bulk Protein in Local Models of Ion-Binding to Proteins: Comparative Study of KcsA, Its Semisynthetic Analog with a Locked-in Binding Site, and Valinomycin
BIOPHYSICAL JOURNAL, 100:1542-1549, MAR 16 2011
abstract,
full text
Parthasarathy, S., Long, F., Miller, Y., Xiao, Y.L., McElheny, D., Thurber, K., Ma, B.Y., Nussinov, R., Ishii, Y.
Molecular-Level Examination of Cu(2+) Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's beta by Solid-State NMR Spectroscopy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3390-3400, MAR 16 2011
abstract,
full text
McCullagh, M., Franco, I., Ratner, M.A., Schatz, G.C.
DNA-Based Optomechanical Molecular Motor
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3452-3459, MAR 16 2011
abstract,
full text
Lee, O.S., Stupp, S.I., Schatz, G.C.
Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3677-3683, MAR 16 2011
abstract,
full text
Wedberg, R., O'Connell, J.P., Peters, G.H., Abildskov, J.
Total and direct correlation function integrals from molecular simulation of binary systems
FLUID PHASE EQUILIBRIA, 302:32-42, MAR 15 2011
abstract,
full text
Haspel, N., Zanuy, D., Nussinov, R., Teesalu, T., Ruoslahti, E., Aleman, C.
Binding of a C-End Rule Peptide to the Neuropilin-1 Receptor: A Molecular Modeling Approach
BIOCHEMISTRY, 50:1755-1762, MAR 15 2011
abstract,
full text
Zhang, Q.C., Yeh, T.L., Leyva, A., Frank, L.G., Miller, J., Kim, Y.E., Langen, R., Finkbeiner, S., Amzel, M.L., Ross, C.A., Poirier, M.A.
A Compact beta Model of huntingtin Toxicity
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:8188-8196, MAR 11 2011
abstract,
full text
Grafmuller, A., Voth, G.A.
Intrinsic Bending of Microtubule Protofilaments
STRUCTURE, 19:409-417, MAR 9 2011
abstract,
full text
Akgun, U., Khademi, S.
Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:3970-3975, MAR 8 2011
abstract,
full text
Uhart, M., Iglesias, A.A., Bustos, D.M.
Structurally Constrained Residues Outside the Binding Motif Are Essential in the Interaction of 14-3-3 and Phosphorylated Partner
JOURNAL OF MOLECULAR BIOLOGY, 406:552-557, MAR 4 2011
abstract,
full text
Ayuso-Tejedor, S., Garcia-Fandino, R., Orozco, M., Sancho, J., Bernado, P.
Structural Analysis of an Equilibrium Folding Intermediate in the Apoflavodoxin Native Ensemble by Small-Angle X-ray Scattering
JOURNAL OF MOLECULAR BIOLOGY, 406:604-619, MAR 4 2011
abstract,
full text
Khan, N.S., Perez-Aguilar, J.M., Kaufmann, T., Hill, P.A., Taratula, O., Lee, O.S., Carroll, P.J., Saven, J.G., Dmochowski, I.J.
Multiple Hindered Rotators in a Gyroscope-Inspired Tribenzylamine Hemicryptophane
JOURNAL OF ORGANIC CHEMISTRY, 76:1418-1424, MAR 4 2011
abstract,
full text
Miller, Y., Ma, B.Y., Nussinov, R.
The Unique Alzheimer's beta-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:2742-2748, MAR 2 2011
abstract,
full text
Cui, H.S., Lyman, E., Voth, G.A.
Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins
BIOPHYSICAL JOURNAL, 100:1271-1279, MAR 2 2011
abstract,
full text
Wallrapp, F.H., Guallar, V.
Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:315-322, MAR-APR 2011
abstract,
full text
Prasad, N.K., Vindal, V., Kumar, V., Kabra, A., Phogat, N., Kumar, M.
Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase
JOURNAL OF MOLECULAR MODELING, 17:533-541, MAR 2011
abstract,
full text
Silvestre-Ryan, J., Lin, Y.C., Chu, J.W.
"Fluctuograms'' Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002023, MAR 2011
abstract,
full text
Mazars, M.
Long ranged interactions in computer simulations and for quasi-2D systems
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 500:43-116, MAR 2011
abstract,
full text
Gonzalez, A., Murcia, M., Benhamu, B., Campillo, M., Lopez-Rodriguez, M.L., Pardo, L.
The importance of solvation in the design of ligands targeting membrane proteins
MEDCHEMCOMM, 2:160-164, MAR 2011
abstract,
full text
Cai, W.S., Wang, T., Liu, Y.Z., Liu, P., Chipot, C., Shao, X.G.
Free Energy Calculations for Cyclodextrin Inclusion Complexes
CURRENT ORGANIC CHEMISTRY, 15:839-847, MAR 2011
abstract,
full text
Heroux, M.S., Mohan, A.D., Olsen, K.W.
Ligand Migration in the Truncated Hemoglobin of Mycobacterium tuberculosis
IUBMB LIFE, 63:214-220, MAR 2011
abstract,
full text
Perez-Sanchez, H., Wenzel, W.
Optimization Methods for Virtual Screening on Novel Computational Architectures
CURRENT COMPUTER-AIDED DRUG DESIGN, 7:44-52, MAR 2011
abstract,
full text
Patra, N., Song, Y.B., Kral, P.
Self-Assembly of Graphene Nanostructures on Nanotubes
ACS NANO, 5:1798-1804, MAR 2011
abstract,
full text
Singh, L.R., Poddar, N.K., Dar, T.A., Rahman, S., Kumar, R., Ahmad, F.
Forty Years of Research on Osmolyte-Induced Protein Folding and Stability
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 8:1-23, MAR 2011
abstract,
full text
Min, S.K., Kim, W.Y., Cho, Y., Kim, K.S.
Fast DNA sequencing with a graphene-based nanochannel device
NATURE NANOTECHNOLOGY, 6:162-165, MAR 2011
abstract,
full text
Beretta, G., Artali, R., Caneva, E., Facino, R.M.
Conformation of the tridimensional structure of 1,2,3,4,6-pentagalloyl-beta-D-glucopyranose (PGG) by (1)H NMR, NOESY and theoretical study and membrane interaction in a simulated phospholipid bilayer: a first insight
MAGNETIC RESONANCE IN CHEMISTRY, 49:132-136, MAR 2011
abstract,
full text
Corry, B.
Water and ion transport through functionalised carbon nanotubes: implications for desalination technology
ENERGY & ENVIRONMENTAL SCIENCE, 4:751-759, MAR 2011
abstract,
full text
Qiu, H., Shen, R., Guo, W.L.
Vibrating carbon nanotubes as water pumps
NANO RESEARCH, 4:284-289, MAR 2011
abstract,
full text
Janovec, L., Kozurkova, M., Sabolova, D., Ungvarsky, J., Paulikova, H., Plsikova, J., Vantova, Z., Imrich, J.
Cytotoxic 3,6-bis((imidazolidinone)imino)acridines: Synthesis, DNA binding and molecular modeling
BIOORGANIC & MEDICINAL CHEMISTRY, 19:1790-1801, MAR 1 2011
abstract,
full text
Gumbart, J., Chipot, C., Schulten, K.
Free-energy cost for translocon-assisted insertion of membrane proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:3596-3601, MAR 1 2011
abstract,
full text,
TCBG publications
Lin, Y.W.
Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:679-684, MAR 2011
abstract,
full text
Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., Trout, B.L.
Prediction of protein binding regions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:888-897, MAR 2011
abstract,
full text
Fogolari, F., Corazza, A., Varini, N., Rotter, M., Gumral, D., Codutti, L., Rennella, E., Viglino, P., Bellotti, V., Esposito, G.
Molecular dynamics simulation of beta(2)-microglobulin in denaturing and stabilizing conditions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:986-1001, MAR 2011
abstract,
full text
Trabuco, L.G., SchreineR, E., Gumbart, J., Hsin, J., Villa, E., Schulten, K.
Applications of the molecular dynamics flexible fitting method
JOURNAL OF STRUCTURAL BIOLOGY, 173:420-427, MAR 2011
abstract,
full text,
TCBG publications
Wang, X., Lee, H.W., Liu, Y.Z., Prestegard, J.H.
Structural NMR of protein oligomers using hybrid methods
JOURNAL OF STRUCTURAL BIOLOGY, 173:515-529, MAR 2011
abstract,
full text
Tsoulos, I.G., Stavrakoudis, A.
Eucb: A C plus plus program for molecular dynamics trajectory analysis
COMPUTER PHYSICS COMMUNICATIONS, 182:834-841, MAR 2011
abstract,
full text
Peplowski, L., Sikora, M., Nowak, W., Cieplak, M.
Molecular jamming-The cystine slipknot mechanical clamp in all-atom simulations
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 085102, FEB 28 2011
abstract,
full text
NategholEslam, M., Holland, B.W., Gray, C.G., Tomberli, B.
Drift-oscillatory steering with the forward-reverse method for calculating the potential of mean force
PHYSICAL REVIEW E, 83: Art. No. 021114, FEB 28 2011
abstract,
full text
Megow, J., Roder, B., Kulesza, A., Bonacic-Koutecky, V., May, V.
A Mixed Quantum-Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Forster Theory and beyond
CHEMPHYSCHEM, 12:645-656, FEB 25 2011
abstract,
full text
Su, C.C., Long, F., Zimmermann, M.T., Rajashankar, K.R., Jernigan, R.L., Yu, E.W.
Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli
NATURE, 470:558-U153, FEB 24 2011
abstract,
full text
Li, X.C., Tobacman, L.S., Mun, J.Y., Craig, R., Fischer, S., Lehman, W.
Tropomyosin Position on F-Actin Revealed by EM Reconstruction and Computational Chemistry
BIOPHYSICAL JOURNAL, 100:1005-1013, FEB 16 2011
abstract,
full text
Spiriti, J., Binder, J.K., Levitus, M., van der Vaart, A.
Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair
BIOPHYSICAL JOURNAL, 100:1049-1057, FEB 16 2011
abstract,
full text
Hsin, J., Schulten, K.
Improved Resolution of Tertiary Structure Elasticity in Muscle Protein
BIOPHYSICAL JOURNAL, 100:L22-L24, FEB 16 2011
abstract,
full text,
TCBG publications
Santiso, E.E., Trout, B.L.
A general set of order parameters for molecular crystals
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 064109, FEB 14 2011
abstract,
full text
Liu, Y.Z., Chipot, C., Shao, X.G., Cai, W.S.
Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide
JOURNAL OF PHYSICAL CHEMISTRY C, 115:1851-1856, FEB 10 2011
abstract,
full text
Mroginski, M.A., Kaminski, S., von Stetten, D., Ringsdorf, S., Gartner, W., Essen, L.O., Hildebrandt, P.
Structure of the Chromophore Binding Pocket in the Pr State of Plant Phytochrome phyA
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1220-1231, FEB 10 2011
abstract,
full text
Shukla, D., Trout, B.L.
Preferential Interaction Coefficients of Proteins in Aqueous Arginine Solutions and Their Molecular Origins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1243-1253, FEB 10 2011
abstract,
full text
Zhou, R.H., Li, J.Y., Hua, L., Yang, Z.X., Berne, B.J.
Comment on "Urea-Mediated Protein Denaturation: A Consensus View"
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1323-1326, FEB 10 2011
full text
Su, Z.Y., Wang, Y.T.
Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:796-802, FEB 10 2011
abstract,
full text
Oliveira, A.F., Gemming, S., Seifert, G.
Conformational Analysis of Aqueous BMP-2 Using Atomistic Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1122-1130, FEB 10 2011
abstract,
full text
Garate, J.A., English, N.J., MacElroy, J.M.D.
Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 055110, FEB 7 2011
abstract,
full text
Yeh, I.C., Wallqvist, A.
On the proper calculation of electrostatic interactions in solid-supported bilayer systems
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 055109, FEB 7 2011
abstract,
full text
Martinez, A.V., DeSensi, S.C., Dominguez, L., Rivera, E., Straub, J.E.
Protein folding in a reverse micelle environment: The role of confinement and dehydration
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 055107, FEB 7 2011
abstract,
full text
Sapir, L., Harries, D.
Linking Trehalose Self-Association with Binary Aqueous Solution Equation of State
JOURNAL OF PHYSICAL CHEMISTRY B, 115:624-634, FEB 3 2011
abstract,
full text
Olbrich, C., Strumpfer, J., Schulten, K., Kleinekathofer, U.
Quest for Spatially Correlated Fluctuations in the FMO Light-Harvesting Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 115:758-764, FEB 3 2011
abstract,
full text,
TCBG publications
Bastug, T., Kuyucak, S.
Comparative Study of the Energetics of Ion Permeation in Kv1.2 and KcsA Potassium Channels
BIOPHYSICAL JOURNAL, 100:629-636, FEB 2 2011
abstract,
full text
Kokhan, O., Shinkarev, V.P.
All-Atom Molecular Dynamics Simulations Reveal Significant Differences in Interaction between Antimycin and Conserved Amino Acid Residues in Bovine and Bacterial bc(1) Complexes
BIOPHYSICAL JOURNAL, 100:720-728, FEB 2 2011
abstract,
full text
Skjevik, A.A., Haug, B.E., Lygre, H., Teigen, K.
Intramolecular hydrogen bonding in articaine can be related to superior bone tissue penetration: A molecular dynamics study
BIOPHYSICAL CHEMISTRY, 154:18-25, FEB 2011
abstract,
full text
Zhang, J.L., Zheng, Q.C., Zhang, H.X.
Theoretical improvement of the specific inhibitor of human carbonic anhydrase VII
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 35:50-56, FEB 2011
abstract,
full text
Kim, S.K., Li, Y.Y., Abrol, R., Heo, J., Goddard, W.A.
Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:420-433, FEB 2011
abstract,
full text
Nowosieski, M., Hoffmann, M., Wyrwicz, L.S., Stepniak, P., Plewczynski, D.M., Lazniewski, M., Ginalski, K., Rychlewski, L.
Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:455-462, FEB 2011
abstract,
full text
Arsawang, U., Saengsawang, O., Rungrotmongkol, T., Sornmee, P., Wittayanarakul, K., Remsungnen, T., Hannongbua, S.
How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system?
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:591-596, FEB 2011
abstract,
full text
Morales-Quintana, L., Fuentes, L., Gaete-Eastman, C., Herrera, R., Moya-Leon, M.A.
Structural characterization and substrate specificity of VpAAT1 protein related to ester biosynthesis in mountain papaya fruit
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:635-642, FEB 2011
abstract,
full text
Yun, S.J., Guy, H.R.
Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:663-675, FEB 2011
abstract,
full text
Grasso, G., Pietropaolo, A., Spoto, G., Pappalardo, G., Tundo, G.R., Ciaccio, C., Coletta, M., Rizzarelli, E.
Copper(I) and Copper(II) Inhibit A beta Peptides Proteolysis by Insulin-Degrading Enzyme Differently: Implications for Metallostasis Alteration in Alzheimer's Disease
CHEMISTRY-A EUROPEAN JOURNAL, 17:2752-2762, FEB 2011
abstract,
full text
Gossett, J.J., Harvey, S.C.
Computational Screening and Design of DNA-Linked Molecular Nanowires
NANO LETTERS, 11:604-608, FEB 2011
abstract,
full text
Kamisetty, H., Ramanathan, A., Bailey-Kellogg, C., Langmead, C.J.
Accounting for conformational entropy in predicting binding free energies of protein-protein interactions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:444-462, FEB 2011
abstract,
full text
Novak, B.R., Moldovan, D., Waldrop, G.L., de Queiroz, M.S.
Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:622-632, FEB 2011
abstract,
full text
Falconi, M., Oteri, F., Di Palma, F., Pandey, S., Battistoni, A., Desideri, A.
Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:181-194, FEB 2011
abstract,
full text
Bowman, G.R., Voelz, V.A., Pande, V.S.
Taming the complexity of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 21:4-11, FEB 2011
abstract,
full text
Chen, W., Lou, J.Z., Hsin, J., Schulten, K., Harvey, S.C., Zhu, C.
Molecular Dynamics Simulations of Forced Unbending of Integrin alpha(V)beta(3)
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1001086, FEB 2011
abstract,
full text,
TCBG publications
Huang, D.Z., Caflisch, A.
The Free Energy Landscape of Small Molecule Unbinding
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002002, FEB 2011
abstract,
full text
Niazi, U.H.K., Bibby, J., Sutcliffe, M.J.
In-silico characterization of the effects of phosphorylated tyrosines 86 and 106 on structure and binding of MAL: insight into hyperinflammatory response to infection by the human malaria parasites
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:53-65, FEB 2011
abstract,
full text
Chakrabarti, B., Bairagya, H.R., Mallik, P., Mukhopadhyay, B.P., Bera, A.K.
An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn(+2) ions in Matrix Metalloproteinase 13 of Human
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:503-516, FEB 2011
abstract,
full text
Olbrich, C., Liebers, J., Kleinekathofer, U.
Modeling of light-harvesting in purple bacteria using a time-dependent Hamiltonian approach
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, 248:393-398, FEB 2011
abstract,
full text
Calderon, C.P.
Estimation and Inference of Diffusion Coefficients in Complex Biomolecular Environments
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:280-290, FEB 2011
abstract,
full text
Kawatsu, T., Lundberg, M., Morokuma, K.
Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:390-401, FEB 2011
abstract,
full text
Qu, Y.Y., Zhou, H., Li, A., Ma, F., Zhou, J.T.
Nitroreductase activity of ferredoxin reductase BphA4 from Dyella ginsengisoli LA-4 by catalytic and structural properties analysis
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 89:655-663, FEB 2011
abstract,
full text
Gushchin, I.Y., Gordeliy, V.I., Grudinin, S.
Role of the HAMP Domain Region of Sensory Rhodopsin Transducers in Signal Transduction
BIOCHEMISTRY, 50:574-580, FEB 1 2011
abstract,
full text
Kalikka, J., Akola, J.
Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:181-194, FEB 2011
abstract,
full text
Mustata, G., Li, M., Zevola, N., Bakan, A., Zhang, L., Epperly, M., Greenberger, J.S., Yu, J., Bahar, I.
Development of Small-Molecule PUMA Inhibitors for Mitigating Radiation-Induced Cell Death
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 11:281-290, FEB 2011
abstract,
full text
Emileh, A., Abrams, C.F.
A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain alpha 1 helix in an engineered HIV-1 gp120
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:537-546, FEB 2011
abstract,
full text
Shim, J.Y., Rudd, J., Ding, T.T.
Distinct second extracellular loop structures of the brain cannabinoid CB(1) receptor: Implication in ligand binding and receptor function
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:581-597, FEB 2011
abstract,
full text
Yan, Q., Murphy-Ullrich, J.E., Song, Y.H.
Molecular and Structural Insight into the Role of Key Residues of Thrombospondin-1 and Calreticulin in Thrombospondin-1-Calreticulin Binding
BIOCHEMISTRY, 50:566-573, FEB 1 2011
abstract,
full text
Henriques, E.S., Brito, R.M.M., Soares, H., Ventura, S., de Oliveira, V.L., Parkhouse, R.M.E.
Modeling of the Toll-like receptor 3 and a putative Toll-like receptor 3 antagonist encoded by the African swine fever virus
PROTEIN SCIENCE, 20:247-255, FEB 2011
abstract,
full text
Khurana, E., DeVane, R.H., Dal Peraro, M., Klein, M.L.
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:530-537, FEB 2011
abstract,
full text
Kotsikorou, E., Lynch, D.L., Abood, M.E., Reggio, P.H.
Lipid bilayer molecular dynamics study of lipid-derived agonists of the putative cannabinoid receptor, GPR55
CHEMISTRY AND PHYSICS OF LIPIDS, 164:131-143, FEB 2011
abstract,
full text
Hilder, T.A., Gordon, D., Chung, S.H.
Synthetic cation-selective nanotube: Permeant cations chaperoned by anions
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 045103, JAN 28 2011
abstract,
full text
Karino, Y., Matubayasi, N.
Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 041105, JAN 28 2011
abstract,
full text
Ramanathan, A., Savol, A.J., Langmead, C.J., Agarwal, P.K., Chennubhotla, C.S.
Discovering Conformational Sub-States Relevant to Protein Function
PLOS ONE, 6: Art. No. e15827, JAN 28 2011
abstract,
full text
Cruz, F.A., Knepley, M.G., Barba, L.A.
PetFMM-A dynamically load-balancing parallel fast multipole library
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, 85:403-428, JAN 28 2011
abstract,
full text
Shan, J.F., Javitch, J.A., Shi, L., Weinstein, H.
The Substrate-Driven Transition to an Inward-Facing Conformation in the Functional Mechanism of the Dopamine Transporter
PLOS ONE, 6: Art. No. e16350, JAN 27 2011
abstract,
full text
Panecka, J., Mura, C., Trylska, J.
Molecular Dynamics of Potential rRNA Binders: Single-Stranded Nucleic Acids and Some Analogues
JOURNAL OF PHYSICAL CHEMISTRY B, 115:532-546, JAN 27 2011
abstract,
full text
Ko, E., Liu, J., Perez, L.M., Lu, G.L., Schaefer, A., Burgess, K.
Universal Peptidomimetics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:462-477, JAN 26 2011
abstract,
full text
Zuniga, L., Marquez, V., Gonzalez-Nilo, F.D., Chipot, C., Cid, L.P., Sepulveda, F.V., Niemeyer, M.I.
Gating of a pH-Sensitive K(2P) Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter
PLOS ONE, 6: Art. No. e16141, JAN 25 2011
abstract,
full text
Liu, L., Fang, Y., Huang, Q.S., Wu, J.H.
A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic alpha-Helical Peptide HP(2-20) and Its Four Analogues
PLOS ONE, 6: Art. No. e16441, JAN 24 2011
abstract,
full text
Jiang, W., Hardy, D.J., Phillips, J.C., MacKerell, A.D., Schulten, K., Roux, B.
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:87-92, JAN 20 2011
abstract,
full text,
TCBG publications
Nury, H., Van Renterghem, C., Weng, Y., Tran, A., Baaden, M., Dufresne, V., Changeux, J.P., Sonner, J.M., Delarue, M., Corringer, P.J.
X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
NATURE, 469:428-+, JAN 20 2011
abstract,
full text
Zerbetto, M., Buck, M., Meirovitch, E., Polimeno, A.
Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain (15)N-(1)H and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1
JOURNAL OF PHYSICAL CHEMISTRY B, 115:376-388, JAN 20 2011
abstract,
full text
Brubaker, W.D., Freites, J.A., Golchert, K.J., Shapiro, R.A., Morikis, V., Tobias, D.J., Martin, R.W.
Separating Instability from Aggregation Propensity in gamma S-Crystallin Variants
BIOPHYSICAL JOURNAL, 100:498-506, JAN 19 2011
abstract,
full text
Fritsch, S., Ivanov, I., Wang, H.L., Cheng, X.L.
Ion Selectivity Mechanism in a Bacterial Pentameric Ligand-Gated Ion Channel
BIOPHYSICAL JOURNAL, 100:390-398, JAN 19 2011
abstract,
full text
Dendzik, Z., Gorny, K., Gwizdala, W., Gburski, Z.
Dipolar relaxation of propylene glycol molecular cluster confined in carbon nanotubes of different chiralities-computer simulation study
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:575-579, JAN 15 2011
abstract,
full text
Kieslich, C.A., Gorham, R.D., Morikis, D.
Is the rigid-body assumption reasonable? Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:707-716, JAN 15 2011
abstract,
full text
Sun, S., Yin, G.Y., Lee, Y.K., Wong, J.T.Y., Zhang, T.Y.
Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:684-688, JAN 14 2011
abstract,
full text
Wang, C.H., Ye, F.B., Velardez, G.F., Peters, G.H., Westh, P.
Affinity of Four Polar Neurotransmitters for Lipid Bilayer Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:196-203, JAN 13 2011
abstract,
full text
Venkatramani, R., Davis, K.L., Wierzbinski, E., Bezer, S., Balaeff, A., Keinan, S., Paul, A., Kocsis, L., Beratan, D.N., Achim, C., Waldeck, D.H.
Evidence for a Near-Resonant Charge Transfer Mechanism for Double-Stranded Peptide Nucleic Acid
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:62-72, JAN 12 2011
abstract,
full text
Hilder, T.A., Chung, S.H.
Carbon nanotube as a gramicidin analogue
CHEMICAL PHYSICS LETTERS, 501:423-426, JAN 7 2011
abstract,
full text
Bossis, F., Palese, L.L.
Molecular dynamics in cytochrome c oxidase Mossbauer spectra deconvolution
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:438-442, JAN 7 2011
abstract,
full text
Sakata, T., Kawashima, Y., Nakano, H.
Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 014501, JAN 7 2011
abstract,
full text
Koksal, M., Jin, Y.H., Coates, R.M., Croteau, R., Christianson, D.W.
Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis
NATURE, 469:116-U138, JAN 6 2011
abstract,
full text
Thomas, M., Jayatilaka, D., Corry, B.
Mapping the Importance of Four Factors in Creating Monovalent Ion Selectivity in Biological Molecules
BIOPHYSICAL JOURNAL, 100:60-69, JAN 5 2011
abstract,
full text
Wang, T., Chipot, C., Shao, X.G., Cai, W.S.
Structural Characterization of Micelles Formed of Cholesteryl-Functionalized Cyclodextrins
LANGMUIR, 27:91-97, JAN 4 2011
abstract,
full text
Wang, Y., Dewdney, T.G., Liu, Z.G., Reiter, S.J., Brunzelle, J.S., Kovari, I.A., Kovari, L.C.
X-RAY CRYSTAL STRUCTURE AND DYNAMICS REVEAL HIV-1 PROTEASE DRUG INTERACTIONS
STUDIA UNIVERSITATIS BABES-BOLYAI CHEMIA, 56:221-230, 2011
abstract,
full text
Tiber, P.M., Orun, O., Nacar, C., Sezerman, U.O., Severcan, F., Severcan, M., Matagne, A., Kan, B.
Structural characterization of recombinant bovine Go alpha by spectroscopy and homology modeling
SPECTROSCOPY-BIOMEDICAL APPLICATIONS, 26:213-229, 2011
abstract,
full text
Gangupomu, V.K., Capaldi, F.M.
Interactions of Carbon Nanotube with Lipid Bilayer Membranes
JOURNAL OF NANOMATERIALS, Art. No. 830436, 2011
abstract,
full text
Reith, D., Mirny, L., Virnau, P.
GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling
PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT, Issue 191, 135-145, 2011
abstract,
full text
Castelletto, V., Moulton, C.M., Cheng, G., Hamley, I.W., Hicks, M.R., Rodger, A., Lopez-Perez, D.E., Revilla-Lopez, G., Aleman, C.
Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif
SOFT MATTER, 7:11405-11415, 2011
abstract,
full text
Orozco, M., Orellana, L., Hospital, A., Naganathan, A.N., Emperador, A., Carrillo, O., Gelpi, J.L.
COARSE-GRAINED REPRESENTATION OF PROTEIN FLEXIBILITY. FOUNDATIONS, SUCCESSES, AND SHORTCOMINGS
ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, VOL 85: COMPUTATIONAL CHEMISTRY METHODS IN STRUCTURAL BIOLOGY, 85:183-215, 2011
abstract,
full text
Chipot, C., Lelievre, T.
ENHANCED SAMPLING OF MULTIDIMENSIONAL FREE-ENERGY LANDSCAPES USING ADAPTIVE BIASING FORCES
SIAM JOURNAL ON APPLIED MATHEMATICS, 71:1673-1695, 2011
abstract,
full text
Dong, X.L., Qi, W., Tao, W., Ma, L.Y., Fu, C.X.
The dynamic behaviours of protein BMP-2 on hydroxyapatite nanoparticles
MOLECULAR SIMULATION, 37:1097-1104, 2011
abstract,
full text
Hughes, M., Xu, H.X., Frederix, P.W.J.M., Smith, A.M., Hunt, N.T., Tuttle, T., Kinloch, I.A., Ulijn, R.V.
Biocatalytic self-assembly of 2D peptide-based nanostructures
SOFT MATTER, 7:10032-10038, 2011
abstract,
full text
Khelashvili, G., Rappolt, M., Chiu, S.W., Pabst, G., Harries, D.
Impact of sterol tilt on membrane bending rigidity in cholesterol and 7DHC-containing DMPC membranes
SOFT MATTER, 7:10299-10312, 2011
abstract,
full text
Teixeira-Dias, B., Zanuy, D., Poater, J., Sola, M., Estrany, F., del Valle, L.J., Aleman, C.
Binding of 6-mer single-stranded homo-nucleotides to poly(3,4-ethylenedioxythiophene): specific hydrogen bonds with guanine
SOFT MATTER, 7:9922-9932, 2011
abstract,
full text
Carr, R., Comer, J., Ginsberg, M.D., Aksimentiev, A.
Atoms-to-microns model for small solute transport through sticky nanochannels
LAB ON A CHIP, 11:3766-3773, 2011
abstract,
full text
Engelbrecht, T., Hauss, T., Suss, K., Vogel, A., Roark, M., Feller, S.E., Neubert, R.H.H., Dobner, B.
Characterisation of a new ceramide EOS species: synthesis and investigation of the thermotropic phase behaviour and influence on the bilayer architecture of stratum corneum lipid model membranes
SOFT MATTER, 7:8998-9011, 2011
abstract,
full text
Jamadagni, S.N., Godawat, R., Garde, S.
Hydrophobicity of Proteins and Interfaces: Insights from Density Fluctuations
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 2, 2:147-171, 2011
abstract,
full text
Zhao, Y.P., Wang, F.C., Chi, M.
Molecular Dynamics Simulation and Molecular Orbital Method
HANDBOOK OF ADHESION TECHNOLOGY, VOL 1 AND 2, DOI 10.1007/978-3-642-01169-6_52, 2011
abstract,
full text
Asghar, W., Billo, J.A., Iqbal, S.M.
Solid State Nanopores for Selective Sensing of DNA
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, DOI 10.1007/978-1-4419-8252-0_5, 2011
abstract,
full text
Gracheva, M.E., Leroux, A., Destine, J., Leburton, J.P.
Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, DOI 10.1007/978-1-4419-8252-0_7, 2011
abstract,
full text
Comer, J., Aksimentiev, A.
Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, DOI 10.1007/978-1-4419-8252-0_14, 2011
abstract,
full text
Wang, Q.M., Shah, N., Zhao, J., Wang, C.S., Zhao, C., Liu, L.Y., Li, L.Y., Zhou, F.M., Zheng, J.
Structural, morphological, and kinetic studies of beta-amyloid peptide aggregation on self-assembled monolayers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:15200-15210, 2011
abstract,
full text
Stavrakoudis, A.
Molecular dynamics study of the human insulin B peptide SHLVEALYLVCGERGG complexed with HLA-DQ8 reveals important hydrogen bond interactions
MOLECULAR SIMULATION, 37:837-845, 2011
abstract,
full text
Lee, O.S., Schatz, G.C.
Computational Simulations of the Interaction of Lipid Membranes with DNA-Functionalized Gold Nanoparticles
BIOMEDICAL NANOETECHNOLOGY: METHODS AND PROTOCOLS, 726:283-296, 2011
abstract,
full text
Nishizawa, K.
Atomistic Molecular Simulation of Gating Modifier Venom Peptides - Two Binding Modes and Effects of Lipid Structure
MECHANOSENSITIVITY AND MECHANOTRANSDUCTION, 4:167-190, 2011
abstract,
full text
Wang, F., Akin-Ojo, O., Pinnick, E., Song, Y.
Approaching post-Hartree-Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method
MOLECULAR SIMULATION, 37:591-605, 2011
abstract,
full text
Deplazes, E., Jayatilaka, D., Corry, B.
Testing the use of molecular dynamics to simulate fluorophore motions and FRET
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:11045-11054, 2011
abstract,
full text
Kawashima, Y., Nakano, H., Jung, J., Ten-no, S.
A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals: implementation for electronic excited states
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:11731-11738, 2011
abstract,
full text
Cheng, X.D., Blumenthal, R.M.
Introduction-Epiphanies in Epigenetics
MODIFICATIONS OF NUCLEAR DNA AND ITS REGULATORY PROTEINS, 101:1-21, 2011
full text
Arce, F.T., Jang, H.B., Ramachandran, S., Landon, P.B., Nussinov, R., Lal, R.
Polymorphism of amyloid beta peptide in different environments: implications for membrane insertion and pore formation
SOFT MATTER, 7:5267-5273, 2011
abstract,
full text
Papadopoulos, T.A., Muccioli, L., Athanasopoulos, S., Walker, A.B., Zannoni, C., Beljonne, D.
Does supramolecular ordering influence exciton transport in conjugated systems? Insight from atomistic simulations
CHEMICAL SCIENCE, 2:1025-1032, 2011
abstract,
full text
Revilla-Lopez, G., Torras, J., Nussinov, R., Aleman, C., Zanuy, D.
Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9986-9994, 2011
abstract,
full text
Telesco, S.E., Shih, A.J., Jia, F., Radhakrishnan, R.
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network
MOLECULAR BIOSYSTEMS, 7:2066-2080, 2011
abstract,
full text
Venturini, A., Zerbetto, F.
Dynamics of a lipid bilayer induced by electric fields
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9216-9222, 2011
abstract,
full text
Suyetin, M.V., Vakhrushev, A.V.
Nanocapsule with pump for methane storage
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9863-9870, 2011
abstract,
full text
Moss, C.L., Chung, T.W., Cerovsky, V., Turecek, F.
ELECTRON TRANSFER DISSOCIATION OF A MELECTIN PEPTIDE: CORRELATING THE PRECURSOR ION STRUCTURE WITH PEPTIDE BACKBONE DISSOCIATIONS
COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, 76:295-309, 2011
abstract,
full text
Banu, M., Patriche, S., Coman, M., Matsushita, S., Tofan, A., Epureanu, A.
Investigation of ubiquitin deformation mechanism under induced stretch-compression loads
ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY, 52:449-454, 2011
abstract,
full text
Chen, L.Y.
Exploring the free-energy landscapes of biological systems with steered molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6176-6183, 2011
abstract,
full text
Guest, W.C., Cashman, N.R., Plotkin, S.S.
A theory for the anisotropic and inhomogeneous dielectric properties of proteins
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6286-6295, 2011
abstract,
full text
Aguilella, V.M., Queralt-Martin, M., Aguilella-Arzo, M., Alcaraz, A.
Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity
INTEGRATIVE BIOLOGY, 3:159-172, 2011
abstract,
full text
Kayser, V., Chennamsetty, N., Voynov, V., Helk, B., Trout, B.L.
Tryptophan-Tryptophan Energy Transfer and Classification of Tryptophan Residues in Proteins Using a Therapeutic Monoclonal Antibody as a Model
JOURNAL OF FLUORESCENCE, 21:275-288, JAN 2011
abstract,
full text
Abroshan, H., Akbarzadeh, H., Taherkhani, F., Parsafar, G.
Effect of water-methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamics study
MOLECULAR PHYSICS, 109:709-724, 2011
abstract,
full text
Bernini, C., Pogni, R., Ruiz-Duenas, F.J., Martinez, A.T., Basosia, R., Sinicropi, A.
EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:5078-5098, 2011
abstract,
full text
Carr, R., Comer, J., Ginsberg, M.D., Aksimentiev, A.
Modeling Pressure-Driven Transport of Proteins Through a Nanochannel
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 10:75-82, JAN 2011
abstract,
full text
Feng, J., Pandey, R.B., Berry, R.J., Farmer, B.L., Naik, R.R., Heinz, H.
Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules
SOFT MATTER, 7:2113-2120, 2011
abstract,
full text
Kayser, V., Chennamsetty, N., Voynov, V., Forrer, K., Helk, B., Trout, B.L.
Glycosylation influences on the aggregation propensity of therapeutic monoclonal antibodies
BIOTECHNOLOGY JOURNAL, 6:38-44, JAN 2011
abstract,
full text
Calero, C., Faraudo, J., Aguilella-Arzo, M.
Molecular dynamics simulations of concentrated aqueous electrolyte solutions
MOLECULAR SIMULATION, 37:123-134, 2011
abstract,
full text
Chung, T.W., Moss, C.L., Zimnicka, M., Johnson, R.S., Moritz, R.L., Turecek, F.
Electron-Capture and -Transfer Dissociation of Peptides Tagged with Tunable Fixed-Charge Groups: Structures and Dissociation Energetics
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22:13-30, JAN 2011
abstract,
full text
Lim, J.B., Klauda, J.B.
Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:323-331, JAN 2011
abstract,
full text
Cashman, D.J., Mamonov, A.B., Bhatt, D., Zuckerman, D.M.
Thermal Motions of the E. coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 11:211-220, JAN 2011
abstract,
full text
Tsaousis, A.D., Gaston, D., Stechmann, A., Walker, P.B., Lithgow, T., Roger, A.J.
A Functional Tom70 in the Human Parasite Blastocystis sp.: Implications for the Evolution of the Mitochondrial Import Apparatus
MOLECULAR BIOLOGY AND EVOLUTION, 28:781-791, JAN 2011
abstract,
full text
Schow, E.V., Freites, J.A., Cheng, P., Bernsel, A., von Heijne, G., White, S.H., Tobias, D.J.
Arginine in Membranes: The Connection Between Molecular Dynamics Simulations and Translocon-Mediated Insertion Experiments
JOURNAL OF MEMBRANE BIOLOGY, 239:35-48, JAN 2011
abstract,
full text
Wagner, C., Olbrich, C., Brutzer, H., Salomo, M., Kleinekathofer, U., Keyser, U.F., Kremer, F.
DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations
JOURNAL OF BIOLOGICAL PHYSICS, 37:117-131, JAN 2011
abstract,
full text
Cazade, P.A., Bordat, P., Baraille, I., Brown, R., Smith, W., Todorov, I.T.
DL_POLY_2 adaptations for solvation studies
MOLECULAR SIMULATION, 37:43-52, 2011
abstract,
full text
Wang, T., Shao, X.G., Cai, W.S., Xue, Y.L., Wang, S.A., Feng, X.Z.
Predicting the coordination geometry for Mg(2+) in the p53 DNA-binding domain: insights from computational studies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:1140-1151, 2011
abstract,
full text
Jiang, J., Mukamel, S.
Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:2394-2400, 2011
abstract,
full text
Zhao, J., Yu, X.A., Liang, G.Z., Zheng, J.
Structural Polymorphism of Human Islet Amyloid Polypeptide (hIAPP) Oligomers Highlights the Importance of Interfacial Residue Interactions
BIOMACROMOLECULES, 12:210-220, JAN 2011
abstract,
full text
Milac, A.L., Anishkin, A., Fatakia, S.N., Chow, C.C., Sukharev, S., Guy, H.R.
Structural models of TREK channels and their gating mechanism
CHANNELS, 5:23-33, JAN-FEB 2011
abstract,
full text
Romo, T.D., Grossfield, A.
Validating and improving elastic network models with molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:23-34, JAN 2011
abstract,
full text
Mustafa, M., Mirza, A., Kannan, N.
Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:99-114, JAN 2011
abstract,
full text
Lynch, R.M., Rong, R., Boliar, S., Sethi, A., Li, B., Mulenga, J., Allen, S., Robinson, J.E., Gnanakaran, S., Derdeyn, C.A.
The B Cell Response Is Redundant and Highly Focused on V1V2 during Early Subtype C Infection in a Zambian Seroconverter
JOURNAL OF VIROLOGY, 85:905-915, JAN 2011
abstract,
full text
Kortagere, S., Cheng, S.Y., Antonio, T., Zhen, J.A., Reith, M.E.A., Dutta, A.K.
Interaction of novel hybrid compounds with the D3 dopamine receptor: Site-directed mutagenesis and homology modeling studies
BIOCHEMICAL PHARMACOLOGY, 81:157-163, JAN 1 2011
abstract,
full text
Comer, J.R., Wells, D.B., Aksimentiev, A.
Modeling Nanopores for Sequencing DNA
DNA NANOTECHNOLOGY: METHODS AND PROTOCOLS, 749:317-358, 2011
abstract,
full text
Sun, S., Wong, J.T.Y., Zhang, T.Y.
Molecular dynamics simulations of phase transition of lamellar lipid membrane in water under an electric field
SOFT MATTER, 7:147-152, 2011
abstract,
full text
Lyubartsev, A.P., Rabinovich, A.L.
Recent development in computer simulations of lipid bilayers
SOFT MATTER, 7:25-39, 2011
abstract,
full text
Shinoda, W., DeVane, R., Klein, M.L.
Coarse-grained force field for ionic surfactants
SOFT MATTER, 7:6178-6186, 2011
abstract,
full text
Gill, J.P., Shaw, K.M., Rountree, B.L., Kehl, C.E., Chiel, H.J.
Simulating Kinetic Processes in Time and Space on a Lattice
MATHEMATICAL MODELLING OF NATURAL PHENOMENA, 6:159-197, 2011
abstract,
full text
Suyetin, M.V., Vakhrushev, A.V.
Temperature-sensitive nanocapsule for drug delivery
MICRO & NANO LETTERS, 6:39-42, JAN 2011
abstract,
full text
Friddle, R.W., Battle, K., Trubetskoy, V., Tao, J.H., Salter, E.A., Moradian-Oldak, J., De Yoreo, J.J., Wierzbicki, A.
Single-Molecule Determination of the Face-Specific Adsorption of Amelogenin's C-Terminus on Hydroxyapatite
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50:7541-7545, 2011
full text
Hsin, J., Strumpfer, J., Lee, E.H., Schulten, K.
Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory
ANNUAL REVIEW OF BIOPHYSICS, VOL 40, 40:187-203, 2011
abstract,
full text,
TCBG publications
Chan, H., Kral, P.
Self-standing nanoparticle membranes and capsules
NANOSCALE, 3:1881-1886, 2011
abstract,
full text
Figueira, A.C.M., Saidemberg, D.M., Souza, P.C.T., Martinez, L., Scanlan, T.S., Baxter, J.D., Skaf, M.S., Palma, M.S., Webb, P., Polikarpov, I.
Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange
MOLECULAR ENDOCRINOLOGY, 25:15-31, JAN 2011
abstract,
full text
Bairagya, H.R., Mukhopadhyay, B.P., Bera, A.K.
Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II
JOURNAL OF MOLECULAR RECOGNITION, 24:35-44, JAN-FEB 2011
abstract,
full text
Pizzirusso, A., Savini, M., Muccioli, L., Zannoni, C.
An atomistic simulation of the liquid-crystalline phases of sexithiophene
JOURNAL OF MATERIALS CHEMISTRY, 21:125-133, 2011
abstract,
full text
Kaila, V.R.I., Sharma, V., Wikstrom, M.
The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:80-84, JAN 2011
abstract,
full text
Chakrapani, S., Cordero-Morales, J.F., Jogini, V., Pan, A.C., Cortes, D.M., Roux, B., Perozo, E.
On the structural basis of modal gating behavior in K(+) channels
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 18:67-+, JAN 2011
abstract,
full text
Yamamoto, T., Ohnishi, S.
Molecular dynamics study on helium nanobubbles in water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:16142-16145, 2011
abstract,
full text
Gubbins, K.E., Liu, Y.C., Moore, J.D., Palmer, J.C.
The role of molecular modeling in confined systems: impact and prospects
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:58-85, 2011
abstract,
full text
Zhang, M.H., Lu, S.Q., Li, G.W., Mao, Z.L., Yu, X., Sun, W.N., Tang, Z.C., Long, M.A., Su, W.A.
Identification of a Residue in Helix 2 of Rice Plasma Membrane Intrinsic Proteins That Influences Water Permeability
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:41982-41992, DEC 31 2010
abstract,
full text
Luan, B.Q., Afzali, A., Harrer, S., Peng, H.B., Waggoner, P., Polonsky, S., Stolovitzky, G., Martyna, G.
Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer
JOURNAL OF PHYSICAL CHEMISTRY B, 114:17172-17176, DEC 30 2010
abstract,
full text
Neumann, A., Baginski, M., Czub, J.
How Do Sterols Determine the Antifungal Activity of Amphotericin B? Free Energy of Binding between the Drug and Its Membrane Targets
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:18266-18272, DEC 29 2010
abstract,
full text
Jia, X.B., Zhang, J., Sun, H.W., Chen, L., Shen, R.X., Lai, C.M.
Molecular Dynamics Simulation Study on the Interaction Mode of Auxin Perception
ACTA CHIMICA SINICA, 68:2500-2508, DEC 28 2010
abstract,
full text
Buch, I., Fishelovitch, D., London, N., Raveh, B., Wolfson, H.J., Nussinov, R.
Allosteric Regulation of Glycogen Synthase Kinase 3 beta: A Theoretical Study
BIOCHEMISTRY, 49:10890-10901, DEC 28 2010
abstract,
full text
Jones, M.K., Zhang, L., Catte, A., Li, L., Oda, M.N., Ren, G., Segrest, J.P.
Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH
JOURNAL OF BIOLOGICAL CHEMISTRY, 285: DOI 10.1074/jbc.M110.187799, DEC 24 2010
abstract,
full text
Kaminski, S., Mroginski, M.A.
Molecular Dynamics of Phycocyanobilin Binding Bacteriophytochromes: A Detailed Study of Structural and Dynamic Properties
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16677-16686, DEC 23 2010
abstract,
full text
Patapati, K.K., Glykos, N.M.
Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study
PLOS ONE, 5: Art. No. e15290, DEC 20 2010
abstract,
full text
Kim, T., Cooper, J.A., Sept, D.
The Interaction of Capping Protein with the Barbed End of the Actin Filament
JOURNAL OF MOLECULAR BIOLOGY, 404:794-802, DEC 17 2010
abstract,
full text
Jang, H., Arce, F.T., Ramachandran, S., Capone, R., Lal, R., Nussinov, R.
beta-Barrel Topology of Alzheimer's beta-Amyloid Ion Channels
JOURNAL OF MOLECULAR BIOLOGY, 404:917-934, DEC 17 2010
abstract,
full text
Du, H.B., Wickramasinghe, R., Qian, X.H.
Effects of Salt on the Lower Critical Solution Temperature of Poly (N-Isopropylacrylamide)
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16594-16604, DEC 16 2010
abstract,
full text
Turgut, D., Atilgan, A.R., Atilgan, C.
Assortative Mixing in Close-Packed Spatial Networks
PLOS ONE, 5: Art. No. e15551, DEC 16 2010
abstract,
full text
Watanabe, A., Choe, S., Chaptal, V., Rosenberg, J.M., Wright, E.M., Grabe, M., Abramson, J.
The mechanism of sodium and substrate release from the binding pocket of vSGLT
NATURE, 468:988-U162, DEC 16 2010
abstract,
full text
DeVane, R., Jusufi, A., Shinoda, W., Chiu, C.C., Nielsen, S.O., Moore, P.B., Klein, M.L.
Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16364-16372, DEC 16 2010
abstract,
full text
Chen, K., Eargle, J., Sarkar, K., Gruebele, M., Luthey-Schulten, Z.
Functional Role of Ribosomal Signatures
BIOPHYSICAL JOURNAL, 99:3930-3940, DEC 15 2010
abstract,
full text
Kaila, V.R.I., Johansson, M.P., Sundholm, D., Wikstrom, M.
Interheme electron tunneling in cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:21470-21475, DEC 14 2010
abstract,
full text
Mirza, A., Mustafa, M., Talevich, E., Kannan, N.
Co-Conserved Features Associated with cis Regulation of ErbB Tyrosine Kinases
PLOS ONE, 5: Art. No. e14310, DEC 13 2010
abstract,
full text
Carnevale, V., Fiorin, G., Levine, B.G., DeGrado, W.F., Klein, M.L.
Multiple Proton Confinement in the M2 Channel from the Influenza A Virus
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20856-20863, DEC 9 2010
abstract,
full text
Nonella, M., Seeger, S.
Monitoring peptide-surface interaction by means of molecular dynamics simulation
CHEMICAL PHYSICS, 378:73-81, DEC 9 2010
abstract,
full text
Davis, W.B., Bjorklund, C.C., Cho, P.S.
Hole Transport Dynamics in Mixed Sequence DNA Can Vary with Salt Concentration: An Experimental and Theoretical Analysis
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20821-20833, DEC 9 2010
abstract,
full text
Lu, S.Q., Zhang, Y., Long, M.A.
Visualization of Allostery in P-Selectin Lectin Domain Using MD Simulations
PLOS ONE, 5: Art. No. e15417, DEC 8 2010
abstract,
full text
Xiao, F., Weng, J.W., Fan, K.N., Wang, W.N.
Mechanism of Ser88 Phosphorylation-Induced Dimer Dissociation in Dynein Light Chain LC8
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15663-15672, DEC 2 2010
abstract,
full text
Gao, M., She, Z.S., Zhou, R.H.
Key Residues that Play a Critical Role in Urea-Induced Lysozyme Unfolding
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15687-15693, DEC 2 2010
abstract,
full text
Sawada, T., Fedorov, D.G., Kitaura, K.
Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15700-15705, DEC 2 2010
abstract,
full text
Kaila, V.R.I., Verkhovsky, M.I., Wikstrom, M.
Proton-Coupled Electron Transfer in Cytochrome Oxidase
CHEMICAL REVIEWS, 110:7062-7081, DEC 2010
full text
Menz, W.J., Penna, M.J., Biggs, M.J.
TNAMD: Implementation of TIGER2 in NAMD
COMPUTER PHYSICS COMMUNICATIONS, 181:2082-2085, DEC 2010
abstract,
full text
Shaikh, S.A., Wen, P.C., Enkavi, G., Huang, Z.J., Tajkhorshid, E.
Capturing Functional Motions of Membrane Channels and Transporters with Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:2481-2500, DEC 2010
abstract,
full text
Lee, O.S., Schatz, G.C.
Conformation of DNA Between Gold Surfaces
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:2568-2573, DEC 2010
abstract,
full text
Janosi, L., Gorfe, A.A.
Segregation of Negatively Charged Phospholipids by the Polycationic and Farnesylated Membrane Anchor of Kras
BIOPHYSICAL JOURNAL, 99:3666-3674, DEC 1 2010
abstract,
full text
Wieden, H.J., Mercier, E., Gray, J., Steed, B., Yawney, D.
A Combined Molecular Dynamics and Rapid Kinetics Approach to Identify Conserved Three-Dimensional Communication Networks in Elongation Factor Tu
BIOPHYSICAL JOURNAL, 99:3735-3743, DEC 1 2010
abstract,
full text
Shafrir, Y., Durell, S.R., Anishkin, A., Guy, H.R.
Beta-barrel models of soluble amyloid beta oligomers and annular protofibrils
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:3458-3472, DEC 2010
abstract,
full text
Dominguez, M., Rezende, M.C.
The Cationic Halochromism of Phenolate Betaines: Molecular Dynamics and Quantum Mechanics Studies
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 7:995-1003, DEC 2010
abstract,
full text
Illingworth, C.J.R., Furini, S., Domene, C.
Computational Studies on Polarization Effects and Selectivity in K(+) Channels
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3780-3792, DEC 2010
abstract,
full text
Banas, P., Hollas, D., Zgarbova, M., Jurecka, P., Orozco, M., Cheatham, T.E., Sponer, J., Otyepka, M.
Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3836-3849, DEC 2010
abstract,
full text
Morcos, F., Chatterjee, S., McClendon, C.L., Brenner, P.R., Lopez-Rendon, R., Zintsmaster, J., Ercsey-Ravasz, M., Sweet, C.R., Jacobson, M.P., Peng, J.W., Izaguirre, J.A.
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1001015, DEC 2010
abstract,
full text
Vogler, C., Huber, C., Waldmann, T., Ettig, R., Braun, L., Izzo, A., Daujat, S., Chassignet, I., Lopez-Contreras, A.J., Fernandez-Capetillo, O., Dundr, M., Rippe, K., Langst, G., Schneider, R.
Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding
PLOS GENETICS, 6: Art. No. e1001234, DEC 2010
abstract,
full text
Jimenez, V.A.
Quantum-Chemical Study on the Bioactive Conformation of Epothilones
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:2176-2190, DEC 2010
abstract,
full text
Matsushita, S., Adachi, T., Inoue, Y., Hojo, M., Sokabe, M.
Evaluation of extensional and torsional stiffness of single actin filaments by molecular dynamics analysis
JOURNAL OF BIOMECHANICS, 43:3162-3167, DEC 1 2010
abstract,
full text
Oliveira, A.F., Gemming, S., Seifert, G.
Molecular dynamics simulations of BMP-2 adsorption on a hydrophobic surface
MATERIALWISSENSCHAFT UND WERKSTOFFTECHNIK, 41:1048-1053, DEC 2010
abstract,
full text
Knapp, B., Lederer, N., Omasits, U., Schreiner, W.
vmdICE: A Plug-In for Rapid Evaluation of Molecular Dynamics Simulations using VMD
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:2868-2873, DEC 2010
abstract,
full text
Papadopoulos, G., Grigoroudis, A.I., Kyriakidis, D.A.
Dimerization of the AtoC response regulator and modelling of its binding to DNA
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:565-572, DEC 2010
abstract,
full text
Gautieri, A., Vesentini, S., Redaelli, A.
How to predict diffusion of medium-sized molecules in polymer matrices. From atomistic to coarse grain simulations
JOURNAL OF MOLECULAR MODELING, 16:1845-1851, DEC 2010
abstract,
full text
Hu, G.D., Chen, L.Y.
In silico experiments of single-chain antibody fragment against drugs of abuse
BIOPHYSICAL CHEMISTRY, 153:97-103, DEC 2010
abstract,
full text
Tipmanee, V., Oberhofer, H., Park, M., Kim, K.S., Blumberger, J.
Prediction of Reorganization Free Energies for Biological Electron Transfer: A Comparative Study of Ru-Modified Cytochromes and a 4-Helix Bundle Protein
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:17032-17040, DEC 1 2010
abstract,
full text
Salsbury, F.R.
Molecular dynamics simulations of protein dynamics and their relevance to drug discovery
CURRENT OPINION IN PHARMACOLOGY, 10:738-744, DEC 2010
abstract,
full text
Tuukkanen, A., Huang, B., Henschel, A., Stewart, F., Schroeder, M.
Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint-based docking
PROTEOMICS, 10:4186-4195, DEC 2010
abstract,
full text
Shi, W., Sorescu, D.C.
Molecular Simulations of CO(2) and H(2) Sorption into Ionic Liquid 1-n-Hexyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)amide ([hmim][Tf(2)N]) Confined in Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15029-15041, NOV 25 2010
abstract,
full text
Furlan, S., Hureau, C., Faller, P., La Penna, G.
Modeling the Cu(+) Binding in the 1-16 Region of the Amyloid-beta Peptide Involved in Alzheimer's Disease
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15119-15133, NOV 25 2010
abstract,
full text
Wang, W., Castelan-Vega, J.A., Jimenez-Alberto, A., Vassell, R., Ye, Z.P., Weiss, C.D.
A mutation in the receptor binding site enhances infectivity of 2009 H1N1 influenza hemagglutinin pseudotypes without changing antigenicity
VIROLOGY, 407:374-380, NOV 25 2010
abstract,
full text
Megow, J., Kulesza, A., Qu, Z.W., Ronneberg, T., Bonacic-Koutecky, V., May, V.
A harmonic approximation of intramolecular vibrations in a mixed quantum-classical methodology: Linear absorbance of a dissolved Pheophorbid-a molecule as an example
CHEMICAL PHYSICS, 377:10-14, NOV 25 2010
abstract,
full text
Li, J.H., Du, L.K., Wang, L.S.
Glycosidic-Bond Hydrolysis Mechanism Catalyzed by Cellulase Cel7A from Trichoderma reesei: A Comprehensive Theoretical Study by Performing MD, QM, and QM/MM Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15261-15268, NOV 25 2010
abstract,
full text
McIntyre, N.R., Lowe, E.W., Belof, J.L., Ivkovic, M., Shafer, J., Space, B., Merkler, D.J.
Evidence for Substrate Preorganization in the Peptidylglycine alpha-Amidating Monooxygenase Reaction Describing the Contribution of Ground State Structure to Hydrogen Tunneling
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:16393-16402, NOV 24 2010
abstract,
full text
Cheng, M.H.Y., Coalson, R.D., Tang, P.
Molecular Dynamics and Brownian Dynamics Investigation of Ion Permeation and Anesthetic Halothane Effects on a Proton-Gated Ion Channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:16442-16449, NOV 24 2010
abstract,
full text
Gnanasambandan, K., Magis, A., Sayeski, P.P.
The Constitutive Activation of Jak2-V617F Is Mediated by a pi Stacking Mechanism Involving Phenylalanines 595 and 617
BIOCHEMISTRY, 49:9972-9984, NOV 23 2010
abstract,
full text
Ma, B.Y., Nussinov, R.
Polymorphic C-terminal beta-Sheet Interactions Determine the Formation of Fibril or Amyloid beta-derived Diffusible Ligand-like Globulomer for the Alzheimer A beta 42 Dodecamer
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:37102-37110, NOV 19 2010
abstract,
full text
Kim, Y., Zhou, M., Moy, S., Morales, J., Cunningham, M.A., Joachimiak, A.
High-Resolution Structure of the Nitrile Reductase QueF Combined with Molecular Simulations Provide Insight into Enzyme Mechanism
JOURNAL OF MOLECULAR BIOLOGY, 404:127-137, NOV 19 2010
abstract,
full text
da Silva, R., Rego, L.G.C., Freire, J.A., Rodriguez, J., Laria, D., Batista, V.S.
Study of Redox Species and Oxygen Vacancy Defects at TiO(2)-Electrolyte Interfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 114:19433-19442, NOV 18 2010
abstract,
full text
Law, R.H.P., Lukoyanova, N., Voskoboinik, I., Caradoc-Davies, T.T., Baran, K., Dunstone, M.A., D'Angelo, M.E., Orlova, E.V., Coulibaly, F., Verschoor, S., Browne, K.A., Ciccone, A., Kuiper, M.J., Bird, P.I., Trapani, J.A., Saibil, H.R., Whisstock, J.C.
The structural basis for membrane binding and pore formation by lymphocyte perforin
NATURE, 468:447-U277, NOV 18 2010
abstract,
full text
Jin, S.Y., Snoeberger, R.C., Issac, A., Stockwell, D., Batista, V.S., Lian, T.Q.
Single-Molecule Interfacial Electron Transfer in Donor-Bridge-Nanoparticle Acceptor Complexes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14309-14319, NOV 18 2010
abstract,
full text
Luan, B.Q., Aksimentiev, A.
Control and reversal of the electrophoretic force on DNA in a charged nanopore
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 454123, NOV 17 2010
abstract,
full text
Trylska, J.
Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 453101, NOV 17 2010
abstract,
full text
Zwolak, M., Wilson, J., Di Ventra, M.
Dehydration and ionic conductance quantization in nanopores
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 454126, NOV 17 2010
abstract,
full text
Jolley, C.C., Douglas, T.
Ion Accumulation in a Protein Nanocage: Finding Noisy Temporal Sequences Using a Genetic Algorithm
BIOPHYSICAL JOURNAL, 99:3385-3393, NOV 17 2010
abstract,
full text
Gangupomu, V.K., Abrams, C.F.
All-Atom Models of the Membrane-Spanning Domain of HIV-1 gp41 from Metadynamics
BIOPHYSICAL JOURNAL, 99:3438-3444, NOV 17 2010
abstract,
full text
Weis, F., Bron, P., Giudice, E., Rolland, J.P., Thomas, D., Felden, B., Gillet, R.
tmRNA-SmpB: a journey to the centre of the bacterial ribosome
EMBO JOURNAL, 29:3810-3818, NOV 17 2010
abstract,
full text
Fu, J., Hashem, Y., Wower, I., Lei, J.L., Liao, H.Y., Zwieb, C., Wower, J., Frank, J.
Visualizing the transfer-messenger RNA as the ribosome resumes translation
EMBO JOURNAL, 29:3819-3825, NOV 17 2010
abstract,
full text
Anishkin, A., Akitake, B., Kamaraju, K., Chiang, C.S., Sukharev, S.
Hydration properties of mechanosensitive channel pores define the energetics of gating
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 454120, NOV 17 2010
abstract,
full text
Demerdash, O.N.A., Buyan, A., Mitchell, J.C.
ReplicOpter: A replicate optimizer for flexible docking
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:3156-3165, NOV 15 2010
abstract,
full text
Llop-Tous, I., Madurga, S., Giralt, E., Marzabal, P., Torrent, M., Ludevid, M.D.
Relevant Elements of a Maize gamma-Zein Domain Involved in Protein Body Biogenesis
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:35633-35644, NOV 12 2010
abstract,
full text
Halder, S., Bhattacharyya, D.
Structural Stability of Tandemly Occurring Noncanonical Basepairs within Double Helical Fragments: Molecular Dynamics Studies of Functional RNA
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14028-14040, NOV 11 2010
abstract,
full text
Meyer, T., D'Abramo, M., Hospital, A., Rueda, M., Ferrer-Costa, C., Perez, A., Carrillo, O., Camps, J., Fenollosa, C., Repchevsky, D., Gelpi, J.L., Orozco, M.
MoDEL (Molecular Dynamics Extended Library): A Database of Atomistic Molecular Dynamics Trajectories
STRUCTURE, 18:1399-1409, NOV 10 2010
abstract,
full text
Kim, H., Hsin, J., Liu, Y.X., Selvin, P.R., Schulten, K.
Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain
STRUCTURE, 18:1443-1449, NOV 10 2010
abstract,
full text,
TCBG publications
Kalantari-Nejad, R., Bahrami, M., Rafii-Tabar, H., Rungger, I., Sanvito, S.
Computational modeling of a carbon nanotube-based DNA nanosensor
NANOTECHNOLOGY, 21: Art. No. 445501, NOV 5 2010
abstract,
full text
Wereszczynski, J., McCammon, J.A.
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3285-3292, NOV 2010
abstract,
full text
Lupieri, P., Ippoliti, E., Altoe, P., Garavelli, M., Mwalaba, M., Carloni, P.
Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car-Parrinello and TDDFT/CASPT2 Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3403-3409, NOV 2010
abstract,
full text
Musiani, F., Bertosa, B., Magistrato, A., Zambelli, B., Turano, P., Losasso, V., Micheletti, C., Ciurli, S., Carloni, P.
Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni(2+)
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3503-3515, NOV 2010
abstract,
full text
Urreizti, R., Moya-Garcia, A.A., Pino-Angeles, A., Cozar, M., Langkilde, A., Fanhoe, U., Esteves, C., Arribas, J., Vilaseca, M.A., Perez-Duenas, B., Pineda, M., Gonzalez, V., Artuch, R., Baldellou, A., Vilarinho, L., Fowler, B., Ribes, A., Sanchez-Jimenez, F., Grinberg, D., Balcells, S.
Molecular characterization of five patients with homocystinuria due to severe methylenetetrahydrofolate reductase deficiency
CLINICAL GENETICS, 78:441-448, NOV 2010
abstract,
full text
Sadiq, S.K., De Fabritiis, G.
Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2873-2885, NOV 1 2010
abstract,
full text
Zhmurov, A., Dima, R.I., Kholodov, Y., Barsegov, V.
SOP-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2984-2999, NOV 1 2010
abstract,
full text
Lugli, F., Toschi, F., Biscarini, F., Zerbetto, F.
Electric Field Effects on Short Fibrils of A beta Amyloid Peptides
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3516-3526, NOV 2010
abstract,
full text
Bauer, A.L., Hlavacek, W.S., Unkefer, P.J., Mu, F.P.
Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1001007, NOV 2010
abstract,
full text
Fatmi, M.Q., Chang, C.E.A.
The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000994, NOV 2010
abstract,
full text
Wang, Q., Mach, R.H., Luedtke, R.R., Reichert, D.E.
Subtype Selectivity of Dopamine Receptor Ligands: Insights from Structure and Ligand-Based Methods
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1970-1985, NOV 2010
abstract,
full text
Karachevtsev, V.A., Plokhotnichenko, A.M., Karachevtsev, M.V., Leontiev, V.S.
Decrease of carbon nanotube UV light absorption induced by pi-pi-stacking interaction with nucleotide bases
CARBON, 48:3682-3691, NOV 2010
abstract,
full text
Rosales-Hernandez, M.C., Mendieta-Wejebe, J.E., Trujillo-Ferrara, J.G., Correa-Basurto, J.
Homology modeling and molecular dynamics of CYP1A1 and CYP2B1 to explore the metabolism of aryl derivatives by docking and experimental assays
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 45:4845-4855, NOV 2010
abstract,
full text
Shu, D., Zhang, H., Petrenko, R., Meller, J., Guo, P.X.
Dual-Channel Single-Molecule Fluorescence Resonance Energy Transfer to Establish Distance Parameters for RNA Nanoparticles
ACS NANO, 4:6843-6853, NOV 2010
abstract,
full text
Kuhn, M.L., Figueroa, C.M., Aleanzi, M., Olsen, K.W., Iglesias, A.A., Ballicora, M.A.
Bi-National and Interdisciplinary Course in Enzyme Engineering
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 38:370-379, NOV-DEC 2010
abstract,
full text
Hsu, C.K., Park, S.
Computational and mutagenesis studies of the streptavidin native dimer interface
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:295-308, NOV 2010
abstract,
full text
Imai, Y., Liu, X.L., Yamagishi, J., Mori, K., Neya, S., Hoshino, T.
Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:461-469, NOV 2010
abstract,
full text
Bhatele, A., Wesolowski, L., Bohm, E., Solomonik, E., Kale, L.V.
Understanding Application Performance via Micro-benchmarks on Three Large Supercomputers: Intrepid, Ranger and Jaguar
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 24:411-427, NOV 2010
abstract,
full text
Duddela, S., Sekhar, P.N., Padmavati, G.V., Banerjee, A.K., Murty, U.S.N.
Probing the structure of human glucose transporter 2 and analysis of protein ligand interactions
MEDICINAL CHEMISTRY RESEARCH, 19:836-853, NOV 2010
abstract,
full text
Fu, Y., Ding, Y.R., Chen, Z.G., Sun, J., Fang, W., Xu, W.B.
Study on the Relationship Between Cyclodextrin Glycosyltransferase Thermostability and Salt Bridge Formation by Molecular Dynamics Simulation
PROTEIN AND PEPTIDE LETTERS, 17:1403-1411, NOV 2010
abstract,
full text
Arcisio-Miranda, M., Muroi, Y., Chowdhury, S., Chanda, B.
Molecular mechanism of allosteric modification of voltage-dependent sodium channels by local anesthetics
JOURNAL OF GENERAL PHYSIOLOGY, 136:541-554, NOV 2010
abstract,
full text
Shukla, D., Trout, B.L.
Interaction of Arginine with Proteins and the Mechanism by Which It Inhibits Aggregation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13426-13438, OCT 28 2010
abstract,
full text
Xia, Z., Gardner, D.P., Gutell, R.R., Ren, P.Y.
Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13497-13506, OCT 28 2010
abstract,
full text
Rogaski, B., Lim, J.B., Klauda, J.B.
Sterol Binding and Membrane Lipid Attachment to the Osh4 Protein of Yeast
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13562-13573, OCT 28 2010
abstract,
full text
Elola, M.D., Rodriguez, J., Laria, D.
Structure and dynamics of liquid methanol confined within functionalized silica nanopores
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 154707, OCT 21 2010
abstract,
full text
Issa, Z.K., Manke, C.W., Jena, B.P., Potoff, J.J.
Ca(2+) Bridging of Apposed Phospholipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13249-13254, OCT 21 2010
abstract,
full text
Dalhaimer, P., Pollard, T.D.
Molecular Dynamics Simulations of Arp2/3 Complex Activation
BIOPHYSICAL JOURNAL, 99:2568-2576, OCT 20 2010
abstract,
full text
Feig, M., Burton, Z.F.
RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation
BIOPHYSICAL JOURNAL, 99:2577-2586, OCT 20 2010
abstract,
full text
Teif, V.B., Ettig, R., Rippe, K.
A Lattice Model for Transcription Factor Access to Nucleosomal DNA
BIOPHYSICAL JOURNAL, 99:2597-2607, OCT 20 2010
abstract,
full text
Kokhan, O., Wraight, C.A., Tajkhorshid, E.
The Binding Interface of Cytochrome c and Cytochrome c(1) in the bc(1) Complex: Rationalizing the Role of Key Residues
BIOPHYSICAL JOURNAL, 99:2647-2656, OCT 20 2010
abstract,
full text
Elli, S., Eusebio, L., Gronchi, P., Ganazzoli, F., Goisis, M.
Modeling the Adsorption Behavior of Linear End-Functionalized Poly(ethylene glycol) on an Ionic Substrate by a Coarse-Grained Monte Carlo Approach
LANGMUIR, 26:15814-15823, OCT 19 2010
abstract,
full text
Kubiak-Ossowska, K., Mulheran, P.A.
Mechanism of Hen Egg White Lysozyme Adsorption on a Charged Solid Surface
LANGMUIR, 26:15954-15965, OCT 19 2010
abstract,
full text
Iturrioz, X., Gerbier, R., Leroux, V., Alvear-Perez, R., Maigret, B., Llorens-Cortes, C.
By Interacting with the C-terminal Phe of Apelin, Phe(255) and Trp(259) in Helix VI of the Apelin Receptor Are Critical for Internalization
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:32627-32637, OCT 15 2010
abstract,
full text
Calandrini, V., Abergel, D., Kneller, G.R.
Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 145101, OCT 14 2010
abstract,
full text
Cerutti, D.S., Freddolino, P.L., Duke, R.E., Case, D.A.
Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12811-12824, OCT 14 2010
abstract,
full text
Bonomi, M., Barducci, A., Gervasio, F.L., Parrinello, M.
Multiple Routes and Milestones in the Folding of HIV-1 Protease Monomer
PLOS ONE, 5: Art. No. e13208, OCT 13 2010
abstract,
full text
Saharay, M., Guo, H., Smith, J.C.
Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS
PLOS ONE, 5: Art. No. e12947, OCT 12 2010
abstract,
full text
Montserret, R., Saint, N., Vanbelle, C., Salvay, A.G., Simorre, J.P., Ebel, C., Sapay, N., Renisio, J.G., Bockmann, A., Steinmann, E., Pietschmann, T., Dubuisson, J., Chipot, C., Penin, F.
NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:31446-31461, OCT 8 2010
abstract,
full text
Guo, Q.L., Weng, J.W., Xu, X.G., Wang, M.H., Wang, X.Y., Ye, X.Y., Wang, W.N., Wang, M.G.
A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis
BMC STRUCTURAL BIOLOGY, 10: Art. No. 33, OCT 8 2010
abstract,
full text
Dang, S.Y., Sun, L.F., Huang, Y.J., Lu, F.R., Liu, Y.F., Gong, H.P., Wang, J.W., Yan, N.E.
Structure of a fucose transporter in an outward-open conformation
NATURE, 467:734-U130, OCT 7 2010
abstract,
full text
Karachevtsev, V.A., Zarudnev, E.S., Stepanian, S.G., Glamazda, A.Y., Karachevtsev, M.V., Adamowicz, L.
Raman Spectroscopy and Theoretical Characterization of Nanohybrids of Porphyrins with Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY C, 114:16215-16222, OCT 7 2010
abstract,
full text
Faraudo, J., Calero, C., Aguilella-Arzo, M.
Ionic Partition and Transport in Multi-Ionic Channels: A Molecular Dynamics Simulation Study of the OmpF Bacterial Porin
BIOPHYSICAL JOURNAL, 99:2107-2115, OCT 6 2010
abstract,
full text
Jardon-Valadez, E., Bondar, A.N., Tobias, D.J.
Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin
BIOPHYSICAL JOURNAL, 99:2200-2207, OCT 6 2010
abstract,
full text
Ho, M.H., De Vivo, M., Dal Peraro, M., Klein, M.L.
Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13702-13712, OCT 6 2010
abstract,
full text
Messner, S., Altmeyer, M., Zhao, H.T., Pozivil, A., Roschitzki, B., Gehrig, P., Rutishauser, D., Huang, D.Z., Caflisch, A., Hottiger, M.O.
PARP1 ADP-ribosylates lysine residues of the core histone tails
NUCLEIC ACIDS RESEARCH, 38:6350-6362, OCT 2010
abstract,
full text
Surdutovich, E., Yakubovich, A.V., Solov'yov, A.V.
Multiscale approach to radiation damage induced by ion beams: complex DNA damage and effects of thermal spikes
EUROPEAN PHYSICAL JOURNAL D, 60:101-108, OCT 2010
abstract,
full text
Ozer, G., Valeev, E.F., Quirk, S., Hernandez, R.
Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3026-3038, OCT 2010
abstract,
full text
Janosi, L., Gorfe, A.A.
Simulating POPC and POPC/POPG Bilayers: Conserved Packing and Altered Surface Reactivity
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3267-3273, OCT 2010
abstract,
full text
Revilla-Lopez, G., Jimenez, A.I., Cativiela, C., Nussinov, R., Aleman, C., Zanuy, D.
Conformational Profile of a Proline-Arginine Hybrid
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1781-1789, OCT 2010
abstract,
full text
Trabuco, L.G., Schreiner, E., Eargle, J., Cornish, P., Ha, T., Luthey-Schulten, Z., Schulten, K.
The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle
JOURNAL OF MOLECULAR BIOLOGY, 402:741-760, OCT 1 2010
abstract,
full text,
TCBG publications
Yang, Y.L., Li, X.Y., Jiang, J.L., Du, H.L., Zhao, L.N., Zhao, Y.L.
Control Performance and Biomembrane Disturbance of Carbon Nanotube Artificial Water Channels by Nitrogen-Doping
ACS NANO, 4:5755-5762, OCT 2010
abstract,
full text
de Araujo, A.S., Martinez, L., Nicoluci, R.D., Skaf, M.S., Polikarpov, I.
Structural modeling of high-affinity thyroid receptor-ligand complexes
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 39:1523-1536, OCT 2010
abstract,
full text
Umeda, H., Inadomi, Y., Watanabe, T., Yagi, T., Ishimoto, T., Ikegami, T., Tadano, H., Sakurai, T., Nagashima, U.
Parallel Fock Matrix Construction with Distributed Shared Memory Model for the FMO-MO Method
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:2381-2388, OCT 2010
abstract,
full text
Xu, J.C., Smith, J.C.
Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants
PROTEIN ENGINEERING DESIGN & SELECTION, 23:759-768, OCT 2010
abstract,
full text
Chen, L.Y.
Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations
BIOPHYSICAL CHEMISTRY, 151:178-180, OCT 2010
abstract,
full text
Corry, B., Hurst, A.C., Pal, P., Nomura, T., Rigby, P., Martinac, B.
An improved open-channel structure of MscL determined from FRET confocal microscopy and simulation
JOURNAL OF GENERAL PHYSIOLOGY, 136:483-494, OCT 2010
abstract,
full text
Liu, J.A., Fan, J.F., Tang, M., Cen, M., Yan, J.F., Liu, Z., Zhou, W.G.
Water Diffusion Behaviors and Transportation Properties in Transmembrane Cyclic Hexa-, Octa- and Decapeptide Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12183-12192, SEP 30 2010
abstract,
full text
Chebil, L., Chipot, C., Archambault, F., Humeau, C., Engasser, J.M., Ghoul, M., Dehez, F.
Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12308-12313, SEP 30 2010
abstract,
full text
Olbrich, C., Kleinekathofer, U.
Time-Dependent Atomistic View on the Electronic Relaxation in Light-Harvesting System II
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12427-12437, SEP 30 2010
abstract,
full text
Foley, M.C., Padow, V.A., Schlick, T.
DNA Pol lambda's Extraordinary Ability To Stabilize Misaligned DNA
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13403-13416, SEP 29 2010
abstract,
full text
Lee, T.S., York, D.M.
Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13505-13518, SEP 29 2010
abstract,
full text
Priet, S., Zlatev, I., Barvik, I., Geerts, K., Leyssen, P., Neyts, J., Dutartre, H., Canard, B., Vasseur, J.J., Morvan, F., Alvarez, K.
3 '-Deoxy Phosphoramidate Dinucleosides as Improved Inhibitors of Hepatitis C Virus Subgenomic Replicon and NS5B Polymerase Activity
JOURNAL OF MEDICINAL CHEMISTRY, 53:6608-6617, SEP 23 2010
abstract,
full text
Long, F., Su, C.C., Zimmermann, M.T., Boyken, S.E., Rajashankar, K.R., Jernigan, R.L., Yu, E.W.
Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport
NATURE, 467:484-U140, SEP 23 2010
abstract,
full text
Veluraja, K., Selvin, J.F.A., Venkateshwari, S., Priyadarzini, T.R.K.
3DSDSCAR-a three dimensional structural database for sialic acid-containing through molecular dynamics simulation
CARBOHYDRATE RESEARCH, 345:2030-2037, SEP 23 2010
abstract,
full text
Khelashvili, G., Mondal, S., Andersen, O.S., Weinstein, H.
Cholesterol Modulates the Membrane Effects and Spatial Organization of Membrane-Penetrating Ligands for G-Protein Coupled Receptors
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12046-12057, SEP 23 2010
abstract,
full text
Jiang, J., Abramavicius, D., Falvo, C., Bulheller, B.M., Hirst, J.D., Mukamel, S.
Simulation of Two-Dimensional Ultraviolet Spectroscopy of Amyloid Fibrils
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12150-12156, SEP 23 2010
abstract,
full text
Hilder, T.A., Gordon, D., Chung, S.H.
Synthetic Chloride-Selective Carbon Nanotubes Examined by Using Molecular and Stochastic Dynamics
BIOPHYSICAL JOURNAL, 99:1734-1742, SEP 22 2010
abstract,
full text
Lyman, E., Cui, H.S., Voth, G.A.
Water under the BAR
BIOPHYSICAL JOURNAL, 99:1783-1790, SEP 22 2010
abstract,
full text
Chen, Q.A., Cheng, M.H., Xu, Y., Tang, P.
Anesthetic Binding in a Pentameric Ligand-Gated Ion Channel: GLIC
BIOPHYSICAL JOURNAL, 99:1801-1809, SEP 22 2010
abstract,
full text
Faustino, I., Perez, A., Orozco, M.
Toward a Consensus View of Duplex RNA Flexibility
BIOPHYSICAL JOURNAL, 99:1876-1885, SEP 22 2010
abstract,
full text
Saito, H., Matubayasi, N., Nishikawa, K., Nagao, H.
Hydration property of globular proteins: An analysis of solvation free energy by energy representation method
CHEMICAL PHYSICS LETTERS, 497:218-222, SEP 20 2010
abstract,
full text
Lai, C.L., Landgraf, K.E., Voth, G.A., Falke, J.J.
Membrane Docking Geometry and Target Lipid Stoichiometry of Membrane-Bound PKC alpha C2 Domain: A Combined Molecular Dynamics and Experimental Study
JOURNAL OF MOLECULAR BIOLOGY, 402:301-310, SEP 17 2010
abstract,
full text
Garcia-Mata, C., Wang, J.W., Gajdanowicz, P., Gonzalez, W., Hills, A., Donald, N., Riedelsberger, J., Amtmann, A., Dreyer, I., Blatt, M.R.
A Minimal Cysteine Motif Required to Activate the SKOR K(+) Channel of Arabidopsis by the Reactive Oxygen Species H(2)O(2)
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:29286-29294, SEP 17 2010
abstract,
full text
Aliaga, C., Briones, L., Rezende, M.C., Tirapegui, C.
The thermochromism of the E(T)(30) betaine in a micro-heterogeneous medium: A spectral and dynamics simulation study
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 349:565-570, SEP 15 2010
abstract,
full text
Pemmaraju, C.D., Rungger, I., Chen, X., Rocha, A.R., Sanvito, S.
Ab initio study of electron transport in dry poly(G)-poly(C) A-DNA strands
PHYSICAL REVIEW B, 82: Art. No. 125426, SEP 14 2010
abstract,
full text
Semenyuk, A., Darian, E., Liu, J., Majumdar, A., Cuenoud, B., Miller, P.S., MacKerell, A.D., Seidman, M.M.
Targeting of an Interrupted Polypurine:Polypyrimidine Sequence in Mammalian Cells by a Triplex-Forming Oligonucleotide Containing a Novel Base Analogue
BIOCHEMISTRY, 49:7867-7878, SEP 14 2010
abstract,
full text
Nurminen, E.M., Pihlavisto, M., Lazar, L., Szakonyi, Z., Pentikainen, U., Fulop, F., Pentikainen, O.T.
Synthesis, in Vitro Activity, and Three-Dimensional Quantitative Structure-Activity Relationship of Novel Hydrazine Inhibitors of Human Vascular Adhesion Protein-1
JOURNAL OF MEDICINAL CHEMISTRY, 53:6301-6315, SEP 9 2010
abstract,
full text
Tsai, C.W., Liu, C.I., Chan, Y.C., Tsai, H.H.G., Ruaan, R.C.
Study of Conformation Effects on the Retention of Small Peptides in Reversed-Phase Chromatography by Thermodynamic Analysis and Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11620-11627, SEP 9 2010
abstract,
full text
Virtanen, J.J., Makowski, L., Sosnick, T.R., Freed, K.F.
Modeling the Hydration Layer around Proteins: HyPred
BIOPHYSICAL JOURNAL, 99:1611-1619, SEP 8 2010
abstract,
full text
Wang, Z.J., Deserno, M.
Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field
NEW JOURNAL OF PHYSICS, 12: Art. No. 095004, SEP 8 2010
abstract,
full text
Chen, Q., Moore, J.D., Liu, Y.C., Roussel, T.J., Wang, Q., Wu, T., Gubbins, K.E.
Transition from single-file to Fickian diffusion for binary mixtures in single-walled carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 094501, SEP 7 2010
abstract,
full text
Kim, S.K., Li, Y.Y., Park, C., Abrol, R., Goddard, W.A.
Prediction of the Three-Dimensional Structure for the Rat Urotensin II Receptor, and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat Receptors from Atomistic Simulations
CHEMMEDCHEM, 5:1594-1608, SEP 3 2010
abstract,
full text
Pisani, L., Catto, M., Giangreco, I., Leonetti, F., Nicolotti, O., Stefanachi, A., Cellamare, S., Carotti, A.
Design, Synthesis, and Biological Evaluation of Coumarin Derivatives Tethered to an Edrophonium-like Fragment as Highly Potent and Selective Dual Binding Site Acetylcholinesterase Inhibitors
CHEMMEDCHEM, 5:1616-1630, SEP 3 2010
abstract,
full text
Ziemys, A., Grattoni, A., Fine, D., Hussain, F., Ferrari, M.
Confinement Effects on Monosaccharide Transport in Nanochannels
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11117-11126, SEP 2 2010
abstract,
full text
Wang, Z.J., Deserno, M.
A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11207-11220, SEP 2 2010
abstract,
full text
Elenewski, J.E., Hackett, J.C.
Free Energy Landscape of the Retinol/Serum Retinol Binding Protein Complex: A Biological Host-Guest System
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11315-11322, SEP 2 2010
abstract,
full text
Hameroff, S.R., Craddock, T.J.A., Tuszynski, J.A.
"MEMORY BYTES" - MOLECULAR MATCH FOR CaMKII PHOSPHORYLATION ENCODING OF MICROTUBULE LATTICES
JOURNAL OF INTEGRATIVE NEUROSCIENCE, 9:253-267, SEP 2010
abstract,
full text
Maffeo, C., Aksimentiev, A.
Single molecule force measurements: Insights from molecular simulations Comment on "Biophysical characterization of DNA binding from single molecule force measurements" by Kathy R. Chaurasiya et al.
PHYSICS OF LIFE REVIEWS, 7:353-354, SEP 2010
full text
Stavrakoudis, A.
Conformational Flexibility in Designing Peptides for Immunology: The Molecular Dynamics Approach
CURRENT COMPUTER-AIDED DRUG DESIGN, 6:207-222, SEP 2010
abstract,
full text
Bucher, D., Gray-Weale, A., Kuyucak, S.
Ab Initio Study of Water Polarization in the Hydration Shell of Aqueous Hydroxide: Comparison between Polarizable and Nonpolarizable Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2888-2895, SEP 2010
abstract,
full text
Sit, P.H.L., Migliore, A., Ho, M.H., Klein, M.L.
Quantum Mechanical and Quantum Mechanical/Molecular Mechanical Studies of the Iron-Dioxygen Intermediates and Proton Transfer in Superoxide Reductase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2896-2909, SEP 2010
abstract,
full text
Le, L., Lee, E.H., Hardy, D.J., Truong, T.N., Schulten, K.
Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000939, SEP 2010
abstract,
full text,
TCBG publications
Zhuravlev, P.I., Wu, S., Potoyan, D.A., Rubinstein, M., Papoian, G.A.
Computing free energies of protein conformations from explicit solvent simulations
METHODS, 52:115-121, SEP 2010
abstract,
full text
Yancey, J.A., Vellore, N.A., Collier, G., Stuart, S.J., Latour, R.A.
Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms
BIOINTERPHASES, 5:85-95, SEP 2010
abstract,
full text
Stone, J.E., Hardy, D.J., Ufimtsev, I.S., Schulten, K.
GPU-accelerated molecular modeling coming of age
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:116-125, SEP 2010
abstract,
full text,
TCBG publications
Vistoli, G., Pedretti, A., Mazzolari, A., Testa, B.
Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 24:771-787, SEP 2010
abstract,
full text
Abroshan, H., Akbarzadeh, H., Parsafar, G.A.
Molecular dynamics simulation and MM-PBSA calculations of sickle cell hemoglobin in dimer form with Val, Trp, or Phe at the lateral contact
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 23:866-877, SEP 2010
abstract,
full text
Lee, H.W., Wylie, G., Bansal, S., Wang, X., Barb, A.W., Macnaughtan, M.A., Ertekin, A., Montelione, G.T., Prestegard, J.H.
Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping
PROTEIN SCIENCE, 19:1673-1685, SEP 2010
abstract,
full text
Barucha-Kraszewska, J., Kraszewski, S., Jurkiewicz, P., Ramseyer, C., Hof, M.
Numerical studies of the membrane fluorescent dyes dynamics in ground and excited states
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:1724-1734, SEP 2010
abstract,
full text
Anitescu, M., Park, S.
A linear assignment approach for the least-squares protein morphing problem
MATHEMATICAL PROGRAMMING, 125:195-203, SEP 2010
abstract,
full text
Vivcharuk, V., Kaznessis, Y.N.
Dimerization of Protegrin-1 in Different Environments
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 11:3177-3194, SEP 2010
abstract,
full text
Stabenfeldt, S.E., Gossett, J.J., Barker, T.H.
Building better fibrin knob mimics: an investigation of synthetic fibrin knob peptide structures in solution and their dynamic binding with fibrinogen/fibrin holes
BLOOD, 116:1352-1359, AUG 26 2010
abstract,
full text
Acharya, R., Carnevale, V., Fiorin, G., Levine, B.G., Polishchuk, A.L., Balannik, V., Samish, I., Lamb, R.A., Pinto, L.H., DeGrado, W.F., Klein, M.L.
Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:15075-15080, AUG 24 2010
abstract,
full text
Zahran, M., Daidone, I., Smith, J.C., Imhof, P.
Mechanism of DNA Recognition by the Restriction Enzyme EcoRV
JOURNAL OF MOLECULAR BIOLOGY, 401:415-432, AUG 20 2010
abstract,
full text
Cardone, A., Hassan, S.A., Albers, R.W., Sriram, R.D., Pant, H.C.
Structural and Dynamic Determinants of Ligand Binding and Regulation of Cyclin-Dependent Kinase 5 by Pathological Activator p25 and Inhibitory Peptide CIP
JOURNAL OF MOLECULAR BIOLOGY, 401:478-492, AUG 20 2010
abstract,
full text
Casanovas, J., Rodriguez-Ropero, F., Zanuy, D., Aleman, C.
Microscopic details of the sensing ability of 15-crown-5-ether functionalized poly(bithiophene)
POLYMER, 51:4267-4272, AUG 19 2010
abstract,
full text
Roos, W.H., Gibbons, M.M., Arkhipov, A., Uetrecht, C., Watts, N.R., Wingfield, P.T., Steven, A.C., Heck, A.J.R., Schulten, K., Klug, W.S., Wuite, G.J.L.
Squeezing Protein Shells: How Continuum Elastic Models, Molecular Dynamics Simulations, and Experiments Coalesce at the Nanoscale
BIOPHYSICAL JOURNAL, 99:1175-1181, AUG 18 2010
abstract,
full text,
TCBG publications
Zou, X.Q., Liu, Y.X., Chen, Z.Z., Cardenas-Jiron, G.I., Schulten, K.
Flow-Induced beta-Hairpin Folding of the Glycoprotein Ib alpha beta-Switch
BIOPHYSICAL JOURNAL, 99:1182-1191, AUG 18 2010
abstract,
full text,
TCBG publications
Kurkcuoglu, O., Bates, P.A.
Mechanism of Cohesin Loading onto Chromosomes: A Conformational Dynamics Study
BIOPHYSICAL JOURNAL, 99:1212-1220, AUG 18 2010
abstract,
full text
Piton, J., Petrella, S., Delarue, M., Andre-Leroux, G., Jarlier, V., Aubry, A., Mayer, C.
Structural Insights into the Quinolone Resistance Mechanism of Mycobacterium tuberculosis DNA Gyrase
PLOS ONE, 5: Art. No. e12245, AUG 18 2010
abstract,
full text
Illingworth, C.J.R., Loenarz, C., Schofield, C.J., Domene, C.
Chemical Basis for the Selectivity of the von Hippel Lindau Tumor Suppressor pVHL for Prolyl-Hydroxylated HIF-1 alpha
BIOCHEMISTRY, 49:6936-6944, AUG 17 2010
abstract,
full text
Raabe, G., Maginn, E.J.
A Force Field for 3,3,3-Fluoro-1-propenes, Including HFO-1234yf
JOURNAL OF PHYSICAL CHEMISTRY B, 114:10133-10142, AUG 12 2010
abstract,
full text
Roxbury, D., Manohar, S., Jagota, A.
Molecular Simulation of DNA beta-Sheet and beta-Barrel Structures on Graphite and Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY C, 114:13267-13276, AUG 12 2010
abstract,
full text
Turecek, F., Chung, T.W., Moss, C.L., Wyer, J.A., Ehlerding, A., Holm, A.I.S., Zettergren, H., Nielsen, S.B., Hvelplund, P., Chamot-Rooke, J., Bythell, B., Paizs, B.
The Histidine Effect. Electron Transfer and Capture Cause Different Dissociations and Rearrangements of Histidine Peptide Cation-Radicals
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:10728-10740, AUG 11 2010
abstract,
full text
Brannigan, G., LeBard, D.N., Henin, J., Eckenhoff, R.G., Klein, M.L.
Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:14122-14127, AUG 10 2010
abstract,
full text
Miller, Y., Ma, B.Y., Tsai, C.J., Nussinov, R.
Hollow core of Alzheimer's A beta(42) amyloid observed by cryoEM is relevant at physiological pH
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:14128-14133, AUG 10 2010
abstract,
full text
Saam, J., Rosini, E., Molla, G., Schulten, K., Pollegioni, L., Ghisla, S.
O(2) Reactivity of Flavoproteins DYNAMIC ACCESS OF DIOXYGEN TO THE ACTIVE SITE AND ROLE OF A H(+) RELAY SYSTEM IN D-AMINO ACID OXIDASE
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:24439-24446, AUG 6 2010
abstract,
full text,
TCBG publications
He, X.B., Guvench, O., MacKerell, A.I., Klein, M.L.
Atomistic Simulation Study of Linear Alkylbenzene Sulfonates at the Water/Air Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9787-9794, AUG 5 2010
abstract,
full text
Priyakumar, U.D.
Atomistic Details of the Ligand Discrimination Mechanism of S(MK)/SAM-III Riboswitch
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9920-9925, AUG 5 2010
abstract,
full text
Liu, J., Nussinov, R.
Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation
BIOPHYSICAL JOURNAL, 99:736-744, AUG 4 2010
abstract,
full text
Broemstrup, T., Reuter, N.
Molecular Dynamics Simulations of Mixed Acidic/Zwitterionic Phospholipid Bilayers
BIOPHYSICAL JOURNAL, 99:825-833, AUG 4 2010
abstract,
full text
Wereszczynski, J., Andricioaei, I.
Free Energy Calculations Reveal Rotating-Ratchet Mechanism for DNA Supercoil Relaxation by Topoisomerase IB and its Inhibition
BIOPHYSICAL JOURNAL, 99:869-878, AUG 4 2010
abstract,
full text
Sen, K., Hackett, J.C.
Peroxo-Iron Mediated Deformylation in Sterol 14 alpha-Demethylase Catalysis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:10293-10305, AUG 4 2010
abstract,
full text
Kurland, M.D., Newcomer, M.B., Peterlin, Z., Ryan, K., Firestein, S., Batista, V.S.
Discrimination of Saturated Aldehydes by the Rat I7 Olfactory Receptor
BIOCHEMISTRY, 49:6302-6304, AUG 3 2010
abstract,
full text
Wang, Q.M., Zhao, J., Yu, X.A., Zhao, C., Li, L.Y., Zheng, J.
Alzheimer A beta(1-42) Monomer Adsorbed on the Self-Assembled Monolayers
LANGMUIR, 26:12722-12732, AUG 3 2010
abstract,
full text
Herrera, A.I., Al-Rawi, A., Cook, G.A., Gao, J.A., Iwamoto, T., Prakash, O., Tomich, J.M., Chen, J.H.
Structural characterization of two pore-forming peptides: Consequences of introducing a C-terminal tryptophan
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2238-2250, AUG 1 2010
abstract,
full text
Khienova, M.G., Nemukhin, A.V., Grigorenko, B.L., Krylov, A.I., Domratcheva, T.M.
Quantum Chemistry Calculations Provide Support to the Mechanism of the Light-Induced Structural Changes in the Flavin-Binding Photoreceptor Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2293-2302, AUG 2010
abstract,
full text
Zhao, R.J., Shen, J.F., Skeel, R.D.
Maximum Flux Transition Paths of Conformational Change
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2411-2423, AUG 2010
abstract,
full text
Mura, C., McCrimmon, C.M., Vertrees, J., Sawaya, M.R.
An Introduction to Biomolecular Graphics
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000918, AUG 2010
full text
Pan, Y.P., Nussinov, R.
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000878, AUG 2010
abstract,
full text
Shaikh, S.A., Tajkhorshid, E.
Modeling and Dynamics of the Inward-Facing State of a Na(+)/Cl(-) Dependent Neurotransmitter Transporter Homologue
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000905, AUG 2010
abstract,
full text
Wong-Ekkabut, J., Miettinen, M.S., Dias, C., Karttunen, M.
Static charges cannot drive a continuous flow of water molecules through a carbon nanotube
NATURE NANOTECHNOLOGY, 5:555-557, AUG 2010
full text
Banerjee, A., Bairagya, H.R., Mukhopadhyay, B.P., Nandi, T.K., Bera, A.K.
Structural insight to mutated Y116S transthyretin by molecular dynamics simulation
INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS, 47:197-202, AUG 2010
abstract,
full text
Popov, A.V., Vorob'ev, Y.N.
GUI-BioPASED: A program for molecular dynamics simulations of biopolymers with a graphical user interface
MOLECULAR BIOLOGY, 44:648-654, AUG 2010
abstract,
full text
Cruz-Chu, E.R., Schulten, K.
Computational Microscopy of the Role of Protonable Surface Residues in Nanoprecipitation Oscillations
ACS NANO, 4:4463-4474, AUG 2010
abstract,
full text,
TCBG publications
Durrant, J.D., Hall, L., Swift, R.V., Landon, M., Schnaufer, A., Amaro, R.E.
Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1
PLOS NEGLECTED TROPICAL DISEASES, 4: Art. No. e803, AUG 2010
abstract,
full text
Chirkova, A., Erlacher, M.D., Clementi, N., Zywicki, M., Aigner, M., Polacek, N.
The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center
NUCLEIC ACIDS RESEARCH, 38:4844-4855, AUG 2010
abstract,
full text
Yuan, Y., Knaggs, M.H., Poole, L.B., Fetrow, J.S., Salsbury, F.R.
Conformational and Oligomeric Effects on the Cysteine pK(a) of Tryparedoxin Peroxidase
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:51-70, AUG 2010
abstract,
full text
Kunji, E.R.S., Robinson, A.J.
Coupling of proton and substrate translocation in the transport cycle of mitochondrial carriers
CURRENT OPINION IN STRUCTURAL BIOLOGY, 20:440-447, AUG 2010
abstract,
full text
Seibold, S.A., Singh, B.N., Zhang, C.F., Kireeva, M., Domecq, C., Bouchard, A., Nazione, A.M., Feig, M., Cukier, R.I., Coulombe, B., Kashlev, M., Hampsey, M., Burton, Z.F.
Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1799:575-587, AUG 2010
abstract,
full text
Shen, R., Guo, W.L., Zhong, W.Y.
Hydration valve controlled non-selective conduction of Na(+) and K(+) in the NaK channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:1474-1479, AUG 2010
abstract,
full text
Mihajlovic, M., Lazaridis, T.
Antimicrobial peptides in toroidal and cylindrical pores
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:1485-1493, AUG 2010
abstract,
full text
Sharma, V., Wikstrom, M., Kaila, V.R.I.
Redox-coupled proton transfer in the active site of cytochrome cbb(3)
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1797:1512-1520, AUG 2010
abstract,
full text
Phogat, N., Vindal, V., Kumar, V., Inampudi, K.K., Prasad, N.K.
Sequence analysis, in silico modeling and docking studies of Caffeoyl CoA-O-methyltransferase of Populus trichopora
JOURNAL OF MOLECULAR MODELING, 16:1461-1471, AUG 2010
abstract,
full text
Novak, M., Jager, C.M., Rumpel, A., Kropp, H., Peukert, W., Clark, T., Halik, M.
The morphology of integrated self-assembled monolayers and their impact on devices - A computational and experimental approach
ORGANIC ELECTRONICS, 11:1476-1482, AUG 2010
abstract,
full text
Jang, H., Arce, F.T., Ramachandran, S., Capone, R., Lal, R., Nussinov, R.
Structural Convergence Among Diverse, Toxic beta-Sheet Ion Channels
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9445-9451, JUL 29 2010
abstract,
full text
Fidelak, J., Juraszek, J., Branduardi, D., Bianciotto, M., Gervasio, F.L.
Free-Energy-Based Methods for Binding Profile Determination in a Congeneric Series of CDK2 Inhibitors
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9516-9524, JUL 29 2010
abstract,
full text
He, Y.H., Shao, L.B., Scheicher, R.H., Grigoriev, A., Ahuja, R., Long, S.B., Ji, Z.Y., Yu, Z.A., Liu, M.
Differential conductance as a promising approach for rapid DNA sequencing with nanopore-embedded electrodes
APPLIED PHYSICS LETTERS, 97: Art. No. 043701, JUL 26 2010
abstract,
full text
Wang, X.Q., Yu, T., Sang, J.P., Zou, X.W., Chen, T.Y., Bolser, D., Zou, X.Q.
A Three-State Multi-Ion Kinetic Model for Conduction Properties of ClC-0 Chloride Channel
BIOPHYSICAL JOURNAL, 99:464-471, JUL 21 2010
abstract,
full text
Balaraman, G.S., Bhattacharya, S., Vaidehi, N.
Structural Insights into Conformational Stability of Wild-Type and Mutant beta(1)-Adrenergic Receptor
BIOPHYSICAL JOURNAL, 99:568-577, JUL 21 2010
abstract,
full text
Prakash, M.K., Barducci, A., Parrinello, M.
Probing the Mechanism of pH-Induced Large-Scale Conformational Changes in Dengue Virus Envelope Protein Using Atomistic Simulations
BIOPHYSICAL JOURNAL, 99:588-594, JUL 21 2010
abstract,
full text
Wells, D.B., Aksimentiev, A.
Mechanical Properties of a Complete Microtubule Revealed through Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 99:629-637, JUL 21 2010
abstract,
full text
Vashisth, H., Abrams, C.F.
All-Atom Structural Models for Complexes of Insulin-Like Growth Factors IGF1 and IGF2 with Their Cognate Receptor
JOURNAL OF MOLECULAR BIOLOGY, 400:645-658, JUL 16 2010
abstract,
full text
Kokhan, O., Shinkarev, V.P., Wraight, C.A.
Binding of Imidazole to the Heme of Cytochrome c(1) and Inhibition of the bc(1) Complex from Rhodobacter sphaeroides I. EQUILIBRIUM AND MODELING STUDIES
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:22513-22521, JUL 16 2010
abstract,
full text
Shah, J.K., Maginn, E.J.
Molecular dynamics investigation of biomimetic ionic liquids
FLUID PHASE EQUILIBRIA, 294:197-205, JUL 15 2010
abstract,
full text
Kumar, R.A., Pilz, D.T., Babatz, T.D., Cushion, T.D., Harvey, K., Topf, M., Yates, L., Robb, S., Uyanik, G., Mancini, G.M.S., Rees, M.I., Harvey, R.J., Dobyns, W.B.
TUBA1A mutations cause wide spectrum lissencephaly (smooth brain) and suggest that multiple neuronal migration pathways converge on alpha tubulins
HUMAN MOLECULAR GENETICS, 19:2817-2827, JUL 15 2010
abstract,
full text
Liu, L.T., Xu, Y., Tang, P.
Mechanistic Insights into Xenon Inhibition of NMDA Receptors from MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9010-9016, JUL 15 2010
abstract,
full text
Utesch, T., Mroginski, M.A.
Three-Dimensional Structural Model of Chicken Liver Sulfite Oxidase in its Activated Form
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:2159-2164, JUL 15 2010
abstract,
full text
Bondar, A.N., del Val, C., Freites, J.A., Tobias, D.J., White, S.H.
Dynamics of SecY Translocons with Translocation-Defective Mutations
STRUCTURE, 18:847-857, JUL 14 2010
abstract,
full text
Ng, Y.W., Raghunathan, D., Chan, P.M., Baskaran, Y., Smith, D.J., Lee, C.H., Verma, C., Manser, E.
Why an A-Loop Phospho-Mimetic Fails to Activate PAK1: Understanding an Inaccessible Kinase State by Molecular Dynamics Simulations
STRUCTURE, 18:879-890, JUL 14 2010
abstract,
full text
Melloni, A., Paccani, R.R., Donati, D., Zanirato, V., Sinicropi, A., Parisi, M.L., Martin, E., Ryazantsev, M., Ding, W.J., Frutos, L.M., Basosi, R., Fusi, S., Latterini, L., Ferre, N., Olivucci, M.
Modeling, Preparation, and Characterization of a Dipole Moment Switch Driven by Z/E Photoisomerization
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:9310-9319, JUL 14 2010
abstract,
full text
Durrant, J.D., Urbaniak, M.D., Ferguson, M.A.J., McCammon, J.A.
Computer-Aided Identification of Trypanosoma brucei Uridine Diphosphate Galactose 4 '-Epimerase Inhibitors: Toward the Development of Novel Therapies for African Sleeping Sickness
JOURNAL OF MEDICINAL CHEMISTRY, 53:5025-5032, JUL 8 2010
abstract,
full text
Cuello, L.G., Jogini, V., Cortes, D.M., Pan, A.C., Gagnon, D.G., Dalmas, O., Cordero-Morales, J.F., Chakrapani, S., Roux, B., Perozo, E.
Structural basis for the coupling between activation and inactivation gates in K(+) channels
NATURE, 466:272-U154, JUL 8 2010
abstract,
full text
Jiao, W.T., McDonald, Q., Coxon, J.M., Parker, E.J.
Molecular Modeling Studies of Peptide Inhibitors Highlight the Importance of Conformational Prearrangement for Inhibition of Calpain
BIOCHEMISTRY, 49:5533-5539, JUL 6 2010
abstract,
full text
Brun, S., Chaloin, L., Gay, B., Bernard, E., Devaux, C., Lionne, C., Chazal, N., Briant, L.
Electrostatic repulsion between HIV-1 capsid proteins modulates hexamer plasticity and in vitro assembly
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2144-2156, JUL 2010
abstract,
full text
Dubey, D.K., Tomar, V.
Tensile and Compressive Loading Effects on Texture Dependent Nanoscale Mechanical Behavior of Model Tropocollagen-Hydroxyapatite Biomaterials
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:1306-1316, JUL 2010
abstract,
full text
de Serrano, V.S., Davis, M.F., Gaff, J.F., Zhang, Q., Chen, Z., D'Antonio, E.L., Bowden, E.F., Rose, R., Franzen, S.
X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 66:770-782, JUL 2010
abstract,
full text
Schafer, N., Negrut, D.
A Quantitative Assessment of the Potential of Implicit Integration Methods for Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL AND NONLINEAR DYNAMICS, 5: Art. No. 031012, JUL 2010
abstract,
full text
Palpant, N.J., Houang, E.M., Delport, W., Hastings, K.E.M., Onufriev, A.V., Sham, Y.Y., Metzger, J.M.
Pathogenic peptide deviations support a model of adaptive evolution of chordate cardiac performance by troponin mutations
PHYSIOLOGICAL GENOMICS, 42:287-299, JUL 2010
abstract,
full text
Kraszewski, S., Tarek, M., Treptow, W., Ramseyer, C.
Affinity of C(60) Neat Fullerenes with Membrane Proteins: A Computational Study on Potassium Channels
ACS NANO, 4:4158-4164, JUL 2010
abstract,
full text
Elmore, D.E., Guayasamin, R.C., Kieffer, M.E.
A Series of Molecular Dynamics and Homology Modeling Computer Labs for an Undergraduate Molecular Modeling Course
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 38:216-223, JUL-AUG 2010
abstract,
full text
Berjanskii, M., Liang, Y.J., Zhou, J.J., Tang, P., Stothard, P., Zhou, Y., Cruz, J., MacDonell, C., Lin, G.H., Lu, P., Wishart, D.S.
PROSESS: a protein structure evaluation suite and server
NUCLEIC ACIDS RESEARCH, 38:W633-W640, JUL 2010
abstract,
full text
Porollo, A., Meller, J.
POLYVIEW-MM: web-based platform for animation and analysis of molecular simulations
NUCLEIC ACIDS RESEARCH, 38:W662-W666, JUL 2010
abstract,
full text
Russell, J., Kral, P.
Configuration-sensitive molecular sensing on doped graphene sheets
NANO RESEARCH, 3:472-480, JUL 2010
abstract,
full text
Lambry, J.C., Beaumont, E., Tarus, B., Blanchard-Desce, M., Slama-Schwok, A.
Selective probing of a NADPH site controlled light-induced enzymatic catalysis
JOURNAL OF MOLECULAR RECOGNITION, 23:379-388, JUL-AUG 2010
abstract,
full text
Claxton, D.P., Quick, M., Shi, L., de Carvalho, F.D., Weinstein, H., Javitch, J.A., Mchaourab, H.S.
Ion/substrate-dependent conformational dynamics of a bacterial homolog of neurotransmitter: sodium symporters
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 17:822-U68, JUL 2010
abstract,
full text
Castelan-Vega, J.A., Jimenez-Alberto, A., Ribas-Aparicio, R.M.
Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: Catalytic mechanism and interactions with DNA
JOURNAL OF MOLECULAR MODELING, 16:1213-1222, JUL 2010
abstract,
full text
Kaszuba, K., Rog, T., Bryl, K., Vattulainen, I., Karttunen, M.
Molecular Dynamics Simulations Reveal Fundamental Role of Water As Factor Determining Affinity of Binding of beta-Blocker Nebivolol to beta(2)-Adrenergic Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 114:8374-8386, JUL 1 2010
abstract,
full text
Krems, M., Pershin, Y.V., Di Ventra, M.
Ionic Memcapacitive Effects in Nanopores
NANO LETTERS, 10:2674-2678, JUL 2010
abstract,
full text
Jiang, J., Abramavicius, D., Bulheller, B.M., Hirst, J.D., Mukamel, S.
Ultraviolet Spectroscopy of Protein Backbone Transitions in Aqueous Solution: Combined QM and MM Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:8270-8277, JUN 24 2010
abstract,
full text
Neelov, A., Holm, C.
Interlaced P3M algorithm with analytical and ik-differentiation
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 234103, JUN 21 2010
abstract,
full text
Katti, D.R., Pradhan, S.M., Katti, K.S.
Directional dependence of hydroxyapatite-collagen interactions on mechanics of collagen
JOURNAL OF BIOMECHANICS, 43:1723-1730, JUN 18 2010
abstract,
full text
Nygaard, R., Valentin-Hansen, L., Mokrosinski, J., Frimurer, T.M., Schwartz, T.W.
Conserved Water-mediated Hydrogen Bond Network between TM-I, -II, -VI, and -VII in 7TM Receptor Activation
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:19625-19636, JUN 18 2010
abstract,
full text
Klauda, J.B., Venable, R.M., Freites, J.A., O'Connor, J.W., Tobias, D.J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, A.D., Pastor, R.W.
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7830-7843, JUN 17 2010
abstract,
full text
Liu, P., Cai, W.S., Chipot, C., Shao, X.G.
Thermodynamic Insights into the Dynamic Switching of a Cyclodextrin in a Bistable Molecular Shuttle
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:1776-1780, JUN 17 2010
abstract,
full text
Schow, E.V., Freites, J.A., Gogna, K., White, S.H., Tobias, D.J.
Down-State Model of the Voltage-Sensing Domain of a Potassium Channel
BIOPHYSICAL JOURNAL, 98:2857-2866, JUN 16 2010
abstract,
full text
Adelman, J.L., Chodera, J.D., Kuo, I.F.W., Miller, T.F., Barsky, D.
The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp
BIOPHYSICAL JOURNAL, 98:3062-3069, JUN 16 2010
abstract,
full text
Treptow, W., Klein, M.L.
The Membrane-Bound State of K(2P) Potassium Channels
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:8145-8151, JUN 16 2010
abstract,
full text
Feig, M., Gebreyohannes, K.G., McGuffin, V.L.
Conformational sampling of S- and R-warfarin in polar solvents: Implications for stereoselective complex formation
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 949:41-51, JUN 15 2010
abstract,
full text
Henkel, M., Mitzner, D., Henklein, P., Meyer-Almes, F.J., Moroni, A., DiFrancesco, M.L., Henkes, L.M., Kreim, M., Kast, S.M., Schubert, U., Thiel, G.
The Proapoptotic Influenza A Virus Protein PB1-F2 Forms a Nonselective Ion Channel
PLOS ONE, 5: Art. No. e11112, JUN 15 2010
abstract,
full text
Ko, J.A., Choi, H.J., Ha, M.Y., Hong, S.D., Yoon, H.S.
A Study on the Behavior of Water Droplet Confined between an Atomic Force Microscope Tip and Rough Surfaces
LANGMUIR, 26:9728-9735, JUN 15 2010
abstract,
full text
Mowrey, D., Haddadian, E.J., Liu, L.T., Willenbring, D., Xu, Y., Tang, P.
Unresponsive Correlated Motion in alpha 7 nAChR to Halothane Binding Explains Its Functional Insensitivity to Volatile Anesthetics
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7649-7655, JUN 10 2010
abstract,
full text
Luan, B.Q., Peng, H.B., Polonsky, S., Rossnagel, S., Stolovitzky, G., Martyna, G.
Base-By-Base Ratcheting of Single Stranded DNA through a Solid-State Nanopore
PHYSICAL REVIEW LETTERS, 104: Art. No. 238103, JUN 10 2010
abstract,
full text
Abramavicius, D., Jiang, J., Bulheller, B.M., Hirst, J.D., Mukamel, S.
Simulation Study of Chiral Two-Dimensional Ultraviolet Spectroscopy of the Protein Backbone
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:7769-7775, JUN 9 2010
abstract,
full text
Giussani, L., Fois, E., Gianotti, E., Tabacchi, G., Gamba, A., Coluccia, S.
On the Compatibility Criteria for Protein Encapsulation inside Mesoporous Materials
CHEMPHYSCHEM, 11:1757-1762, JUN 7 2010
abstract,
full text
Rungger, I., Chen, X., Schwingenschlogl, U., Sanvito, S.
Finite-bias electronic transport of molecules in a water solution
PHYSICAL REVIEW B, 81: Art. No. 235407, JUN 4 2010
abstract,
full text
Zhang, J.L., Zheng, Q.C., Zhang, H.X.
Insight into the Dynamic Interaction of Different Carbohydrates with Human Surfactant Protein D: Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7383-7390, JUN 3 2010
abstract,
full text
Revilla-Lopez, G., Torras, J., Curco, D., Casanovas, J., Calaza, M.I., Zanuy, D., Jimenez, A.I., Cativiela, C., Nussinov, R., Grodzinski, P., Aleman, C.
NCAD, a Database Integrating the Intrinsic Conformational Preferences of Non-Coded Amino Acids
JOURNAL OF PHYSICAL CHEMISTRY B, 114:7413-7422, JUN 3 2010
abstract,
full text
Capone, R., Mustata, M., Jang, H., Arce, F.T., Nussinov, R., Lal, R.
Antimicrobial Protegrin-1 Forms Ion Channels: Molecular Dynamic Simulation, Atomic Force Microscopy, and Electrical Conductance Studies
BIOPHYSICAL JOURNAL, 98:2644-2652, JUN 2 2010
abstract,
full text
Colizzi, F., Perozzo, R., Scapozza, L., Recanatini, M., Cavalli, A.
Single-Molecule Pulling Simulations Can Discern Active from Inactive Enzyme Inhibitors
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:7361-7371, JUN 2 2010
abstract,
full text
Tainer, J.A., McCammon, J.A., Ivanov, I.
Recognition of the Ring-Opened State of Proliferating Cell Nuclear Antigen by Replication Factor C Promotes Eukaryotic Clamp-Loading
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:7372-7378, JUN 2 2010
abstract,
full text
Morrone, J.A., Zhou, R.H., Berne, B.J.
Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1798-1804, JUN 2010
abstract,
full text
Juneja, A., Numata, J., Nilsson, L., Knapp, E.W.
Merging Implicit with Explicit Solvent Simulations: Polyethylene Glycol
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1871-1883, JUN 2010
abstract,
full text
Morgan, B.R., Massi, F.
Accurate Estimates of Free Energy Changes in Charge Mutations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1884-1893, JUN 2010
abstract,
full text
Schulz, R., Vargiu, A.V., Collu, F., Kleinekathofer, U., Ruggerone, P.
Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000806, JUN 2010
abstract,
full text
Virtanen, S.I., Pentikainen, O.T.
Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1005-1011, JUN 2010
abstract,
full text
Mathew, D.C., Luthey-Schulten, Z.
Influence of Montmorillonite on Nucleotide Oligomerization Reactions: A Molecular Dynamics Study
ORIGINS OF LIFE AND EVOLUTION OF BIOSPHERES, 40:303-317, JUN 2010
abstract,
full text
Hertel, B., Tayefeh, S., Kloss, T., Hewing, J., Gebhardt, M., Baumeister, D., Moroni, A., Thiel, G., Kast, S.M.
Salt bridges in the miniature viral channel Kcv are important for function
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 39:1057-1068, JUN 2010
abstract,
full text
Dubey, D.K., Tomar, V.
Role of Molecular Level Interfacial Forces in Hard Biomaterial Mechanics: A Review
ANNALS OF BIOMEDICAL ENGINEERING, 38:2040-2055, JUN 2010
abstract,
full text
Choudhury, S.R., Singh, S.K., Roy, S., Sengupta, D.N.
An insight into the sequential, structural and phylogenetic properties of banana 1-aminocyclopropane-1-carboxylate synthase 1 and study of its interaction with pyridoxal-5 '-phosphate and aminoethoxyvinylglycine
JOURNAL OF BIOSCIENCES, 35:281-294, JUN 2010
abstract,
full text
Preat, J., Rodriguez-Ropero, F., Torras, J., Bertran, O., Zanuy, D., Aleman, C.
Parameterization of the Torsional Potential for Calix[4]arene-Substituted Poly(thiophene)s
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1741-1751, JUN 2010
abstract,
full text
Chen, W., Lou, J.Z., Zhu, C.
Simulated Thermal Unfolding of the von Willebrand Factor A Domains
CELLULAR AND MOLECULAR BIOENGINEERING, 3:117-127, JUN 2010
abstract,
full text
Zhang, Y.B., Lu, M., Cheng, Y.K., Li, Z.Q.
H-NOX domains display different tunnel systems for ligand migration
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:814-819, JUN 2010
abstract,
full text
Sereda, Y.V., Bishop, T.C.
Evaluation of Elastic Rod Models with Long Range Interactions for Predicting Nucleosome Stability
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:867-887, JUN 2010
abstract,
full text
Kovacic, L., Novinec, M., Petan, T., Krizaj, I.
Structural basis of the significant calmodulin-induced increase in the enzymatic activity of secreted phospholipases A(2)
PROTEIN ENGINEERING DESIGN & SELECTION, 23:479-487, JUN 2010
abstract,
full text
Lin, Y.W.
Expanding Protein Functionalities by Rational Design of Artificial Metal-Binding Sites
PROGRESS IN CHEMISTRY, 22:1203-1211, JUN 2010
abstract,
full text
Morgan, B.R., Massi, F.
A computational study of RNA binding and specificity in the tandem zinc finger domain of TIS11d
PROTEIN SCIENCE, 19:1222-1234, JUN 2010
abstract,
full text
Krah, A., Pogoryelov, D., Langer, J.D., Bond, P.J., Meier, T., Faraldo-Gomez, J.D.
Structural and energetic basis for H(+) versus Na(+) binding selectivity in ATP synthase F(o) rotors
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1797:763-772, JUN-JUL 2010
abstract,
full text
Salsbury, F.R.
Effects of Cisplatin Binding to DNA on the Dynamics of the E. coli MutS Dimer
PROTEIN AND PEPTIDE LETTERS, 17:744-750, JUN 2010
abstract,
full text
Guallar, V., Wallrapp, F.H.
QM/MM methods: Looking inside heme proteins biochemisty
BIOPHYSICAL CHEMISTRY, 149:1-11, JUN 2010
abstract,
full text
Weber, V., Merchant, S., Dixit, P.D., Asthagiri, D.
Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 204509, MAY 28 2010
abstract,
full text
Shinoda, W., DeVane, R., Klein, M.L.
Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6836-6849, MAY 27 2010
abstract,
full text
Sun, T.T., Shao, X.G., Cai, W.S.
Self-assembly behavior of beta-cyclodextrin and imipramine. A Free energy perturbation study
CHEMICAL PHYSICS, 371:84-90, MAY 25 2010
abstract,
full text
Miller, Y., Ma, B.Y., Nussinov, R.
Zinc ions promote Alzheimer A beta aggregation via population shift of polymorphic states
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:9490-9495, MAY 25 2010
abstract,
full text
Forbes, J.G., Flaherty, D.B., Ma, K., Qadota, H., Benian, G.M., Wang, K.A.
Extensive and Modular Intrinsically Disordered Segments in C. elegans TTN-1 and Implications in Filament Binding, Elasticity and Oblique Striation
JOURNAL OF MOLECULAR BIOLOGY, 398:672-689, MAY 21 2010
abstract,
full text
Unal, H., Jagannathan, R., Bhat, M.B., Karnik, S.S.
Ligand-specific Conformation of Extracellular Loop-2 in the Angiotensin II Type 1 Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:16341-16350, MAY 21 2010
abstract,
full text
DeVane, R., Klein, M.L., Chiu, C.C., Nielsen, S.O., Shinoda, W., Moore, P.B.
Coarse-Grained Potential Models for Phenyl-Based Molecules: I. Parametrization Using Experimental Data
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6386-6393, MAY 20 2010
abstract,
full text
Chiu, C.C., DeVane, R., Klein, M.L., Shinoda, W., Moore, P.B., Nielsen, S.O.
Coarse-Grained Potential Models for Phenyl-Based Molecules: II. Application to Fullerenes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6394-6400, MAY 20 2010
abstract,
full text
Shi, W., Sorescu, D.C., Luebke, D.R., Keller, M.J., Wickramanayake, S.
Molecular Simulations and Experimental Studies of Solubility and Diffusivity for Pure and Mixed Gases of H(2), CO(2), and Ar Absorbed in the Ionic Liquid 1-n-Hexyl-3-methylimidazolium Bis(Trifluoromethylsulfonyl)amide ([hmim][Tf(2)N])
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6531-6541, MAY 20 2010
abstract,
full text
Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., Trout, B.L.
Prediction of Aggregation Prone Regions of Therapeutic Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 114:6614-6624, MAY 20 2010
abstract,
full text
Ko, Y.J., Jo, W.H.
Secondary Water Pore Formation for Proton Transport in a CIC Exchanger Revealed by an Atomistic Molecular-Dynamics Simulation
BIOPHYSICAL JOURNAL, 98:2163-2169, MAY 19 2010
abstract,
full text
Khalili-Araghi, F., Jogini, V., Yarov-Yarovoy, V., Tajkhorshid, E., Roux, B., Schulten, K.
Calculation of the Gating Charge for the Kv1.2 Voltage-Activated Potassium Channel
BIOPHYSICAL JOURNAL, 98:2189-2198, MAY 19 2010
abstract,
full text,
TCBG publications
Raghunathan, D., Gayen, S., Gruber, G., Verma, C.S.
Crosstalk along the Stalk: Dynamics of the Interaction of Subunits B and F in the A(1)A(O) ATP Synthase of Methanosarcina mazei Gol
BIOCHEMISTRY, 49:4181-4190, MAY 18 2010
abstract,
full text
Jana, G., Jimenez, V., Villa-Freixa, J., Prat-Resina, X., Delgado, E., Alderete, J.
Computational study on the carboligation reaction of acetohidroxyacid synthase: New approach on the role of the HEThDP(-) intermediate
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1774-1788, MAY 15 2010
abstract,
full text
Guo, H.B., Johs, A., Parks, J.M., Olliff, L., Miller, S.M., Summers, A.O., Liang, L.Y., Smith, J.C.
Structure and Conformational Dynamics of the Metalloregulator MerR upon Binding of Hg(II)
JOURNAL OF MOLECULAR BIOLOGY, 398:555-568, MAY 14 2010
abstract,
full text
Pedersen, P.J., Adolph, S.K., Subramanian, A.K., Arouri, A., Andresen, T.L., Mouritsen, O.G., Madsen, R., Madsen, M.W., Peters, G.H., Clausen, M.H.
Liposomal Formulation of Retinoids Designed for Enzyme Triggered Release
JOURNAL OF MEDICINAL CHEMISTRY, 53:3782-3792, MAY 13 2010
abstract,
full text
Trabuco, L.G., Harrison, C.B., Schreiner, E., Schulten, K.
Recognition of the Regulatory Nascent Chain TnaC by the Ribosome
STRUCTURE, 18:627-637, MAY 12 2010
abstract,
full text,
TCBG publications
Zhang, Y.B., Cheng, Y.K., Lu, M., Zhang, H.L., Li, Z.Q.
Function of the Hydrogen-bonding Network Between the Y-S-R Motif and the Heme Propionate Groups in sGC-HNOX Domain
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 31:1039-1044, MAY 10 2010
abstract,
full text
Liu, Y.Z., Chipot, C., Shao, X.G., Cai, W.S.
Solubilizing Carbon Nanotubes through Noncovalent Functionalization. Insight from the Reversible Wrapping of Alginic Acid around a Single-Walled Carbon Nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5783-5789, MAY 6 2010
abstract,
full text
Fishelovitch, D., Shaik, S., Wolfson, H.J., Nussinov, R.
How Does the Reductase Help To Regulate the Catalytic Cycle of Cytochrome P450 3A4 Using the Conserved Water Channel?
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5964-5970, MAY 6 2010
abstract,
full text
Biro, I., Pezeshki, S., Weingart, H., Winterhalter, M., Kleinekathofer, U.
Comparing the Temperature-Dependent Conductance of the Two Structurally Similar E. coil Porins OmpC and OmpF
BIOPHYSICAL JOURNAL, 98:1830-1839, MAY 5 2010
abstract,
full text
Nyce, H.L., Stober, S.T., Abrams, C.F., White, M.M.
Mapping Spatial Relationships between Residues in the Ligand-Binding Domain of the 5-Ht(3) Receptor Using a Molecular Ruler
BIOPHYSICAL JOURNAL, 98:1847-1855, MAY 5 2010
abstract,
full text
McGillick, B.E., Balius, T.E., Mukherjee, S., Rizzo, R.C.
Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20
BIOCHEMISTRY, 49:3575-3592, MAY 4 2010
abstract,
full text
Goley, E.D., Rammohan, A., Znameroski, E.A., Firat-Karalar, E.N., Sept, D., Welch, M.D.
An actin-filament-binding interface on the Arp2/3 complex is critical for nucleation and branch stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:8159-8164, MAY 4 2010
abstract,
full text
Kast, D., Espinoza-Fonseca, L.M., Yi, C., Thomas, D.D.
Phosphorylation-induced structural changes in smooth muscle myosin regulatory light chain
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:8207-8212, MAY 4 2010
abstract,
full text
Ohkubo, Y.Z., Morrissey, J.H., Tajkhorshid, E.
Dynamical view of membrane binding and complex formation of human factor VIIa and tissue factor
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 8:1044-1053, MAY 2010
abstract,
full text
Vashisth, H., Abrams, C.F.
Docking of insulin to a structurally equilibrated insulin receptor ectodomain
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1531-1543, MAY 1 2010
abstract,
full text
Sadiq, S.K., Wright, D.W., Kenway, O.A., Coveney, P.V.
Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:890-905, MAY 2010
abstract,
full text
Chiu, C.C., Maher, M.C., Dieckmann, G.R., Nielsen, S.O.
Molecular Dynamics Study of a Carbon Nanotube Binding Reversible Cyclic Peptide
ACS NANO, 4:2539-2546, MAY 2010
abstract,
full text
Collins, L., Parker, A.L., Gehman, J.D., Eckley, L., Perugini, M.A., Separovic, F., Fabre, J.W.
Self-Assembly of Peptides into Spherical Nanoparticles for Delivery of Hydrophilic Moieties to the Cytosol
ACS NANO, 4:2856-2864, MAY 2010
abstract,
full text
Durrant, J.D., Keranen, H., Wilson, B.A., McCammon, J.A.
Computational Identification of Uncharacterized Cruzain Binding Sites
PLOS NEGLECTED TROPICAL DISEASES, 4: Art. No. e676, MAY 2010
abstract,
full text
Cickovski, T., Chatterjee, S., Wenger, J., Sweet, C.R., Izaguirre, J.A.
MDLab: A Molecular Dynamics Simulation Prototyping Environment
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1345-1356, MAY 2010
abstract,
full text
Yang, X.D., Tajkhorshid, E., Chen, L.F.
Functional Interplay between Acetylation and Methylation of the RelA Subunit of NF-kappa B
MOLECULAR AND CELLULAR BIOLOGY, 30:2170-2180, MAY 1 2010
abstract,
full text
Tsukada, M., Watanabe, N., Harada, M., Tagami, K.
Theoretical simulation of noncontact atomic force microscopy in liquids
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B, 28: DOI 10.1116/1.3430541, MAY 2010
abstract,
full text
Cardone, A., Albers, R.W., Sriram, R.D., Pant, H.C.
Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor CIP
JOURNAL OF COMPUTATIONAL BIOLOGY, 17:707-721, MAY 2010
abstract,
full text
Mascayano, C., Nunez, G., Acevedo, W., Rezende, M.C.
Binding of arachidonic acid and two flavonoid inhibitors to human 12-and 15-lipoxygenases: a steered molecular dynamics study
JOURNAL OF MOLECULAR MODELING, 16:1039-1045, MAY 2010
abstract,
full text
Eastman, P., Pande, V.S.
Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:1268-1272, APR 30 2010
abstract,
full text
Aleksandrov, A., Simonson, T.
Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:13807-13815, APR 30 2010
abstract,
full text
Hsin, J., Chandler, D.E., Gumbart, J., Harrison, C.B., Sener, M., Strumpfer, J., Schulten, K.
Self-Assembly of Photosynthetic Membranes
CHEMPHYSCHEM, 11:1154-1159, APR 26 2010
abstract,
full text,
TCBG publications
Mroginski, M.A., Kaminski, S., Hildebrandt, P.
Raman Spectra of the Phycoviolobilin Cofactor in Phycoerythrocyanin Calculated by QM/MM Methods
CHEMPHYSCHEM, 11:1265-1274, APR 26 2010
abstract,
full text
Sgourakis, N.G., Garcia, A.E.
The Membrane Complex between Transducin and Dark-State Rhodopsin Exhibits Large-Amplitude Interface Dynamics on the Sub-Microsecond Timescale: Insights from All-Atom MD Simulations
JOURNAL OF MOLECULAR BIOLOGY, 398:161-173, APR 23 2010
abstract,
full text
Carrascal, N., Green, D.F.
Energetic Decomposition with the Generalized-Born and Poisson-Boltzmann Solvent Models: Lessons from Association of G-Protein Components
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5096-5116, APR 22 2010
abstract,
full text
Vidossich, P., Florin, G., Alfonso-Prieto, M., Derat, E., Shaik, S., Rovira, C.
On the Role of Water in Peroxidase Catalysis: A Theoretical Investigation of HRP Compound I Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5161-5169, APR 22 2010
abstract,
full text
Chen, X.B., Gao, L.H., Fang, W.H., Phillips, D.L.
Theoretical Insight into the Photodegradation of a Disulfide Bridged Cyclic Tetrapeptide in Solution and Subsequent Fast Unfolding-Refolding Events
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5206-5214, APR 22 2010
abstract,
full text
McCullagh, M., Hariharan, M., Lewis, F.D., Markovitsi, D., Douki, T., Schatz, G.C.
Conformational Control of TT Dimerization in DNA Conjugates. A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 114:5215-5221, APR 22 2010
abstract,
full text
Miao, L., Schulten, K.
Probing a Structural Model of the Nuclear Pore Complex Channel through Molecular Dynamics
BIOPHYSICAL JOURNAL, 98:1658-1667, APR 21 2010
abstract,
full text,
TCBG publications
Utiramerur, S., Paulaitis, M.E.
Cooperative hydrophobic/hydrophilic interactions in the hydration of dimethyl ether
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 155102, APR 21 2010
abstract,
full text
Pfaendtner, J., De La Cruz, E.M., Voth, G.A.
Actin filament remodeling by actin depolymerization factor/cofilin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:7299-7304, APR 20 2010
abstract,
full text
Nesmelova, I.V., Ermakova, E., Daragan, V.A., Pang, M., Menendez, M., Lagartera, L., Solis, D., Baum, L.G., Mayo, K.H.
Lactose Binding to Galectin-1 Modulates Structural Dynamics, Increases Conformational Entropy, and Occurs with Apparent Negative Cooperativity
JOURNAL OF MOLECULAR BIOLOGY, 397:1209-1230, APR 16 2010
abstract,
full text
Pyrkosz, A.B., Eargle, J., Sethi, A., Luthey-Schulten, Z.
Exit Strategies for Charged tRNA from GluRS
JOURNAL OF MOLECULAR BIOLOGY, 397:1350-1371, APR 16 2010
abstract,
full text
Sotomayor, M., Weihofen, W.A., Gaudet, R., Corey, D.P.
Structural Determinants of Cadherin-23 Function in Hearing and Deafness
NEURON, 66:85-100, APR 15 2010
abstract,
full text
Watanabe, H., Yamaguchi, S., Sen, S., Morita, A., Tahara, T.
"Half-hydration" at the air/water interface revealed by heterodyne-detected electronic sum frequency generation spectroscopy, polarization second harmonic generation, and molecular dynamics simulation
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 144701, APR 14 2010
abstract,
full text
Steijl, R., Barakos, G.N.
Coupled Navier-Stokes-Molecular dynamics simulations using a multi-physics flow simulation framework
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, 62:1081-1106, APR 10 2010
abstract,
full text
Lian, P., Liu, L.A., Shi, Y.X., Bu, Y.X., Wei, D.Q.
Tethered-Hopping Model for Protein-DNA Binding and Unbinding Based on Sox2-Oct1-Hoxb1 Ternary Complex Simulations
BIOPHYSICAL JOURNAL, 98:1285-1293, APR 7 2010
abstract,
full text
Gubbins, K.E., Moore, J.D.
Molecular Modeling of Matter: Impact and Prospects in Engineering
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 49:3026-3046, APR 7 2010
full text
Maginn, E.J., Elliott, J.R.
Historical Perspective and Current Outlook for Molecular Dynamics As a Chemical Engineering Tool
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 49:3059-3078, APR 7 2010
full text
Ishii, S., Yano, T., Ebihara, A., Okamoto, A., Manzoku, M., Hayashi, H.
Crystal Structure of the Peptidase Domain of Streptococcus ComA, a Bifunctional ATP-binding Cassette Transporter Involved in the Quorum-sensing Pathway
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:10777-10785, APR 2 2010
abstract,
full text
Zhang, J.F., Wang, Q.G., Barz, B.D., He, Z.Q., Kosztin, I., Shang, Y., Xu, D.
MUFOLD: A new solution for protein 3D structure prediction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1137-1152, APR 2010
abstract,
full text
Luan, B.Q., Carr, R., Caffrey, M., Aksimentiev, A.
The effect of calcium on the conformation of cobalamin transporter BtuB
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1153-1162, APR 2010
abstract,
full text
Tchesnokova, V., McVeigh, A.L., Kidd, B., Yakovenko, O., Thomas, W.E., Sokurenko, E.V., Savarino, S.J.
Shear-enhanced binding of intestinal colonization factor antigen I of enterotoxigenic Escherichia coli
MOLECULAR MICROBIOLOGY, 76:489-502, APR 2010
abstract,
full text
Mazorra-Manzano, M.A., Tanaka, T., Dee, D.R., Yada, R.Y.
Structure-function characterization of the recombinant aspartic proteinase A1 from Arabidopsis thaliana
PHYTOCHEMISTRY, 71:515-523, APR 2010
abstract,
full text
Minoukadeh, K., Chipot, C., Lelievre, T.
Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1008-1017, APR 2010
abstract,
full text
Bellucci, L., Laino, T., Tafi, A., Botta, M.
Metadynamics Simulations of Enantioselective Acylation Give Insights into the Catalytic Mechanism of Burkholderia cepacia Lipase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1145-1156, APR 2010
abstract,
full text
Glass, D.C., Krishnan, M., Nutt, D.R., Smith, J.C.
Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1390-1400, APR 2010
abstract,
full text
Lundberg, M., Sasakura, Y., Zheng, G.S., Morokuma, K.
Case Studies of ONIOM(DFT:DFTB) and ONIOM(DFT:DFTB:MM) for Enzymes and Enzyme Mimics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:1413-1427, APR 2010
abstract,
full text
Hilder, T.A., Yang, R., Ganesh, V., Gordon, D., Bliznyuk, A., Rendell, A.P., Chung, S.H.
Validity of current force fields for simulations on boron nitride nanotubes
MICRO & NANO LETTERS, 5:150-156, APR 2010
abstract,
full text
Chinappi, M., Casciola, C.M.
Intrinsic slip on hydrophobic self-assembled monolayer coatings
PHYSICS OF FLUIDS, 22: Art. No. 042003, APR 2010
abstract,
full text
Belyy, V., Anishkin, A., Kamaraju, K., Liu, N.L., Sukharev, S.
The tension-transmitting 'clutch' in the mechanosensitive channel MscS
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 17:451-U92, APR 2010
abstract,
full text
Giambasxu, G.M., Lee, T.S., Sosa, C.P., Robertson, M.P., Scott, W.G., York, D.M.
Identification of dynamical hinge points of the L1 ligase molecular switch
RNA-A PUBLICATION OF THE RNA SOCIETY, 16:769-780, APR 2010
abstract,
full text
Schwander, P., Fung, R., Phillips, G.N., Ourmazd, A.
Mapping the conformations of biological assemblies
NEW JOURNAL OF PHYSICS, 12: Art. No. 035007, MAR 31 2010
abstract,
full text
Van Schouwen, B.M.B., Nakano, M., Watanabe, H., Tanaka, S., Gordon, H.L., Rothstein, S.M.
Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 944:12-20, MAR 30 2010
abstract,
full text
Yamtich, J., Starcevic, D., Lauper, J., Smith, E., Shi, I., Rangarajan, S., Jaeger, J., Sweasy, J.B.
Hinge Residue I174 Is Critical for Proper dNTP Selection by DNA Polymerase beta
BIOCHEMISTRY, 49:2326-2334, MAR 23 2010
abstract,
full text
Palmer, D.S., Christensen, A.U., Sorensen, J., Celik, L., Qvist, K.B., Schiott, B.
Bovine Chymosin: A Computational Study of Recognition and Binding of Bovine kappa-Casein
BIOCHEMISTRY, 49:2563-2573, MAR 23 2010
abstract,
full text
Limongelli, V., Bonomi, M., Marinelli, L., Gervasio, F.L., Cavalli, A., Novellino, E., Parrinello, M.
Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:5411-5416, MAR 23 2010
full text
Timko, J., Bucher, D., Kuyucak, S.
Dissociation of NaCl in water from ab initio molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 114510, MAR 21 2010
abstract,
full text
Volkmann, G., Murphy, P.W., Rowland, E.E., Cronan, J.E., Liu, X.Q., Blouin, C., Byers, D.M.
Intein-mediated Cyclization of Bacterial Acyl Carrier Protein Stabilizes Its Folded Conformation but Does Not Abolish Function
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:8605-8614, MAR 19 2010
abstract,
full text
Diaz, J.A.C., Cagin, T.
Thermo-mechanical stability and strength of peptide nanostructures from molecular dynamics: self-assembled cyclic peptide nanotubes
NANOTECHNOLOGY, 21: Art. No. 115703, MAR 19 2010
abstract,
full text
Lee, E.H., Hsin, J., von Castelmur, E., Mayans, O., Schulten, K.
Tertiary and Secondary Structure Elasticity of a Six-Ig Titin Chain
BIOPHYSICAL JOURNAL, 98:1085-1095, MAR 17 2010
abstract,
full text,
TCBG publications
Wijesinha-Bettoni, R., Alexeev, Y., Johnson, P., Marsh, J., Sancho, A.I., Abdullah, S.U., Mackie, A.R., Shewry, P.R., Smith, L.J., Mills, E.N.C.
The Structural Characteristics of Nonspecific Lipid Transfer Proteins Explain Their Resistance to Gastroduodenal Proteolysis
BIOCHEMISTRY, 49:2130-2139, MAR 16 2010
abstract,
full text
Abrams, C.F., Vanden-Eijnden, E.
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:4961-4966, MAR 16 2010
abstract,
full text
Westrich, L., Gil-Mast, S., Kortagere, S., Kuzhikandathil, E.V.
Development of tolerance in D3 dopamine receptor signaling is accompanied by distinct changes in receptor conformation
BIOCHEMICAL PHARMACOLOGY, 79:897-907, MAR 15 2010
abstract,
full text
Priyakumar, U.D., MacKerell, A.D.
Role of the Adenine Ligand on the Stabilization of the Secondary and Tertiary Interactions in the Adenine Riboswitch
JOURNAL OF MOLECULAR BIOLOGY, 396:1422-1438, MAR 12 2010
abstract,
full text
Liu, J., Nussinov, R.
Molecular Dynamics Reveal the Essential Role of Linker Motions in the Function of Cullin-RING E3 Ligases
JOURNAL OF MOLECULAR BIOLOGY, 396:1508-1523, MAR 12 2010
abstract,
full text
Rykunov, D., Fiser, A.
New statistical potential for quality assessment of protein models and a survey of energy functions
BMC BIOINFORMATICS, 11: Art. No. 128, MAR 12 2010
abstract,
full text
Knox, C.K., Voth, G.A.
Probing Selected Morphological Models of Hydrated Nation Using Large-Scale Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:3205-3218, MAR 11 2010
abstract,
full text
Vassiliev, S., Comte, P., Mahboob, A., Bruce, D.
Tracking the Flow of Water through Photosystem II Using Molecular Dynamics and Streamline Tracing
BIOCHEMISTRY, 49:1873-1881, MAR 9 2010
abstract,
full text
Antipova, O., Orgel, J.P.R.O.
In Situ D-periodic Molecular Structure of Type II Collagen
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:7087-7096, MAR 5 2010
abstract,
full text
Ponder, J.W., Wu, C.J., Ren, P.Y., Pande, V.S., Chodera, J.D., Schnieders, M.J., Haque, I., Mobley, D.L., Lambrecht, D.S., DiStasio, R.A., Head-Gordon, M., Clark, G.N.I., Johnson, M.E., Head-Gordon, T.
Current Status of the AMOEBA Polarizable Force Field
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2549-2564, MAR 4 2010
abstract,
full text
Khalfa, A., Tarek, M.
On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2676-2684, MAR 4 2010
abstract,
full text
Vivcharuk, V., Kaznessis, Y.
Free Energy Profile of the Interaction between a Monomer or a Dimer of Protegrin-1 in a Specific Binding Orientation and a Model Lipid Bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2790-2797, MAR 4 2010
abstract,
full text
Kang, Y., Wang, Q., Liu, Y.C., Shen, J.W., Wu, T.
Diameter Selectivity of Protein Encapsulation in Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2869-2875, MAR 4 2010
abstract,
full text
Vorobyev, D.Y., Kuo, C.H., Kuroda, D.G., Scott, J.N., Vanderkooi, J.M., Hochstrasser, R.M.
Water-Induced Relaxation of a Degenerate Vibration of Guanidium Using 2D IR Echo Spectroscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2944-2953, MAR 4 2010
abstract,
full text
Wang, Q.M., Zhao, C., Zhao, J., Wang, J.D., Yang, J.C., Yu, X., Zhen, J.
Comparative Molecular Dynamics Study of A beta Adsorption on the Self-Assembled Monolayers
LANGMUIR, 26:3308-3316, MAR 2 2010
abstract,
full text
Hicks, S.D., Henley, C.L.
Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations
PHYSICAL REVIEW E, 81: Art. No. 030903, MAR 2010
abstract,
full text
Havel, N., Geisbrecht, B.V., Lambris, J., Kavraki, L.
Multi-scale characterization of the energy landscape of proteins with application to the C3d/Efb-C complex
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:1004-1014, MAR 2010
abstract,
full text
Gedeon, P.C., Indarte, M., Surratt, C.K., Madura, J.D.
Molecular dynamics of leucine and dopamine transporter proteins in a model cell membrane lipid bilayer
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:797-811, MAR 2010
abstract,
full text
Anishkin, A., Milac, A.L., Guy, H.R.
Symmetry-restrained molecular dynamics simulations improve homology models of potassium channels
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:932-949, MAR 2010
abstract,
full text
Cilurzo, F., Gennari, C.G.M., Selmin, F., Vistoli, G.
Effects of Metal Ions on Entero-Soluble Poly(methacrylic acid-methyl methacrylate) Coating: A Combined Analysis by ATR-FTIR Spectroscopy and Computational Approaches
MOLECULAR PHARMACEUTICS, 7:421-430, MAR-APR 2010
abstract,
full text
Liwo, A., Oldziej, S., Czaplewski, C., Kleinerman, D.S., Blood, P., Scheraga, H.A.
Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:890-909, MAR 2010
abstract,
full text
Lash-Van Wyhe, L.L., Postila, P.A., Tsubone, K., Sasaki, M., Pentikainen, O.T., Sakai, R., Swanson, G.T.
Pharmacological activity of C10-substituted analogs of the high-affinity kainate receptor agonist dysiherbaine
NEUROPHARMACOLOGY, 58:640-649, MAR 2010
abstract,
full text
Buch, I., Harvey, M.J., Giorgino, T., Anderson, D.P., De Fabritiis, G.
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:397-403, MAR 2010
abstract,
full text
Yamaguchi, T., Ishikawa, T., Imai, Y., Matsuki, N., Xenos, M., Deng, Y.F., Bluestein, D.
Particle-Based Methods for Multiscale Modeling of Blood Flow in the Circulation and in Devices: Challenges and Future Directions
ANNALS OF BIOMEDICAL ENGINEERING, 38:1225-1235, MAR 2010
abstract,
full text
Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., MacKerell, A.D.
CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:671-690, MAR 2010
abstract,
full text
Feng, J.H., Lucchinetti, E., Enkavi, G., Wang, Y., Gehrig, P., Roschitzki, B., Schaub, M.C., Tajkhorshid, E., Zaugg, K., Zaugg, M.
Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY, 298:C740-C748, MAR 2010
abstract,
full text
Swain, M., Silva, C.G., Loureiro-Ferreira, N., Ostropytskyy, V., Brito, J., Riche, O., Stahl, F., Dubitzky, W., Brito, R.M.M.
P-found: Grid-enabling distributed repositories of protein folding and unfolding simulations for data mining
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING-THEORY METHODS AND APPLICATIONS, 26:424-433, MAR 2010
abstract,
full text
Dendzik, Z., Gorny, K., Kosmider, M., Zurek, S.
CONFINEMENT SIZE EFFECT IN DIPOLAR RELAXATION OF GLYCEROL MOLECULES CLUSTER ENCAPSULATED INSIDE CARBON NANOTUBES - COMPUTER SIMULATION STUDY
REVIEWS ON ADVANCED MATERIALS SCIENCE, 23:42-51, MAR 2010
abstract,
full text
Branschadel, M., Aird, A., Zappe, A., Tietz, C., Krippner-Heidenreich, A., Scheurich, P.
Dual function of cysteine rich domain (CRD) 1 of TNF receptor type 1: Conformational stabilization of CRD2 and control of receptor responsiveness
CELLULAR SIGNALLING, 22:404-414, MAR 2010
abstract,
full text
Qiu, H., Ma, S.J., Shen, R., Guo, W.L.
Dynamic and energetic mechanisms for the distinct permeation rate in AQP1 and AQP0
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:318-326, MAR 2010
abstract,
full text
Ramanathan, A., Agarwal, P.K., Kurnikova, M., Langmead, C.J.
An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL BIOLOGY, 17:309-324, MAR 2010
abstract,
full text
Soriano-Ursua, M.A., Trujillo-Ferrara, J.G., Alvarez-Cedillo, J., Correa-Basurto, J.
Docking studies on a refined human beta(2) adrenoceptor model yield theoretical affinity values in function with experimental values for R-ligands, but not for S-antagonists
JOURNAL OF MOLECULAR MODELING, 16:401-409, MAR 2010
abstract,
full text
Varin, T., Gutierrez-de-Teran, H., Castro, M., Brea, J., Fabis, F., Dauphin, F., Aqvist, J., Lepailleur, A., Perez, P., Burgueno, J., Vela, J.M., Loza, M.I., Rodrigo, J.
Phe369(7.38) at human 5-HT(7) receptors confers interspecies selectivity to antagonists and partial agonists
BRITISH JOURNAL OF PHARMACOLOGY, 159:1069-1081, MAR 2010
abstract,
full text
Gburski, Z., Gorny, K., Raczynski, P.
The impact of a carbon nanotube on the cholesterol domain localized on a protein surface
SOLID STATE COMMUNICATIONS, 150:415-418, MAR 2010
abstract,
full text
Tan, J.J., Cong, X.J., Hu, L.M., Wang, C.X., Jia, L., Liang, X.J.
Therapeutic strategies underpinning the development of novel techniques for the treatment of HIV infection
DRUG DISCOVERY TODAY, 15:186-197, MAR 2010
abstract,
full text
Wang, Y.T., Chan, C.H., Su, Z.Y., Chen, C.L.
Homology modeling, docking, and molecular dynamics reveal HR1039 as a potent inhibitor of 2009 A(H1N1) influenza neuraminidase
BIOPHYSICAL CHEMISTRY, 147:74-80, MAR 2010
abstract,
full text
Diao, J.K., Maniotis, A.J., Folberg, R., Tajkhorshid, E.
Interplay of mechanical and binding properties of Fibronectin type I
THEORETICAL CHEMISTRY ACCOUNTS, 125:397-405, MAR 2010
abstract,
full text
Bahar, I., Lezon, T.R., Bakan, A., Shrivastava, I.H.
Normal Mode Analysis of Biomolecular Structures: Functional Mechanisms of Membrane Proteins
CHEMICAL REVIEWS, 110:1463-1497, MAR 2010
full text
Isea, R., Ramirez, J.L., Hoebeke, J.
Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics
MEMORIAS DO INSTITUTO OSWALDO CRUZ, 105:123-126, MAR 2010
abstract,
full text
Choudhary, O.P., Ujwal, R., Kowallis, W., Coalson, R., Abramson, J., Grabe, M.
The Electrostatics of VDAC: Implications for Selectivity and Gating
JOURNAL OF MOLECULAR BIOLOGY, 396:580-592, FEB 26 2010
abstract,
full text
Artavanis-Tsakonas, K., Weihofen, W.A., Antos, J.M., Coleman, B.I., Comeaux, C.A., Duraisingh, M.T., Gaudet, R., Ploegh, H.L.
Characterization and Structural Studies of the Plasmodium falciparum Ubiquitin and Nedd8 Hydrolase UCHL3
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:6857-6866, FEB 26 2010
abstract,
full text
Barakat, K., Mane, J., Friesen, D., Tuszynski, J.
Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:555-568, FEB 26 2010
abstract,
full text
Harmon, C.W., Grimm, R.L., McIntire, T.M., Peterson, M.D., Njegic, B., Angel, V.M., Alshawa, A., Underwood, J.S., Tobias, D.J., Gerber, R.B., Gordon, M.S., Hemminger, J.C., Nizkorodov, S.A.
Hygroscopic Growth and Deliquescence of NaCl Nanoparticles Mixed with Surfactant SDS
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2435-2449, FEB 25 2010
abstract,
full text
Cheluvaraja, S., Ortoleva, P.
Thermal nanostructure: An order parameter multiscale ensemble approach
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 075102, FEB 21 2010
abstract,
full text
Pfaendtner, J., Lyman, E., Pollard, T.D., Voth, G.A.
Structure and Dynamics of the Actin Filament
JOURNAL OF MOLECULAR BIOLOGY, 396:252-263, FEB 19 2010
abstract,
full text
Kim, H.J., Choi, M.Y., Kim, H.J., Llinas, M.
Conformational Dynamics and Ligand Binding in the Multi-Domain Protein PDC109
PLOS ONE, 5: Art. No. e9180, FEB 18 2010
abstract,
full text
Liu, J., Fan, J.F., Tang, M., Zhou, W.Q.
Molecular Dynamics Simulation for the Structure of the Water Chain in a Transmembrane Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY A, 114:2376-2383, FEB 18 2010
abstract,
full text
Pedersen, U.R., Peters, G.H., Schroder, T.B., Dyre, J.C.
Correlated Volume-Energy Fluctuations of Phospholipid Membranes: A Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2124-2130, FEB 18 2010
abstract,
full text
Furini, S., Domene, C., Cavalcanti, S.
Insights into the Sliding Movement of the Lac Repressor Nonspecifically Bound to DNA
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2238-2245, FEB 18 2010
abstract,
full text
Waegele, M.M., Gai, F.
Computational Modeling of the Nitrile Stretching Vibration of 5-Cyanoindole in Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:781-786, FEB 18 2010
abstract,
full text
Zhang, H., Wang, P., Papangelopoulos, N., Xu, Y., Sette, A., Bourne, P.E., Lund, O., Ponomarenko, J., Nielsen, M., Peters, B.
Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
PLOS ONE, 5: Art. No. e9272, FEB 17 2010
abstract,
full text
Latawiec, D., Herrera, F., Bek, A., Losasso, V., Candotti, M., Benetti, F., Carlino, E., Kranjc, A., Lazzarino, M., Gustincich, S., Carloni, P., Legname, G.
Modulation of Alpha-Synuclein Aggregation by Dopamine Analogs
PLOS ONE, 5: Art. No. e9234, FEB 16 2010
abstract,
full text
Enkavi, G., Tajkhorshid, E.
Simulation of Spontaneous Substrate Binding Revealing the Binding Pathway and Mechanism and Initial Conformational Response of GlpT
BIOCHEMISTRY, 49:1105-1114, FEB 16 2010
abstract,
full text
Hartshorn, C.M., Jewett, C.M., Brozik, J.A.
Molecular Effects of a Nanocrystalline Quartz Support upon Planar Lipid Bilayers
LANGMUIR, 26:2609-2617, FEB 16 2010
abstract,
full text
Wang, Y., Tajkhorshid, E.
Nitric oxide conduction by the brain aquaporin AQP4
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:661-670, FEB 15 2010
abstract,
full text
Zhang, J.L., Hou, R.Z., Li, Z., Zheng, Q.C., Zhang, H.X.
Homology Modeling of Human Extracellular Signal-regulated Kinase 1 and Docking and Reconstitution of Its Inhibitors
ACTA CHIMICA SINICA, 68:222-226, FEB 14 2010
abstract,
full text
Gu, F.F., Jones, M.K., Chen, J.G., Patterson, J.C., Catte, A., Jerome, W.G., Li, L., Segrest, J.P.
Structures of Discoidal High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:4652-4665, FEB 12 2010
abstract,
full text
Freire, M.G., Neves, C.M.S.S., Silva, A.M.S., Santos, L.M.N.B.F., Marrucho, I.M., Rebelo, L.P.N., Shah, J.K., Maginn, E.J., Coutinho, J.A.P.
(1)H NMR and Molecular Dynamics Evidence for an Unexpected Interaction on the Origin of Salting-In/Salting-Out Phenomena
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2004-2014, FEB 11 2010
abstract,
full text
Sterpone, F., Stirnemann, G., Hynes, J.T., Laage, D.
Water Hydrogen-Bond Dynamics around Amino Acids: The Key Role of Hydrophilic Hydrogen-Bond Acceptor Groups
JOURNAL OF PHYSICAL CHEMISTRY B, 114:2083-2089, FEB 11 2010
abstract,
full text
Mori, T., Ishitani, R., Tsukazaki, T., Nureki, O., Sugita, Y.
Molecular Mechanisms Underlying the Early Stage of Protein Translocation through the Sec Translocon
BIOCHEMISTRY, 49:945-950, FEB 9 2010
abstract,
full text
Holst, B., Nygaard, R., Valentin-Hansen, L., Bach, A., Engelstoft, M.S., Petersen, P.S., Frimurer, T.M., Schwartz, T.W.
A Conserved Aromatic Lock for the Tryptophan Rotameric Switch in TM-VI of Seven-transmembrane Receptors
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:3973-3985, FEB 5 2010
abstract,
full text
Guzman, D.L., Randall, A., Baldi, P., Guan, Z.B.
Computational and single-molecule force studies of a macro domain protein reveal a key molecular determinant for mechanical stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:1989-1994, FEB 2 2010
abstract,
full text
Deeb, O., Rosales-Hernandez, M.C., Gomez-Castro, C., Garduno-Juarez, R., Correa-Basurto, J.
Exploration of Human Serum Albumin Binding Sites by Docking and Molecular Dynamics Flexible Ligand-Protein Interactions
BIOPOLYMERS, 93:161-170, FEB 2010
abstract,
full text
Kanth, J.M.P., Vemparala, S., Anishetty, R.
Long-distance correlations in molecular orientations of liquid water and shape-dependent hydrophobic force
PHYSICAL REVIEW E, 81: Art. No. 021201, FEB 2010
abstract,
full text
Stopa, B., Piekarska, B., Konieczny, L., Krol, M., Rybarska, J., Jagusiak, A., Spolnik, P., Roterman, I., Urbanowicz, B., Piwowar, P., Lewinski, K.
Formation of amyloid-like aggregates through the attachment of protein molecules to a Congo red scaffolding framework ordered under the influence of an electric field
CENTRAL EUROPEAN JOURNAL OF CHEMISTRY, 8:41-50, FEB 2010
abstract,
full text
Eichenbaum, K.D., Rodriguez, Y., Mezei, M., Osman, R.
The energetics of the acetylation switch in p53-mediated transcriptional activation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:447-456, FEB 1 2010
abstract,
full text
Devireddy, R.V.
Statistical thermodynamics of biomembranes
CRYOBIOLOGY, 60:80-90, FEB 2010
abstract,
full text
Bjelkmar, P., Larsson, P., Cuendet, M.A., Hess, B., Lindahl, E.
Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:459-466, FEB 2010
abstract,
full text
Postila, P.A., Swanson, G.T., Pentikainen, O.T.
Exploring kainate receptor pharmacology using molecular dynamics simulations
NEUROPHARMACOLOGY, 58:515-527, FEB 2010
abstract,
full text
Abate, C., Elenewski, J., Niso, M., Berardi, F., Colabufo, N.A., Azzariti, A., Perrone, R., Glennon, R.A.
Interaction of the sigma(2) Receptor Ligand PB28 with the Human Nucleosome: Computational and Experimental Probes of Interaction with the H2A/H2B Dimer
CHEMMEDCHEM, 5:268-273, FEB 2010
abstract,
full text
Espinoza-Fonseca, L.M., Wong-Ramirez, C., Trujillo-Ferrara, J.G.
Tyr74 is essential for the formation, stability and function of Plasmodium falciparum triosephosphate isomerase dimer
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 494:46-57, FEB 1 2010
abstract,
full text
Park, J.W., Jo, W.H.
Computational design of novel, high-affinity neuraminidase inhibitors for H5N1 avian influenza virus
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 45:536-541, FEB 2010
abstract,
full text
Gannon, G., Greer, J.C., Larsson, J.A., Thompson, D.
Molecular Dynamics Study of Naturally Occurring Defects in Self-Assembled Monolayer Formation
ACS NANO, 4:921-932, FEB 2010
abstract,
full text
Qin, W., Li, X., Bian, W.W., Fan, X.J., Qi, J.Y.
Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces
BIOMATERIALS, 31:1007-1016, FEB 2010
abstract,
full text
Ko, Y.J., Jo, W.H.
Chloride Ion Conduction Without Water Coordination in the Pore of ClC Protein
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:603-611, FEB 2010
abstract,
full text
Gorantla, S., Avdoshenko, S., Borrnert, F., Bachmatiuk, A., Dimitrakopoulou, M., Schaffel, F., Schonfelder, R., Thomas, J., Gemming, T., Warner, J.H., Cuniberti, G., Eckert, J., Buchner, B., Rummeli, M.
Enhanced pi-pi interactions between a C(60) fullerene and a buckle bend on a double-walled carbon nanotube
NANO RESEARCH, 3:92-97, FEB 2010
abstract,
full text
Tuszynska, I., Bujnicki, J.M.
Predicting Atomic Details of the Unfolding Pathway for YibK, a Knotted Protein from the SPOUT Superfamily
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:511-520, FEB 2010
abstract,
full text
Rodrigues, J.R., Simoes, C.J.V., Silva, C.G., Brito, R.M.M.
Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: Insights from molecular dynamics simulations
PROTEIN SCIENCE, 19:202-219, FEB 2010
abstract,
full text
Costache, A.D., Ghosh, J., Knight, D.D., Kohn, J.
Computational Methods for the Development of Polymeric Biomaterials
ADVANCED ENGINEERING MATERIALS, 12:B3-B17, FEB 2010
abstract,
full text
Salimi, N.L., Ho, B., Agard, D.A.
Unfolding Simulations Reveal the Mechanism of Extreme Unfolding Cooperativity in the Kinetically Stable alpha-Lytic Protease
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000689, FEB 2010
abstract,
full text
Floquet, N., MiKadmi, C., Perahia, D., Gagne, D., Berge, G., Marie, J., Baneres, J.L., Galleyrand, J.C., Fehrentz, J.A., Martinez, J.
Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR)
JOURNAL OF MOLECULAR BIOLOGY, 395:769-784, JAN 29 2010
abstract,
full text
Ovchinnikov, V., Trout, B.L., Karplus, M.
Mechanical Coupling in Myosin V: A Simulation Study
JOURNAL OF MOLECULAR BIOLOGY, 395:815-833, JAN 29 2010
abstract,
full text
Weng, J.W., Fan, K.N., Wang, W.N.
The Conformational Transition Pathway of ATP Binding Cassette Transporter MsbA Revealed by Atomistic Simulations
JOURNAL OF BIOLOGICAL CHEMISTRY, 285: Art. No. 3053, JAN 29 2010
abstract,
full text
Basse, N., Kaar, J.L., Settanni, G., Joerger, A.C., Rutherford, T.J., Fersht, A.R.
Toward the Rational Design of p53-Stabilizing Drugs: Probing the Surface of the Oncogenic Y220C Mutant
CHEMISTRY & BIOLOGY, 17:46-56, JAN 29 2010
abstract,
full text
Kuroda, D.G., Vorobyev, D.Y., Hochstrasser, R.M.
Ultrafast relaxation and 2D IR of the aqueous trifluorocarboxylate ion
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 044501, JAN 28 2010
abstract,
full text
Yang, L., Fishbine, B.H., Migliori, A., Pratt, L.R.
Dielectric saturation of liquid propylene carbonate in electrical energy storage applications
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 044701, JAN 28 2010
abstract,
full text
Maekawa, H., Ge, N.H.
Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1434-1446, JAN 28 2010
abstract,
full text
Martinez, L., Souza, P.C.T., Garcia, W., Batista, F.A.H., Portugal, R.V., Nascimento, A.S., Nakahira, M., Lima, L.M.T.R., Polikarpov, I., Skaf, M.S.
On the Denaturation Mechanisms of the Ligand Binding Domain of Thyroid Hormone Receptors
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1529-1540, JAN 28 2010
abstract,
full text
Grimm, R.L., Tobias, D.J., Hemminger, J.C.
D2O Water Interaction with Textured Carboxylic Acid-Terminated Monolayer Surfaces Characterized by Temperature-Programmed Desorption and Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 114:1570-1579, JAN 28 2010
abstract,
full text
Landstrom, J., Widmalm, G.
Glycan flexibility: insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect
CARBOHYDRATE RESEARCH, 345:330-333, JAN 26 2010
abstract,
full text
Durer, Z.A.O., Diraviyam, K., Sept, D., Kudryashov, D.S., Reisler, E.
F-Actin Structure Destabilization and DNase I Binding Loop Fluctuations Mutational Cross-Linking and Electron Microscopy Analysis of Loop States and Effects on F-Actin
JOURNAL OF MOLECULAR BIOLOGY, 395:544-557, JAN 22 2010
abstract,
full text
Morriss-Andrews, A., Rottler, J., Plotkin, S.S.
A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
JOURNAL OF CHEMICAL PHYSICS, 132: Art. No. 035105, JAN 21 2010
abstract,
full text
Titov, A.V., Wang, B.Y., Sint, K., Kral, P.
Controllable Synthetic Molecular Channels: Biomimetic Ammonia Switch
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1174-1179, JAN 21 2010
abstract,
full text
Sul, S., Feng, Y., Le, U., Tobias, D.J., Ge, N.H.
Interactions of Tyrosine in Leu-Enkephalin at a Membrane-Water Interface: An Ultrafast Two-Dimensional Infrared Study Combined with Density Functional Calculations and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:1180-1190, JAN 21 2010
abstract,
full text
Goldsmith, J., Martens, C.C.
Molecular Dynamics Simulation of Salt Rejection in Model Surface-Modified Nanopores
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:528-535, JAN 21 2010
abstract,
full text
Lupyan, D., Mezei, M., Logothetis, D.E., Osman, R.
A Molecular Dynamics Investigation of Lipid Bilayer Perturbation by PIP(2)
BIOPHYSICAL JOURNAL, 98:240-247, JAN 20 2010
abstract,
full text
Gonnet, P.
Using piecewise polynomials for faster potential function evaluation
JOURNAL OF COMPUTATIONAL PHYSICS, 229:313-324, JAN 20 2010
abstract,
full text
Asthagiri, D., Dixit, P.D., Merchant, S., Paulaitis, M.E., Pratt, L.R., Rempe, S.B., Varma, S.
Ion selectivity from local configurations of ligands in solutions and ion channels
CHEMICAL PHYSICS LETTERS, 485:1-7, JAN 18 2010
abstract,
full text
Armishaw, C.J., Singh, N., Medina-Franco, J.L., Clark, R.J., Scott, K.C.M., Houghten, R.A., Jensen, A.A.
A Synthetic Combinatorial Strategy for Developing alpha-Conotoxin Analogs as Potent alpha(7) Nicotinic Acetylcholine Receptor Antagonists
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:1809-1821, JAN 15 2010
abstract,
full text
Zheng, J., Yu, X., Wang, J.D., Yang, J.C., Wang, Q.M.
Molecular Modeling of Two Distinct Triangular Oligomers in Amyloid beta-protein
JOURNAL OF PHYSICAL CHEMISTRY B, 114:463-470, JAN 14 2010
abstract,
full text
Henin, J., Brannigan, G., Dailey, W.P., Eckenhoff, R., Klein, M.L.
An Atomistic Model for Simulations of the General Anesthetic Isoflurane
JOURNAL OF PHYSICAL CHEMISTRY B, 114:604-612, JAN 14 2010
abstract,
full text
Liu, L.T., Haddadian, E.J., Willenbring, D., Xu, Y., Tang, P.
Higher Susceptibility to Halothane Modulation in Open- Than in Closed-Channel alpha 4 beta 2 nAChR Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:626-632, JAN 14 2010
abstract,
full text
Agarwal, M., Kushwaha, H.R., Chakravarty, C.
Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 114:651-659, JAN 14 2010
abstract,
full text
Golosov, A.A., Warren, J.J., Beese, L.S., Karplus, M.
The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis
STRUCTURE, 18:83-93, JAN 13 2010
abstract,
full text
Krah, A., Pogoryelov, D., Meier, T., Faraldo-Gomez, J.D.
On the Structure of the Proton-Binding Site in the F(o) Rotor of Chloroplast ATP Synthases
JOURNAL OF MOLECULAR BIOLOGY, 395:20-27, JAN 8 2010
abstract,
full text
Sept, D., MacKintosh, F.C.
Microtubule Elasticity: Connecting All-Atom Simulations with Continuum Mechanics
PHYSICAL REVIEW LETTERS, 104: Art. No. 018101, JAN 8 2010
abstract,
full text
Zhang, J.L., Zheng, Q.C., Zhang, H.X.
Unbinding of glucose from human pulmonary surfactant protein D studied by steered molecular dynamics simulations
CHEMICAL PHYSICS LETTERS, 484:338-343, JAN 7 2010
abstract,
full text
Romo, T.D., Grossfield, A., Pitman, M.C.
Concerted Interconversion between Ionic Lock Substates of the beta(2) Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics
BIOPHYSICAL JOURNAL, 98:76-84, JAN 6 2010
abstract,
full text
Rodriguez-Ropero, F., Zanuy, D., Aleman, C.
Electronic characterization of all-thiophene conducting dendrimers: Molecules and assemblies
POLYMER, 51:308-315, JAN 6 2010
abstract,
full text
Tsybovsky, Y., Molday, R.S., Palczewski, K.
The ATP-Binding Cassette Transporter ABCA4: Structural and Functional Properties and Role in Retinal Disease
INFLAMMATION AND RETINAL DISEASE: COMPLEMENT BIOLOGY AND PATHOLOGY, 703:105-125, 2010
abstract,
full text
Nemkevich, A., Burgi, H.B., Spackman, M.A., Corry, B.
Molecular dynamics simulations of structure and dynamics of organic molecular crystals
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:14916-14929, 2010
abstract,
full text
Topal, K.G., Atilgan, C., Demir, A.S., Aviyente, V.
Understanding the Mode of Action of ThDP in Benzoylformate Decarboxylase
BIOPOLYMERS, 93:32-46, JAN 2010
abstract,
full text
Miao, Y.L., Ortoleva, P.J.
Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation
BIOPOLYMERS, 93:61-73, JAN 2010
abstract,
full text
Roy, A., Carpentier, P., Bourgeois, D., Field, M.
Diffusion pathways of oxygen species in the phototoxic fluorescent protein KillerRed
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 9:1342-1350, 2010
abstract,
full text
Sikdar, D., Katti, D.R., Katti, K.S., Bhowmik, R.
TAILORING CRYSTALLINITY AND NANOMECHANICAL PROPERTIES OF CLAY POLYMER NANOCOMPOSITES: A MOLECULAR DYNAMICS STUDY
INTERNATIONAL JOURNAL FOR MULTISCALE COMPUTATIONAL ENGINEERING, 8:561-584, 2010
abstract,
full text
Calderon, C.P., Martinez, J.G., Carroll, R.J., Sorensen, D.C.
P-SPLINES USING DERIVATIVE INFORMATION
MULTISCALE MODELING & SIMULATION, 8:1562-1580, 2010
abstract,
full text
Zhang, L., Berlyand, L., Fedorov, M.V., Owhadi, H.
GLOBAL ENERGY MATCHING METHOD FOR ATOMISTIC-TO-CONTINUUM MODELING OF SELF-ASSEMBLING BIOPOLYMER AGGREGATES
MULTISCALE MODELING & SIMULATION, 8:1958-1980, 2010
abstract,
full text
Emperador, A., Meyer, T., Orozco, M.
Protein flexibility from discrete molecular dynamics simulations using quasi-physical potentials
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:83-94, JAN 2010
abstract,
full text
Fuchs, P.F.J.
Molecular Dynamics of Membrane Peptides and Proteins: Principles and Comparison to Experimental Data
MEMBRANE PROTEIN STRUCTURE DETERMINATION: METHODS AND PROTOCOLS, 654:403-421, 2010
abstract,
full text
Liu, M.S., Todd, B.D., Sadus, R.J.
Allosteric Conformational Transition in Adenylate Kinase: Dynamic Correlations and Implication for Allostery
AUSTRALIAN JOURNAL OF CHEMISTRY, 63:405-412, 2010
abstract,
full text
Langham, A., Kaznessis, Y.N.
Molecular Simulations of Antimicrobial Peptides
ANTIMICROBIAL PEPTIDES: METHODS AND PROTOCOLS, 618:267-285, 2010
abstract,
full text
Wang, H., Laughton, C.A.
Molecular Modelling Methods to Quantitate Drug-DNA Interactions
DRUG-DNA INTERACTION PROTOCOLS, SECOND EDITION, 613:119-131, 2010
abstract,
full text
Henin, J., Fiorin, G., Chipot, C., Klein, M.L.
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:35-47, JAN 2010
abstract,
full text
Zomot, E., Bahar, I.
The sodium/galactose symporter crystal structure is a dynamic, not so occluded state
MOLECULAR BIOSYSTEMS, 6:1040-1046, 2010
abstract,
full text
Halverson, J.D., Maldarelli, C., Couzis, A., Koplik, J.
Atomistic simulations of the wetting behavior of nanodroplets of water on homogeneous and phase separated self-assembled monolayers
SOFT MATTER, 6:1297-1307, 2010
abstract,
full text
Luan, B.Q., Aksimentiev, A.
Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes
SOFT MATTER, 6:243-246, 2010
abstract,
full text
Aguilella-Arzo, M., Calero, C., Faraudo, J.
Simulation of electrokinetics at the nanoscale: inversion of selectivity in a bio-nanochannel
SOFT MATTER, 6:6079-6082, 2010
abstract,
full text
Volkova, E.I., Suyetin, M.V., Vakhrushev, A.V.
Temperature Sensitive Nanocapsule of Complex Structural Form for Methane Storage
NANOSCALE RESEARCH LETTERS, 5:205-210, JAN 2010
abstract,
full text
Kumar, S., Li, M.S.
Biomolecules under mechanical force
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 486:1-74, JAN 2010
abstract,
full text
Zuo, G.C., Shen, R., Ma, S.J., Guo, W.L.
Transport Properties of Single-File Water Molecules inside a Carbon Nanotube Biomimicking Water Channel
ACS NANO, 4:205-210, JAN 2010
abstract,
full text
Titov, A.V., Kral, P., Pearson, R.
Sandwiched Graphene-Membrane Superstructures
ACS NANO, 4:229-234, JAN 2010
abstract,
full text
Al-Hilli, S., Willander, M.
ZNO NANO-STRUCTURES FOR BIOSENSING APPLICATIONS: MOLECULAR DYNAMICS SIMULATIONS
ADVANCES IN NANOTECHNOLOGY, VOLUME 4, 4:123-153, 2010
abstract,
full text
Hodak, M., Bernholc, J.
Insights into prion protein function from atomistic simulations
PRION, 4:13-19, JAN-MAR 2010
abstract,
full text
Xu, L., Zhao, W.J., Wang, X.C.
Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 39:327-336, JAN 2010
abstract,
full text
Xu, J., Ren, Y., Ge, W., Yu, X.A., Yang, X.Z., Li, J.H.
Molecular dynamics simulation of macromolecules using graphics processing unit
MOLECULAR SIMULATION, 36:1131-1140, 2010
abstract,
full text
Peters, B.
Recent advances in transition path sampling: accurate reaction coordinates, likelihood maximisation and diffusive barrier-crossing dynamics
MOLECULAR SIMULATION, 36:1265-1281, 2010
abstract,
full text
Stavrakoudis, A.
Computational modelling and molecular dynamics simulations of a cyclic peptide mimotope of the CD52 antigen complexed with CAMPATH-1H antibody
MOLECULAR SIMULATION, 36:127-137, 2010
abstract,
full text
Roth, M.W., Kaspar, M., Wexler, C., Firlej, L., Kuchta, B.
Molecular dynamics simulations of submonolayer hexane and pentane films on graphite
MOLECULAR SIMULATION, 36:326-333, 2010
abstract,
full text
Duff, N., Peters, B.
Mitosis method for directly calculating the interfacial free energy of nuclei
MOLECULAR SIMULATION, 36:498-504, 2010
abstract,
full text
Voulgarakis, N.K., Satish, S., Chu, J.W.
Modelling the viscoelasticity and thermal fluctuations of fluids at the nanoscale
MOLECULAR SIMULATION, 36:552-559, 2010
abstract,
full text
Bajaj, C., Zhao, W.Q.
FAST MOLECULAR SOLVATION ENERGETICS AND FORCES COMPUTATION
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 31:4524-4552, 2010
abstract,
full text
Malawski, M., Bartynski, T., Bubak, M.
Invocation of operations from script-based Grid applications
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING AND ESCIENCE, 26:138-146, JAN 2010
abstract,
full text
Coveney, P.V., Giupponi, G., Jha, S., Manos, S., MacLaren, J., Pickles, S.M., Saksena, R.S., Soddemann, T., Suter, J.L., Thyveetil, M., Zasada, S.J.
Large scale computational science on federated international grids: The role of switched optical networks
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING-THEORY METHODS AND APPLICATIONS, 26:99-110, JAN 2010
abstract,
full text
Dubey, D.K., Tomar, V.
Effect of changes in tropocollagen residue sequence and hydroxyapatite mineral texture on the strength of ideal nanoscale tropocollagen-hydroxyapatite biomaterials
JOURNAL OF MATERIALS SCIENCE-MATERIALS IN MEDICINE, 21:161-171, JAN 2010
abstract,
full text
Schlick, T.
Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd Edition
MOLECULAR MODELING AND SIMULATION: AN INTERDISCIPLINARY GUIDE, 2ND EDITION, 21:1-723, 2010
full text
Norata, G.D., Garlaschelli, K., Grigore, L., Raselli, S., Tramontana, S., Meneghetti, F., Artali, R., Noto, D., Cefalu, A.B., Buccianti, G., Averna, M., Catapano, A.L.
Effects of PCSK9 variants on common carotid artery intima media thickness and relation to ApoE alleles
ATHEROSCLEROSIS, 208:177-182, JAN 2010
abstract,
full text
Yin, Y., Arkhipov, A., Schulten, K.
Multi-scale Simulations of Membrane Sculpting by N-BAR Domains
MOLECULAR SIMULATIONS AND BIOMEMBRANES: FROM BIOPHYSICS TO FUNCTION, 20:146-176, 2010
full text,
TCBG publications
Wen, P.C., Huang, Z.J., Enkavi, G., Wang, Y., Gumbart, J., Tajkhorshid, E.
Molecular Mechanisms of Active Transport Across the Cellular Membrane
MOLECULAR SIMULATIONS AND BIOMEMBRANES: FROM BIOPHYSICS TO FUNCTION, 20:248-286, 2010
full text
Aksimentiev, A.
Deciphering ionic current signatures of DNA transport through a nanopore
NANOSCALE, 2:468-483, 2010
abstract,
full text
Bellesia, G., Jewett, A.I., Shea, J.E.
Sequence periodicity and secondary structure propensity in model proteins
PROTEIN SCIENCE, 19:141-154, JAN 2010
abstract,
full text
Vistoli, G., Pedretti, A., Mazzolari, A., Testa, B.
In silico prediction of human carboxylesterase-1 (hCES1) metabolism combining docking analyses and MD simulations
BIOORGANIC & MEDICINAL CHEMISTRY, 18:320-329, JAN 1 2010
abstract,
full text
Karachevtsev, V.A., Karachevtsev, M.V., Leontiev, V.S., Lytvyn, O.S., Bogorosh, A.T.
Nanohybrid Structures Formed by Carbon Nanotubes with Long Polynucleotide
FULLERENES NANOTUBES AND CARBON NANOSTRUCTURES, 18:531-537, 2010
abstract,
full text
Stirnemann, G., Rossky, P.J., Hynes, J.T., Laage, D.
Water reorientation, hydrogen-bond dynamics and 2D-IR spectroscopy next to an extended hydrophobic surface
FARADAY DISCUSSIONS, 146:263-281, 2010
abstract,
full text
Li, S.J., Bai, B.F.
Multi-Vapor Embryos Nucleation Process and Spinodal Analyses of Expandable Superheated Water System
NANOSCALE AND MICROSCALE THERMOPHYSICAL ENGINEERING, 14:174-185, 2010
abstract,
full text
Mernea, M., Calborean, O., Dinca, M.P., Leca, A., Apostol, D., Dascalu, T., Mihailescu, D.
The simulation of bovine serum albumin vibration spectrum in THz domain
JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS, 12:135-140, JAN 2010
abstract,
full text
Willenbring, D., Xu, Y., Tang, P.
The role of structured water in mediating general anesthetic action on alpha 4 beta 2 nAChR
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:10263-10269, 2010
abstract,
full text
Yamamoto, T., Ohnishi, S.
Nano bubbles in liquid of a noble-gas mixture
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:1033-1037, 2010
abstract,
full text
Schmeer, G., Maurer, A.
Development of thermodynamic properties of electrolyte solutions with the help of RISM-calculations at the Born-Oppenheimer level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:2407-2417, 2010
abstract,
full text
Abou Hamad, I., Novotny, M.A., Wipf, D.O., Rikvold, P.A.
A new battery-charging method suggested by molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:2740-2743, 2010
abstract,
full text
Batista, P.R., Robert, C.H., Marechal, J.D., Ben Hamida-Rebai, M., Pascutti, P.G., Bisch, P.M., Perahia, D.
Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:2850-2859, 2010
abstract,
full text
Liang, H.Q., Li, Z.Y., Yang, J.L.
Single-stranded DNA adsorption on chiral molecule coated Au surface: a molecular dynamics study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:4431-4434, 2010
abstract,
full text
Denysenkov, V., Prandolini, M.J., Gafurov, M., Sezer, D., Endeward, B., Prisner, T.F.
Liquid state DNP using a 260 GHz high power gyrotron
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:5786-5790, 2010
abstract,
full text
Chen, L.Y., Bastien, D.A., Espejel, H.E.
Determination of equilibrium free energy from nonequilibrium work measurements
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:6579-6582, 2010
abstract,
full text
Liu, Y.C., Moore, J.D., Roussel, T.J., Gubbins, K.E.
Dual diffusion mechanism of argon confined in single-walled carbon nanotube bundles
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:6632-6640, 2010
abstract,
full text
Broemstrup, T., Reuter, N.
How does Proteinase 3 interact with lipid bilayers?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:7487-7496, 2010
abstract,
full text
Yamamoto, T., Uda, T., Yamasaki, T., Ohno, T.
Hydration effect on the optical property of a DNA fiber: First-principles and molecular dynamics studies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:9300-9311, 2010
abstract,
full text
Yakubovich, A.V., Solov'yov, A.V., Greiner, W.
Conformational Changes in Polypeptides and Proteins
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 110:257-269, JAN 2010
abstract,
full text
Dieterich, J.M., Hartke, B.
OGOLEM: Global cluster structure optimisation for arbitrary mixtures of flexible molecules. A multiscaling, object-oriented approach
MOLECULAR PHYSICS, 108:279-291, 2010
abstract,
full text
Abroshan, H., Akbarzadeh, H., Taherkhani, F., Parsafar, G.
Effect of a monomeric sequence on the structure of hydrated Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamic study
MOLECULAR PHYSICS, 108:3393-3404, 2010
abstract,
full text
Amaro, R.E., Li, W.W.
Emerging Methods for Ensemble-Based Virtual Screening
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 10:3-13, JAN 2010
abstract,
full text
Luo, Y., Roux, B.
Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 1:183-189, JAN 2010
abstract,
full text
Schneider, O., Sternberg, U., Vondrous, A.
PARALLEL MOLECULAR DYNAMICS SIMULATION USING A HYBRID FORCE FIELD WITH QUANTUM CHEMICAL CHARGE CALCULATIONS
CLUSTER COMPUTING AND MULTI-HOP NETWORK RESEARCH, , 2010
abstract,
full text
Buehler, M.J.
Computational Scale Linking in Biological Protein Materials
COMPUTATIONAL MODELING IN BIOMECHANICS, DOI 10.1007/978-90-481-3575-2_17, 2010
abstract,
full text
Vohra, S., Hall, B.A., Holdbrook, D.A., Khalid, S., Biggin, P.C.
Bookshelf: a simple curation system for the storage of biomolecular simulation data
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, Art. No. baq033, 2010
abstract,
full text
Glowacki, D.R., Paci, E., Shalashilin, D.V.
Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems
JOURNAL OF PHYSICAL CHEMISTRY B, 113:16603-16611, DEC 31 2009
abstract,
full text
Chen, C., Li, W.Z., Song, Y.C., Yang, J.
A molecular dynamics study of cryoprotective agent - Water-sodium chloride ternary solutions
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 916:37-46, DEC 30 2009
abstract,
full text
Hamaneh, M.B., Buck, M.
Refinement of the Primary Hydration Shell Model for Molecular Dynamics Simulations of Large Proteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:2635-2644, DEC 30 2009
abstract,
full text
Puklin-Faucher, E., Vogel, V.
Integrin Activation Dynamics between the RGD-binding Site and the Headpiece Hinge
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:36557-36568, DEC 25 2009
abstract,
full text
Yeung, N., Lin, Y.W., Gao, Y.G., Zhao, X., Russell, B.S., Lei, L.Y., Miner, K.D., Robinson, H., Lu, Y.
Rational design of a structural and functional nitric oxide reductase
NATURE, 462:1079-U144, DEC 24 2009
abstract,
full text
Yang, L.J., Zou, J., Xie, H.Z., Li, L.L., Wei, Y.Q., Yang, S.Y.
Steered Molecular Dynamics Simulations Reveal the Likelier Dissociation Pathway of Imatinib from Its Targeting Kinases c-Kit and Abl
PLOS ONE, 4: Art. No. e8470, DEC 24 2009
abstract,
full text
Voulgarakis, N.K., Satish, S., Chu, J.W.
Modeling the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics and molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 234115, DEC 21 2009
abstract,
full text
Anisimov, V.M., Bugaenko, V.L., Cavasotto, C.N.
Quantum Mechanical Dynamics of Charge Transfer in Ubiquitin in Aqueous Solution
CHEMPHYSCHEM, 10:3194-3196, DEC 21 2009
full text
Heyes, D.J., Levy, C., Lafite, P., Roberts, I.S., Goldrick, M., Stachulski, A.V., Rossington, S.B., Stanford, D., Rigby, S.E.J., Scrutton, N.S., Leys, D.
Structure-based Mechanism of CMP-2-keto-3-deoxymanno-octulonic Acid Synthetase CONVERGENT EVOLUTION OF A SUGAR-ACTIVATING ENZYME WITH DNA/RNA POLYMERASES
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:35514-35523, DEC 18 2009
abstract,
full text
McLean, K.J., Lafite, P., Levy, C., Cheesman, M.R., Mast, N., Pikuleva, I.A., Leys, D., Munro, A.W.
The Structure of Mycobacterium tuberculosis CYP125 MOLECULAR BASIS FOR CHOLESTEROL BINDING IN A P450 NEEDED FOR HOST INFECTION
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:35524-35533, DEC 18 2009
abstract,
full text
Chen, H.S., Kolahi, K.S., Mofrad, M.R.K.
Phosphorylation Facilitates the Integrin Binding of Filamin under Force
BIOPHYSICAL JOURNAL, 97:3095-3104, DEC 16 2009
abstract,
full text
Wang, S.J., Xin, F.X., Liu, X.Y., Wang, Y.X., An, Z.Y., Qi, Q.S., Wang, P.G.
N-Terminal Deletion of Peptide: N-Glycanase Results in Enhanced Deglycosylation Activity
PLOS ONE, 4: Art. No. e8335, DEC 16 2009
abstract,
full text
Al-Hilli, S., Willander, M.
Ionic current flow through ZnO nanotubes
NANOTECHNOLOGY, 20: Art. No. 505504, DEC 16 2009
abstract,
full text
Vukovic, L., Kral, P.
Coulombically Driven Rolling of Nanorods on Water
PHYSICAL REVIEW LETTERS, 103: Art. No. 246103, DEC 11 2009
abstract,
full text
Taylor, D.J., Devkota, B., Huang, A.D., Topf, M., Narayanan, E., Sali, A., Harvey, S.C., Frank, J.
Comprehensive Molecular Structure of the Eukaryotic Ribosome
STRUCTURE, 17:1591-1604, DEC 9 2009
abstract,
full text
Khavrutskii, I.V., Grant, B., Taylor, S.S., McCammon, J.A.
A Transition Path Ensemble Study Reveals a Linchpin Role for Mg(2+) during Rate-Limiting ADP Release from Protein Kinase A
BIOCHEMISTRY, 48:11532-11545, DEC 8 2009
abstract,
full text
Martinez, L., Nascimento, A.S., Nunes, F.M., Phillips, K., Aparicio, R., Dias, S.M.G., Figueira, A.C.M., Lin, J.H., Nguyen, P., Apriletti, J.W., Neves, F.A.R., Baxter, J.D., Webb, P., Skaf, M.S., Polikarpov, I.
Gaining ligand selectivity in thyroid hormone receptors via entropy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:20717-20722, DEC 8 2009
abstract,
full text
Kouza, M., Hu, C.K., Zung, H., Li, M.S.
Protein mechanical unfolding: Importance of non-native interactions
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 215103, DEC 7 2009
abstract,
full text
Hilder, T.A., Gordon, D., Chung, S.H.
Boron Nitride Nanotubes Selectively Permeable to Cations or Anions
SMALL, 5:2870-2875, DEC 4 2009
abstract,
full text
Neumann, A., Czub, J., Baginski, M.
On the Possibility of the Amphotericin B-Sterol Complex Formation in Cholesterol- and Ergosterol-Containing Lipid Bilayers: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 113:15875-15885, DEC 3 2009
abstract,
full text
Daigle, R., Rousseau, J.A., Guertin, M., Lague, P.
Theoretical Investigations of Nitric Oxide Channeling in Mycobacterium tuberculosis Truncated Hemoglobin N
BIOPHYSICAL JOURNAL, 97:2967-2977, DEC 2 2009
abstract,
full text
Chandler, D.E., Gumbart, J., Stack, J.D., Chipot, C., Schulten, K.
Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s
BIOPHYSICAL JOURNAL, 97:2978-2984, DEC 2 2009
abstract,
full text,
TCBG publications
Jang, H., Arce, F.T., Capone, R., Ramachandran, S., Lal, R., Nussinov, R.
Misfolded Amyloid Ion Channels Present Mobile beta-Sheet Subunits in Contrast to Conventional Ion Channels
BIOPHYSICAL JOURNAL, 97:3029-3037, DEC 2 2009
abstract,
full text
Hsin, J., Chipot, C., Schulten, K.
A Glycophorin A-Like Framework for the Dimerization of Photosynthetic Core Complexes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:17096-+, DEC 2 2009
abstract,
full text,
TCBG publications
Newhouse, E.I., Xu, D., Markwick, P.R.L., Amaro, R.E., Pao, H.C., Wu, K.J., Alam, M., McCammon, J.A., Li, W.W.
Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine, and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:17430-17442, DEC 2 2009
abstract,
full text
Rezende, M.C., Onate, R., Nunez, G., Dominguez, M., Mascayano, C.
Lipophilic contributions to the solvatochromism of analogous betaines
DYES AND PIGMENTS, 83:391-395, DEC 2009
abstract,
full text
Liu, L., Koharudin, L.M.I., Gronenborn, A.M., Bahar, I.
A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR, X-ray, and computations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:927-939, DEC 2009
abstract,
full text
Martinez, L., Laine, E., Malliavin, T.E., Nilges, M., Blondel, A.
ATP conformations and ion binding modes in the active site of anthrax edema factor: A computational analysis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:971-983, DEC 2009
abstract,
full text
Asses, Y., Leroux, V., Tairi-Kellou, S., Dono, R., Maina, F., Maigret, B.
Analysis of c-Met Kinase Domain Complexes: A New Specific Catalytic Site Receptor Model for Defining Binding Modes of ATP-Competitive Ligands
CHEMICAL BIOLOGY & DRUG DESIGN, 74:560-570, DEC 2009
abstract,
full text
Paliy, M., Melnik, R., Shapiro, B.A.
Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization
PHYSICAL BIOLOGY, 6: Art. No. 046003, DEC 2009
abstract,
full text
Genchev, G.Z., Kallberg, M., Gursoy, G., Mittal, A., Dubey, L., Perisic, O., Feng, G., Langlois, R., Lu, H.
Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics
CELL BIOCHEMISTRY AND BIOPHYSICS, 55:141-152, DEC 2009
abstract,
full text
Fadouloglou, V.E., Stavrakoudis, A., Bouriotis, V., Kokkinidis, M., Glykos, N.M.
Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:3299-3311, DEC 2009
abstract,
full text
Park, J.W., Jo, W.H.
Infiltration of Water Molecules into the Oseltamivir-Binding Site of H274Y Neuraminidase Mutant Causes Resistance to Oseltamivir
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:2735-2741, DEC 2009
abstract,
full text
Jones, M.K., Catte, A., Li, L., Segrest, J.P.
Dynamics of Activation of Lecithin: Cholesterol Acyltransferase by Apolipoprotein A-I
BIOCHEMISTRY, 48:11196-11210, DEC 1 2009
abstract,
full text
Garzon, D., Bond, P.J., Faraldo-Gomez, J.D.
Predicted structural basis for CD1c presentation of mycobacterial branched polyketides and long lipopeptide antigens
MOLECULAR IMMUNOLOGY, 47:253-260, DEC 2009
abstract,
full text
Chae, K., Kieslich, C.A., Morikis, D., Kim, S.C., Lord, E.M.
A Gain-of-Function Mutation of Arabidopsis Lipid Transfer Protein 5 Disturbs Pollen Tube Tip Growth and Fertilization
PLANT CELL, 21:3902-3914, DEC 2009
abstract,
full text
Zasada, S.J., Coveney, P.V.
Virtualizing access to scientific applications with the Application Hosting Environment
COMPUTER PHYSICS COMMUNICATIONS, 180:2513-2525, DEC 2009
abstract,
full text
Hu, K.K., Tanaka, T.
S(1) site residues of Lactococcus lactis prolidase affect substrate specificity and allosteric behaviour
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1794:1715-1724, DEC 2009
abstract,
full text
Stavrakoudis, A.
Conformational Studies of the 313-320 and 313-332 Peptide Fragments Derived from the alpha(IIb) Subunit of Integrin Receptor with Molecular Dynamics Simulations
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 15:263-272, DEC 2009
abstract,
full text
Khafizov, K.
GoLoco motif proteins binding to G alpha(i1): insights from molecular simulations
JOURNAL OF MOLECULAR MODELING, 15:1491-1499, DEC 2009
abstract,
full text
Arinaminpathy, Y., Khurana, E., Engelman, D.M., Gerstein, M.B.
Computational analysis of membrane proteins: the largest class of drug targets
DRUG DISCOVERY TODAY, 14:1130-1135, DEC 2009
abstract,
full text
Crowley, M.F., Williamson, M.J., Walker, R.C.
CHAMBER: Comprehensive Support for CHARMM Force Fields Within the AMBER Software
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 109:3767-3772, DEC 2009
abstract,
full text
Vargas, D.A., Zaman, M.H.
Serine at Phosphorylation Site Regulates the Mechanical and Structural Behavior of Fascin
CELLULAR AND MOLECULAR BIOENGINEERING, 2:504-513, DEC 2009
abstract,
full text
Delalande, O., Ferey, N., Grasseau, G., Baaden, M.
Complex Molecular Assemblies at Hand via Interactive Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:2375-2387, NOV 30 2009
abstract,
full text
Li, B., Zhu, H.M., Wang, Y., Zhao, B., Li, L., Shen, J.
Molecular Dynamics Simulation of the Effect of Different Materials Surface on Natural Behavior of Nine Peptides of Coagulation Factor XII
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 30:23-28, NOV 30 2009
abstract,
full text
Krepkiy, D., Mihailescu, M., Freites, J.A., Schow, E.V., Worcester, D.L., Gawrisch, K., Tobias, D.J., White, S.H., Swartz, K.J.
Structure and hydration of membranes embedded with voltage-sensing domains
NATURE, 462:473-U168, NOV 26 2009
abstract,
full text
Vagenende, V., Yap, M.G.S., Trout, B.L.
Mechanisms of Protein Stabilization and Prevention of Protein Aggregation by Glycerol
BIOCHEMISTRY, 48:11084-11096, NOV 24 2009
abstract,
full text
Arkhipov, A., Yin, Y., Schulten, K.
Membrane-Bending Mechanism of Amphiphysin N-BAR Domains
BIOPHYSICAL JOURNAL, 97:2727-2735, NOV 18 2009
abstract,
full text,
TCBG publications
Cui, H.S., Ayton, G.S., Voth, G.A.
Membrane Binding by the Endophilin N-BAR Domain
BIOPHYSICAL JOURNAL, 97:2746-2753, NOV 18 2009
abstract,
full text
Krammer, E.M., Ravaud, S., Dehez, F., Frelet-Barrand, A., Pebay-Peyroula, E., Chipot, C.
High-Chloride Concentrations Abolish the Binding of Adenine Nucleotides in the Mitochondrial ADP/ATP Carrier Family
BIOPHYSICAL JOURNAL, 97:L25-L27, NOV 18 2009
abstract,
full text
Halverson, J.D., Maldarelli, C., Couzis, A., Koplik, J.
Wetting of hydrophobic substrates by nanodroplets of aqueous trisiloxane and alkyl polyethoxylate surfactant solutions
CHEMICAL ENGINEERING SCIENCE, 64:4657-4667, NOV 16 2009
abstract,
full text
Carotti, A., Macchiarulo, A., Giacche, N., Pellicciari, R.
Targeting the conformational transitions of MDM2 and MDMX: Insights into key residues affecting p53 recognition
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:524-535, NOV 15 2009
abstract,
full text
Tournassat, C., Chapron, Y., Leroy, P., Bizi, M., Boulahya, F.
Comparison of molecular dynamics simulations with triple layer and modified Gouy-Chapman models in a 0.1 M NaCl-montmorillonite system
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 339:533-541, NOV 15 2009
abstract,
full text
Gorecki, A., Szypowski, M., Dlugosz, M., Trylska, J.
RedMD-Reduced Molecular Dynamics Package
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:2364-2373, NOV 15 2009
abstract,
full text
Gumbart, J., Wiener, M.C., Tajkhorshid, E.
Coupling of Calcium and Substrate Binding through Loop Alignment in the Outer-Membrane Transporter BtuB
JOURNAL OF MOLECULAR BIOLOGY, 393:1129-1142, NOV 13 2009
abstract,
full text
Rodriguez-Ropero, F., Canales, M., Zanuy, D., Zhang, A., Schluter, D., Aleman, C.
Helical Dendronized Polymers with Chiral Second-Generation Dendrons: Atomistic View and Driving Forces for Structure Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 113:14868-14876, NOV 12 2009
abstract,
full text
Gumbart, J., Trabuco, L.G., Schreiner, E., Villa, E., Schulten, K.
Regulation of the Protein-Conducting Channel by a Bound Ribosome
STRUCTURE, 17:1453-1464, NOV 11 2009
abstract,
full text,
TCBG publications
Knapp, J.E., Pahl, R., Cohen, J., Nichols, J.C., Schulten, K., Gibson, Q.H., Srajer, V., Royer, W.E.
Ligand Migration and Cavities within Scapharca Dimeric Hbl: Studies by Time-Resolved Crystallography, Xe Binding, and Computational Analysis
STRUCTURE, 17:1494-1504, NOV 11 2009
abstract,
full text,
TCBG publications
Ziemys, A., Ferrari, M., Cavasotto, C.N.
Molecular Modeling of Glucose Diffusivity in Silica Nanochannels
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 9:6349-6359, NOV 2009
abstract,
full text
Patra, N., Wang, B.Y., Kral, P.
Nanodroplet Activated and Guided Folding of Graphene Nanostructures
NANO LETTERS, 9:3766-3771, NOV 2009
abstract,
full text
Sharma, G., Rege, K., Budil, D.E., Yarmush, M., Mavroidis, C.
Biological Force Measurement in a Protein-Based Nanoactuator
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 8:684-691, NOV 2009
abstract,
full text
Palmai, Z., Chaloin, L., Lionne, C., Fidy, J., Perahia, D., Balog, E.
Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 77:319-329, NOV 1 2009
abstract,
full text
Li, S.J., Bai, B.F.
Multi-vapor embryos nucleation process and spinodal temperature analysis of expandable superheated water system
ACTA PHYSICA SINICA, 58:7596-7602, NOV 2009
abstract,
full text
Suyetin, M.V., Vakhrushev, A.V.
Nanocapsule for Safe and Effective Methane Storage
NANOSCALE RESEARCH LETTERS, 4:1267-1270, NOV 2009
abstract,
full text
Hong, S.D., Ha, M.Y., Balachandar, S.
Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 339:187-195, NOV 1 2009
abstract,
full text
Sekhar, P.N., Reddy, L.A., De Maeyer, M., Kumar, K.P., Srinivasulu, Y.S., Sunitha, M.S.L., Sphoorthi, I.S.N., Jayasree, G., Rao, A.M., Kothekar, V.S., Narayana, P.V.B.S., Kishor, P.B.K.
Genome wide analysis and comparative docking studies of new diaryl furan derivatives against human cyclooxygenase-2, lipoxygenase, thromboxane synthase and prostacyclin synthase enzymes involved in inflammatory pathway
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:313-329, NOV 2009
abstract,
full text
Lin, J.P., Buettner, R., Yuan, Y.C., Yip, R., Horne, D., Jove, R., Vaidehi, N.
Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 28:347-356, NOV 2009
abstract,
full text
Wang, S.C., Yang, S., Yin, Y.J., Xi, J.H., Li, S.Y., Hao, D.Y.
Molecular dynamics simulations reveal the disparity in specific recognition of GCC-box by AtERFs transcription factors super family in Arabidopsis
JOURNAL OF MOLECULAR RECOGNITION, 22:474-479, NOV-DEC 2009
abstract,
full text
Moretti, S., De Falco, V., Tamburrino, A., Barbi, F., Tavano, M., Avenia, N., Santeusanio, F., Santoro, M., Macchiarulo, A., Puxeddu, E.
Insights into the molecular function of the inactivating mutations of B-Raf involving the DFG motif
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH, 1793:1634-1645, NOV 2009
abstract,
full text
Pickholz, M., Fraceto, L.F., de Paula, E.
Preferential location of prilocaine and etidocaine in phospholipid bilayers: A molecular dynamics study
SYNTHETIC METALS, 159:2157-2158, NOV 2009
abstract,
full text
Krone, M., Bidmon, K., Ertl, T.
Interactive Visualization of Molecular Surface Dynamics
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 15:1391-1398, NOV-DEC 2009
abstract,
full text
Pentikainen, U., Ylanne, J.
The Regulation Mechanism for the Auto-Inhibition of Binding of Human Filamin A to Integrin
JOURNAL OF MOLECULAR BIOLOGY, 393:644-657, OCT 30 2009
abstract,
full text
Hajjar, E., Dejaegere, A., Reuter, N.
Challenges in pK(a) Predictions for Proteins: The case of Asp213 in Human Proteinase 3
JOURNAL OF PHYSICAL CHEMISTRY A, 113:11783-11792, OCT 29 2009
abstract,
full text
Olivier, Y., Muccioli, L., Lemaur, V., Geerts, Y.H., Zannoni, C., Cornil, J.
Theoretical Characterization of the Structural and Hole Transport Dynamics in Liquid-Crystalline Phthalocyanine Stacks
JOURNAL OF PHYSICAL CHEMISTRY B, 113:14102-14111, OCT 29 2009
abstract,
full text
Mori, T., Okamoto, Y.
Folding simulations of gramicidin A into the beta-helix conformations: Simulated annealing molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 165103, OCT 28 2009
abstract,
full text
Xu, W., Cai, P., Yan, M., Xu, L., Ouyang, P.K.
Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase
CHINESE JOURNAL OF CHEMICAL PHYSICS, 22:467-472, OCT 27 2009
abstract,
full text
Lafleur, K., Huang, D.Z., Zhou, T., Caflisch, A., Nevado, C.
Structure-Based Optimization of Potent and Selective Inhibitors of the Tyrosine Kinase Erythropoietin Producing Human Hepatocellular Carcinoma Receptor B4 (EphB4)
JOURNAL OF MEDICINAL CHEMISTRY, 52:6433-6446, OCT 22 2009
abstract,
full text
Pantano, D.A., Klein, M.L.
Characterization of Membrane-Protein Interactions for the Leucine Transporter from Aquifex aeolicus by Molecular Dynamics Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13715-13722, OCT 22 2009
abstract,
full text
Legge, F.S., Binger, K.J., Griffin, M.D.W., Howlett, G.J., Scanlon, D., Treutlein, H., Yarovsky, I.
Effect of Oxidation and Mutation on the Conformational Dynamics and Fibril Assembly of Amyloidogenic Peptides Derived from Apolipoprotein C-II
JOURNAL OF PHYSICAL CHEMISTRY B, 113:14006-14014, OCT 22 2009
abstract,
full text
Freddolino, P.L., Schulten, K.
Common Structural Transitions in Explicit-Solvent Simulations of Villin Headpiece Folding
BIOPHYSICAL JOURNAL, 97:2338-2347, OCT 21 2009
abstract,
full text,
TCBG publications
Dendzik, Z., Gorny, K., Gburski, Z.
Cooperative dipolar relaxation of a glycerol molecular cluster in nanoscale confinement-a computer simulation study
JOURNAL OF PHYSICS-CONDENSED MATTER, 21: Art. No. 425101, OCT 21 2009
abstract,
full text
Wang, T.J., Hoy, J.A., Lamm, M.H., Nilsen-Hamilton, M.
Computational and Experimental Analyses Converge to Reveal a Coherent Yet Malleable Aptamer Structure That Controls Chemical Reactivity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:14747-14755, OCT 21 2009
abstract,
full text
Mustata, M., Capone, R., Jang, H., Arce, F.T., Ramachandran, S., Lal, R., Nussinov, R.
K3 Fragment of Amyloidogenic beta(2)-Microglobulin Forms Ion Channels: Implication for Dialysis Related Amyloidosis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:14938-14945, OCT 21 2009
abstract,
full text
Materese, C.K., Savelyev, A., Papoian, G.A.
Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:15005-15013, OCT 21 2009
abstract,
full text
Tarrago, T., Martin-Benito, J., Sabido, E., Claasen, B., Madurga, S., Gairi, M., Valpuesta, J.M., Giralt, E.
A new side opening on prolyl oligopeptidase revealed by electron microscopy
FEBS LETTERS, 583:3344-3348, OCT 20 2009
abstract,
full text
Fatmi, M.Q., Ai, R., Chang, C.E.A.
Synergistic Regulation and Ligand-Induced Conformational Changes of Tryptophan Synthase
BIOCHEMISTRY, 48:9921-9931, OCT 20 2009
abstract,
full text
Dixit, A., Yi, L., Gowthaman, R., Torkamani, A., Schork, N.J., Verkhivker, G.M.
Sequence and Structure Signatures of Cancer Mutation Hotspots in Protein Kinases
PLOS ONE, 4: Art. No. e7485, OCT 16 2009
abstract,
full text
Xu, L., Liu, X., Zhao, W.J., Wang, X.C.
Locally Enhanced Sampling Study of Dioxygen Diffusion Pathways in Homoprotocatechuate 2,3-Dioxygenase
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13596-13603, OCT 15 2009
abstract,
full text
Lee, E.H., Hsin, J., Sotomayor, M., Comellas, G., Schulten, K.
Discovery Through the Computational Microscope
STRUCTURE, 17:1295-1306, OCT 14 2009
abstract,
full text,
TCBG publications
Zhong, W.Y., Guo, W.L.
Mixed modes in opening of KcsA potassium channel from a targeted molecular dynamics simulation
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 388:86-90, OCT 9 2009
abstract,
full text
Lvov, A., Greitzer, D., Berlin, S., Chikvashvili, D., Tsuk, S., Lotan, I., Michaelevski, I.
Rearrangements in the Relative Orientation of Cytoplasmic Domains Induced by a Membrane-anchored Protein Mediate Modulations in Kv Channel Gating
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:28276-28291, OCT 9 2009
abstract,
full text
Cavallari, M., Garbesi, A., Di Felice, R.
Porphyrin Intercalation in G4-DNA Quadruplexes by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13152-13160, OCT 8 2009
abstract,
full text
Pezeshki, S., Chimerel, C., Bessonov, A.N., Winterhalter, M., Kleinekathofer, U.
Understanding Ion Conductance on a Molecular Level: An All-Atom Modeling of the Bacterial Porin OmpF
BIOPHYSICAL JOURNAL, 97:1898-1906, OCT 7 2009
abstract,
full text
Krems, M., Zwolak, M., Pershin, Y.V., Di Ventra, M.
Effect of Noise on DNA Sequencing via Transverse Electronic Transport
BIOPHYSICAL JOURNAL, 97:1990-1996, OCT 7 2009
abstract,
full text
Arkhipov, A., Roos, W.H., Wuite, G.J.L., Schulten, K.
Elucidating the Mechanism behind Irreversible Deformation of Viral Capsids
BIOPHYSICAL JOURNAL, 97:2061-2069, OCT 7 2009
abstract,
full text,
TCBG publications
Okan, O.B., Atilgan, A.R., Atilgan, C.
Nanosecond Motions in Proteins Impose Bounds on the Timescale Distributions of Local Dynamics
BIOPHYSICAL JOURNAL, 97:2080-2088, OCT 7 2009
abstract,
full text
Fogolari, F., Haridas, H., Corazza, A., Viglino, P., Cora, D., Caselle, M., Esposito, G., Xodo, L.E.
Molecular models for intrastrand DNA G-quadruplexes
BMC STRUCTURAL BIOLOGY, 9: Art. No. 64, OCT 7 2009
abstract,
full text
Cho, H.M., Chu, J.W.
Inversion of radial distribution functions to pair forces by solving the Yvon-Born-Green equation iteratively
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 134107, OCT 7 2009
abstract,
full text
Gordon, D., Krishnamurthy, V., Chung, S.H.
Generalized Langevin models of molecular dynamics simulations with applications to ion channels
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 134102, OCT 7 2009
abstract,
full text
Shih, A.Y., Sligar, S.G., Schulten, K.
Maturation of high-density lipoproteins
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 6:863-871, OCT 6 2009
abstract,
full text,
TCBG publications
Hilder, T.A., Gordon, D., Chung, S.H.
Salt Rejection and Water Transport Through Boron Nitride Nanotubes
SMALL, 5:2183-2190, OCT 2 2009
abstract,
full text
Metcalf, D.G., Kulp, D.W., Bennett, J.S., DeGrado, W.F.
Multiple Approaches Converge on the Structure of the Integrin alpha IIb/beta 3 Transmembrane Heterodimer
JOURNAL OF MOLECULAR BIOLOGY, 392:1087-1101, OCT 2 2009
abstract,
full text
Trivedi, M., Davis, R.A., Shabaik, Y., Roy, A., Verkhivker, G., Laurence, J.S., Middaugh, C.R., Siahaan, T.J.
The Role of Covalent Dimerization on the Physical and Chemical Stability of the EC1 Domain of Human E-Cadherin
JOURNAL OF PHARMACEUTICAL SCIENCES, 98:3562-3574, OCT 2009
abstract,
full text
Talbert-Slagle, K., Marlatt, S., Barrera, F.N., Khurana, E., Oates, J., Gerstein, M., Engelman, D.M., Dixon, A.M., DiMaio, D.
Artificial Transmembrane Oncoproteins Smaller than the Bovine Papillomavirus E5 Protein Redefine Sequence Requirements for Activation of the Platelet-Derived Growth Factor beta Receptor
JOURNAL OF VIROLOGY, 83:9773-9785, OCT 2009
abstract,
full text
Gutowski, K.E., Gurkan, B., Maginn, E.J.
Force field for the atomistic simulation of the properties of hydrazine, organic hydrazine derivatives, and energetic hydrazinium ionic liquids
PURE AND APPLIED CHEMISTRY, 81:1799-1828, OCT 2009
abstract,
full text
Lim, M.C.G., Zhong, Z.W.
Effects of fluid flow on the oligonucleotide folding in single-walled carbon nanotubes
PHYSICAL REVIEW E, 80: Art. No. 041915, OCT 2009
abstract,
full text
Ahn, K.H., Bertalovitz, A.C., Mierke, D.F., Kendall, D.A.
Dual Role of the Second Extracellular Loop of the Cannabinoid Receptor 1: Ligand Binding and Receptor Localization
MOLECULAR PHARMACOLOGY, 76:833-842, OCT 2009
abstract,
full text
Dubey, D.K., Tomar, V.
Understanding the influence of structural hierarchy and its coupling with chemical environment on the strength of idealized tropocollagen-hydroxyapatite biomaterials
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS, 57:1702-1717, OCT 2009
abstract,
full text
Phillips, J.C., Stone, J.E.
Probing Biomolecular Machines with Graphics Processors
COMMUNICATIONS OF THE ACM, 52:34-41, OCT 2009
full text
Maragliano, L., Vanden-Eijnden, E., Roux, B.
Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2589-2594, OCT 2009
abstract,
full text
Schulz, R., Lindner, B., Petridis, L., Smith, J.C.
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2798-2808, OCT 2009
abstract,
full text
Atilgan, C., Atilgan, A.R.
Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000544, OCT 2009
abstract,
full text
Baris, I., Tuncel, A., Ozber, N., Keskin, O., Kavakli, I.H.
Investigation of the Interaction between the Large and Small Subunits of Potato ADP-Glucose Pyrophosphorylase
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000546, OCT 2009
abstract,
full text
Liu, J., Nussinov, R.
The Mechanism of Ubiquitination in the Cullin-RING E3 Ligase Machinery: Conformational Control of Substrate Orientation
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000527, OCT 2009
abstract,
full text
Dagliyan, O., Kavakli, I.H., Turkay, M.
Classification of Cytochrome P450 Inhibitors with Respect to Binding Free Energy and pIC(50) Using Common Molecular Descriptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:2403-2411, OCT 2009
abstract,
full text
Roopra, S., Knapp, B., Omasits, U., Schreiner, W.
jSimMacs for GROMACS: A Java Application for Advanced Molecular Dynamics Simulations with Remote Access Capability
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:2412-2417, OCT 2009
abstract,
full text
Trabuco, L.G., Villa, E., Schreiner, E., Harrison, C.B., Schulten, K.
Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
METHODS, 49:174-180, OCT 2009
abstract,
full text,
TCBG publications
Huang, W., Kim, J., Jha, S., Aboul-Ela, F.
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm
NUCLEIC ACIDS RESEARCH, 37:6528-6539, OCT 2009
abstract,
full text
Bairagya, H.R., Mukhopadhyay, B.P., Sekar, K.
An Insight to the Dynamics of Conserved Water Molecular Triad in IMPDH II (Human): Recognition of Cofactor and Substrate to Catalytic Arg 322
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:149-158, OCT 2009
abstract,
full text
Bonomi, M., Branduardi, D., Bussi, G., Camilloni, C., Provasi, D., Raiteri, P., Donadio, D., Marinelli, F., Pietrucci, F., Broglia, R.A., Parrinello, M.
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
COMPUTER PHYSICS COMMUNICATIONS, 180:1961-1972, OCT 2009
abstract,
full text
Penev, E.S., Lampoudi, S., Shea, J.E.
TiREX: Replica-exchange molecular dynamics using TINKER
COMPUTER PHYSICS COMMUNICATIONS, 180:2013-2019, OCT 2009
abstract,
full text
Perlmutter, J.D., Sachs, J.N.
Experimental verification of lipid bilayer structure through multi-scale modeling
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:2284-2290, OCT 2009
abstract,
full text
Kaila, V.R.I., Verkhovsky, M.I., Hummer, G., Wikstrom, M.
Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1787:1205-1214, OCT 2009
abstract,
full text
Monfregola, L., Vitale, R.M., Amodeo, P., De Luca, S.
A SPR strategy for high-throughput ligand screenings based on synthetic peptides mimicking a selected subdomain of the target protein: A proof of concept on HER2 receptor
BIOORGANIC & MEDICINAL CHEMISTRY, 17:7015-7020, OCT 1 2009
abstract,
full text
Soriano-Ursua, M.A., Trujillo-Ferrara, J.G., Correa-Basurto, J.
Homology modeling and flex-ligand docking studies on the guinea pig beta(2) adrenoceptor: structural and experimental similarities differences with the human beta(2)
JOURNAL OF MOLECULAR MODELING, 15:1203-1211, OCT 2009
abstract,
full text
Walker, K.D., Causgrove, T.P.
Contribution of arginine-glutamate salt bridges to helix stability
JOURNAL OF MOLECULAR MODELING, 15:1213-1219, OCT 2009
abstract,
full text
Pomata, M.H.H., Sonoda, M.T., Skaf, M.S., Elola, M.D.
Anomalous Dynamics of Hydration Water in Carbohydrate Solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12999-13006, OCT 1 2009
abstract,
full text
Fishelovitch, D., Shaik, S., Wolfson, H.J., Nussinov, R.
Theoretical Characterization of Substrate Access/Exit Channels in the Human Cytochrome P450 3A4 Enzyme: Involvement of Phenylalanine Residues in the Gating Mechanism
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13018-13025, OCT 1 2009
abstract,
full text
Foley, M.C., Schlick, T.
Relationship Between Conformational Changes in Pol lambda's Active Site Upon Binding Incorrect Nucleotides and Mismatch Incorporation Rates
JOURNAL OF PHYSICAL CHEMISTRY B, 113:13035-13047, OCT 1 2009
abstract,
full text
Moraru, A., Svab, I., Mihailescu, D.F.
CHARMM FORCE FIELD PARAMETERIZATION OF BACTERIAL LIPOPOLYSACCHARIDES
REVUE ROUMAINE DE CHIMIE, 54:799-+, OCT 2009
abstract,
full text
Lin, Y.W., Nie, C.M., Liao, L.F.
Folding behaviors of apocytochrome b(5) and its mutants: Insights from high temperature molecular dynamics simulations
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 910:154-162, SEP 30 2009
abstract,
full text
Taskent-Sezgin, H., Chung, J., Patsalo, V., Miyake-Stoner, S.J., Miller, A.M., Brewer, S.H., Mehl, R.A., Green, D.F., Raleigh, D.P., Carrico, I.
Interpretation of p-Cyanophenylalanine Fluorescence in Proteins in Terms of Solvent Exposure and Contribution of Side-Chain Quenchers: A Combined Fluorescence, IR and Molecular Dynamics Study
BIOCHEMISTRY, 48:9040-9046, SEP 29 2009
abstract,
full text
Tsai, C.W., Hsu, N.Y., Wang, C.H., Lu, C.Y., Chang, Y., Tsai, H.H.G., Ruaan, R.C.
Coupling Molecular Dynamics Simulations with Experiments for the Rational Design of Indolicidin-Analogous Antimicrobial Peptides
JOURNAL OF MOLECULAR BIOLOGY, 392:837-854, SEP 25 2009
abstract,
full text
De Angeli, A., Moran, O., Wege, S., Filleur, S., Ephritikhine, G., Thomine, S., Barbier-Brygoo, H., Gambale, F.
ATP Binding to the C Terminus of the Arabidopsis thaliana Nitrate/Proton Antiporter, AtCLCa, Regulates Nitrate Transport into Plant Vacuoles
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:26526-26532, SEP 25 2009
abstract,
full text
Furini, S., Domene, C.
Atypical mechanism of conduction in potassium channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:16074-16077, SEP 22 2009
abstract,
full text
Bellesia, G., Shea, J.E.
Diversity of kinetic pathways in amyloid fibril formation
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 111102, SEP 21 2009
abstract,
full text
Garate, J.A., English, N.J., MacElroy, J.M.D.
Static and alternating electric field and distance-dependent effects on carbon nanotube-assisted water self-diffusion across lipid membranes
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 114508, SEP 21 2009
abstract,
full text
Zhang, H.M., Kenaan, C., Hamdane, D., Hoa, G.H.B., Hollenberg, P.F.
Effect of Conformational Dynamics on Substrate Recognition and Specificity as Probed by the Introduction of a de Novo Disulfide Bond into Cytochrome P450 2B1
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:25678-25686, SEP 18 2009
abstract,
full text
Carpena, X., Vidossich, P., Schroettner, K., Calisto, B.M., Banerjee, S., Stampler, J., Soudi, M., Furtmuller, P.G., Rovira, C., Fita, I., Obinger, C.
Essential Role of Proximal Histidine-Asparagine Interaction in Mammalian Peroxidases
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:25929-25937, SEP 18 2009
abstract,
full text
Shukla, D., Shinde, C., Trout, B.L.
Molecular Computations of Preferential Interaction Coefficients of Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12546-12554, SEP 17 2009
abstract,
full text
Roy, A., Taraphder, S.
Transition Path Sampling Study of the Conformational Fluctuation of His-64 in Human Carbonic Anhydrase II
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12555-12564, SEP 17 2009
abstract,
full text
Liu, L.T., Willenbring, D., Xu, Y., Tang, P.
General Anesthetic Binding to Neuronal alpha 4 beta 2 Nicotinic Acetylcholine Receptor and Its Effects on Global Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12581-12589, SEP 17 2009
abstract,
full text
Law, R.J., Lightstone, F.C.
Modeling Neuronal Nicotinic and GABA Receptors: Important Interface Salt-Links and Protein Dynamics
BIOPHYSICAL JOURNAL, 97:1586-1594, SEP 16 2009
abstract,
full text
Orgel, J.P.R.O., Eid, A., Antipova, O., Bella, J., Scott, J.E.
Decorin Core Protein (Decoron) Shape Complements Collagen Fibril Surface Structure and Mediates Its Binding
PLOS ONE, 4: Art. No. e7028, SEP 15 2009
abstract,
full text
Gokhan-Kelekci, N., Simsek, O.O., Ercan, A., Yelekci, K., Sahin, Z.S., Isik, S., Ucar, G., Bilgin, A.A.
Synthesis and molecular modeling of some novel hexahydroindazole derivatives as potent monoamine oxidase inhibitors
BIOORGANIC & MEDICINAL CHEMISTRY, 17:6761-6772, SEP 15 2009
abstract,
full text
Kajander, T., Sachs, J.N., Goldman, A., Regan, L.
Electrostatic Interactions of Hsp-organizing Protein Tetratricopeptide Domains with Hsp70 and Hsp90 COMPUTATIONAL ANALYSIS AND PROTEIN ENGINEERING
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:25364-25374, SEP 11 2009
abstract,
full text
Lee, T.S., Ma, W.L., Zhang, X., Kantarjian, H., Albitar, M.
Structural effects of clinically observed mutations in JAK2 exons 13-15: comparison with V617F and exon 12 mutations
BMC STRUCTURAL BIOLOGY, 9: Art. No. 58, SEP 10 2009
abstract,
full text
Wang, T., Sun, H.W., Chen, L., Shen, R.X., Lai, C.M.
Docking and Molecular Dynamics Simulation Studies of Interaction Between Arabidopsis TIR1 and Auxin IAA
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 30:1835-1838, SEP 10 2009
abstract,
full text
Kubiak, K., Mulheran, P.A.
Molecular Dynamics Simulations of Hen Egg White Lysozyme Adsorption at a Charged Solid Surface
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12189-12200, SEP 10 2009
abstract,
full text
Homouz, D., Hoffman, B., Cheung, M.S.
Hydrophobic Interactions of Hexane in Nanosized Water Droplets
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12337-12342, SEP 10 2009
abstract,
full text
Lee, O.S., Schatz, G.C.
Interaction between DNAs on a Gold Surface
JOURNAL OF PHYSICAL CHEMISTRY C, 113:15941-15947, SEP 10 2009
abstract,
full text
Newstead, S., Fowler, P.W., Bilton, P., Carpenter, E.P., Sadler, P.J., Campopiano, D.J., Sansom, M.S.P., Iwata, S.
Insights into How Nucleotide-Binding Domains Power ABC Transport
STRUCTURE, 17:1213-1222, SEP 9 2009
abstract,
full text
Wang, J.P., Cai, K.C., Ma, X.Y.
Ultrafast Structural Dynamics of Biomolecules Examined by Multiple-Mode 2D IR Spectroscopy: Anharmonically Coupled Motions are in Harmony
CHEMPHYSCHEM, 10:2242-2250, SEP 9 2009
abstract,
full text
Balius, T.E., Rizzo, R.C.
Quantitative Prediction of Fold Resistance for Inhibitors of EGFR
BIOCHEMISTRY, 48:8435-8448, SEP 8 2009
abstract,
full text
Takeda, T., Klimov, D.K.
Side Chain Interactions Can Impede Amyloid Fibril Growth: Replica Exchange Simulations of A beta Peptide Mutant
JOURNAL OF PHYSICAL CHEMISTRY B, 113:11848-11857, SEP 3 2009
abstract,
full text
Sengupta, N., Maekawa, H., Zhuang, W., Toniolo, C., Mukamel, S., Tobias, D.J., Ge, N.H.
Sensitivity of 2D IR Spectra to Peptide Helicity: A Concerted Experimental and Simulation Study of an Octapeptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:12037-12049, SEP 3 2009
abstract,
full text
Law, C.J., Enkavi, G., Wang, D.N., Tajkhorshid, E.
Structural Basis of Substrate Selectivity in the Glycerol-3-Phosphate: Phosphate Antiporter GlpT
BIOPHYSICAL JOURNAL, 97:1346-1353, SEP 2 2009
abstract,
full text
Sarkar, K., Meister, K., Sethi, A., Gruebele, M.
Fast Folding of an RNA Tetraloop on a Rugged Energy Landscape Detected by a Stacking-Sensitive Probe
BIOPHYSICAL JOURNAL, 97:1418-1427, SEP 2 2009
abstract,
full text
Liu, M., Cong, X.J., Li, P., Tan, J.J., Chen, W.Z., Wang, C.X.
Study on the Inhibitory Mechanism and Binding Mode of the Hydroxycoumarin Compound NSC158393 to HIV-1 Integrase by Molecular Modeling
BIOPOLYMERS, 91:700-709, SEP 2009
abstract,
full text
Mustafa, M., Henderson, D.J., Busath, D.D.
Free-energy profiles for ions in the influenza M(2)-TMD channel
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 76:794-807, SEP 2009
abstract,
full text
Gaillard, T., Dejaegere, A., Stote, R.H.
Dynamics of beta 3 integrin I-like and Hybrid domains: Insight from simulations on the mechanism of transition between open and closed forms
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 76:977-994, SEP 2009
abstract,
full text
Menor, S.A., de Graff, A.M.R., Thorpe, M.F.
Hierarchical plasticity from pair distance fluctuations
PHYSICAL BIOLOGY, 6: Art. No. 036017, SEP 2009
abstract,
full text
Shi, W., Maginn, E.J.
Molecular Simulation of Ammonia Absorption in the Ionic Liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf(2)N])
AICHE JOURNAL, 55:2414-2421, SEP 2009
abstract,
full text
Dubey, D.K., Tomar, V.
Role of the nanoscale interfacial arrangement in mechanical strength of tropocollagen-hydroxyapatite-based hard biomaterials
ACTA BIOMATERIALIA, 5:2704-2716, SEP 2009
abstract,
full text
Bulo, R.E., Ensing, B., Sikkema, J., Visscher, L.
Toward a Practical Method for Adaptive QM/MM Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2212-2221, SEP 2009
abstract,
full text
Cerutti, D.S., Duke, R.E., Darden, T.A., Lybrand, T.P.
Staggered Mesh Ewald: An Extension of the Smooth Particle-Mesh Ewald Method Adding Great Versatility
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2322-2338, SEP 2009
abstract,
full text
Harvey, M.J., De Fabritiis, G.
An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2371-2377, SEP 2009
abstract,
full text
Qureshi, S.H., Yang, L.K., Manithody, C., Iakhiaev, A.V., Rezaie, A.R.
Mutagenesis Studies toward Understanding Allostery In Thrombin
BIOCHEMISTRY, 48:8261-8270, SEP 1 2009
abstract,
full text
Banerjee, A.K., Arora, N., Murty, U.S.N.
Structural model of the Plasmodium falciparum Thioredoxin reductase: a novel target for antimalarial drugs
JOURNAL OF VECTOR BORNE DISEASES, 46:171-183, SEP 2009
abstract,
full text
Suyetin, M.V., Vakhrushev, A.V.
Temperature-sensitive nanocapsules for methane storage
MICRO & NANO LETTERS, 4:172-176, SEP 2009
abstract,
full text
Song, C., Corry, B.
Computational study of the transmembrane domain of the acetylcholine receptor
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 38:961-970, SEP 2009
abstract,
full text
Sakuraba, S., Kitao, A.
Multiple Markov Transition Matrix Method: Obtaining the Stationary Probability Distribution from Multiple Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1850-1858, SEP 2009
abstract,
full text
Codutti, L., Picotti, P., Marin, O., Dewilde, S., Fogolari, F., Corazza, A., Viglino, P., Moens, L., Esposito, G., Fontana, A.
Conformational stability of neuroglobin helix F - possible effects on the folding pathway within the globin family
FEBS JOURNAL, 276:5177-5190, SEP 2009
abstract,
full text
Yongye, A.B., Li, Y.M., Giulianotti, M.A., Yu, Y.P., Houghten, R.A., Martinez-Mayorga, K.
Modeling of peptides containing D-amino acids: implications on cyclization
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 23:677-689, SEP 2009
abstract,
full text
Sharma, M., Bulusu, G., Mitra, A.
MD simulations of ligand-bound and ligand-free aptamer: Molecular level insights into the binding and switching mechanism of the add A-riboswitch
RNA-A PUBLICATION OF THE RNA SOCIETY, 15:1673-1692, SEP 2009
abstract,
full text
Li, X.C., Nevels, K.J., Gryczynski, Z., Gryczynski, I., Pusztai-Carey, M., Xie, D.X., Butko, P.
A molecular dynamics model of the Bt toxin Cyt1A and its validation by resonance energy transfer
BIOPHYSICAL CHEMISTRY, 144:53-61, SEP 2009
abstract,
full text
Czajkowsky, D.M., Shao, Z.F.
The human IgM pentamer is a mushroom-shaped molecule with a flexural bias
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:14960-14965, SEP 1 2009
abstract,
full text
Yount, N.Y., Kupferwasser, D., Spisni, A., Dutz, S.M., Ramjan, Z.H., Sharma, S., Waring, A.J., Yeaman, M.R.
Selective reciprocity in antimicrobial activity versus cytotoxicity of hBD-2 and crotamine
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:14972-14977, SEP 1 2009
abstract,
full text
Fu, Y., Ding, Y.R., Chen, Z.G., Xu, W.B.
Exploring Unfolding Pathway of CGTase: Insight from Molecular Dynamics Simulation
RIVISTA DI BIOLOGIA-BIOLOGY FORUM, 102:347-364, SEP-DEC 2009
abstract,
full text
Nishizawa, K.
Molecular Dynamics Simulations of Kv Channels and Gating-Modifier Peptide Toxins
CURRENT COMPUTER-AIDED DRUG DESIGN, 5:155-173, SEP 2009
abstract,
full text
Dubey, D.K., Tomar, V.
Role of hydroxyapatite crystal shape in nanoscale mechanical behavior of model tropocollagen-hydroxyapatite hard biomaterials
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 29:2133-2140, AUG 31 2009
abstract,
full text
Bairagya, H.R., Mukhopadhyay, B.P., Bhattacharya, S.
Role of the conserved water molecules in the binding of inhibitor to IMPDH-II (human): A study on the water mimic inhibitor design
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 908:31-39, AUG 30 2009
abstract,
full text
Vagenende, V., Yap, M.G.S., Trout, B.L.
Molecular Anatomy of Preferential Interaction Coefficients by Elucidating Protein Solvation in Mixed Solvents: Methodology and Application for Lysozyme in Aqueous Glycerol
JOURNAL OF PHYSICAL CHEMISTRY B, 113:11743-11753, AUG 27 2009
abstract,
full text
Santaniello, E., Casati, S., Ciuffreda, P., Meroni, G., Pedretti, A., Vistoli, G.
A molecular modelling approach to rationalize the stereochemical outcome of the Burkholderia cepacia lipase-catalyzed transesterification of aromatic primary alcohols with vinyl esters with different chain lengths in chloroform
TETRAHEDRON-ASYMMETRY, 20:1833-1836, AUG 26 2009
abstract,
full text
Aleman, C., Betran, O., Casanovas, J., Houk, K.N., Hall, H.K.
Thermodynamic Control of the Polymerizability of Five-, Six-, and Seven-Membered Lactones
JOURNAL OF ORGANIC CHEMISTRY, 74:6237-6244, AUG 21 2009
abstract,
full text
Miller, Y., Ma, B.Y., Nussinov, R.
Polymorphism of Alzheimer's A beta(17-42) (p3) Oligomers: The Importance of the Turn Location and Its Conformation
BIOPHYSICAL JOURNAL, 97:1168-1177, AUG 19 2009
abstract,
full text
Chennamsetty, N., Helk, B., Voynov, V., Kayser, V., Trout, B.L.
Aggregation-Prone Motifs in Human Immunoglobulin G
JOURNAL OF MOLECULAR BIOLOGY, 391:404-413, AUG 14 2009
abstract,
full text
Meier, T., Krah, A., Bond, P.J., Pogoryelov, D., Diederichs, K., Faraldo-Gomez, J.D.
Complete Ion-Coordination Structure in the Rotor Ring of Na(+)-Dependent F-ATP Synthases
JOURNAL OF MOLECULAR BIOLOGY, 391:498-507, AUG 14 2009
abstract,
full text
Bagchi, S., Falvo, C., Mukamel, S., Hochstrasser, R.M.
2D-IR Experiments and Simulations of the Coupling between Amide-I and Ionizable Side Chains in Proteins: Application to the Villin Headpiece
JOURNAL OF PHYSICAL CHEMISTRY B, 113:11260-11273, AUG 13 2009
abstract,
full text
Mamonov, A.B., Bhatt, D., Cashman, D.J., Ding, Y., Zuckerman, D.M.
General Library-Based Monte Carlo Technique Enables Equilibrium Sampling of Semi-atomistic Protein Models
JOURNAL OF PHYSICAL CHEMISTRY B, 113:10891-10904, AUG 6 2009
abstract,
full text
Pfaendtner, J., Branduardi, D., Parrinello, M., Pollard, T.D., Voth, G.A.
Nucleotide-dependent conformational states of actin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:12723-12728, AUG 4 2009
abstract,
full text
Martin, H.S.C., Jha, S., Howorka, S., Coveney, P.V.
Determination of Free Energy Profiles for the Translocation of Polynucleotides through alpha-Hemolysin Nanopores using Non-Equilibrium Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2135-2148, AUG 2009
abstract,
full text
Ramya, L., Gautham, N.
Effects of Hydration on the Conformational Energy Landscape of the Pentapeptide Met-Enkephalin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:2180-2190, AUG 2009
abstract,
full text
Dixit, A., Verkhivker, G.M.
Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000487, AUG 2009
abstract,
full text
Sogaard, R., Alsterfjord, M., MacAulay, N., Zeuthen, T.
Ammonium ion transport by the AMT/Rh homolog TaAMT1;1 is stimulated by acidic pH
PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY, 458:733-743, AUG 2009
abstract,
full text
Butler, K.V., He, R., McLaughlin, K., Vistoli, G., Langley, B., Kozikowski, A.P.
Stereoselective HDAC Inhibition from Cysteine-Derived Zinc-Binding Groups
CHEMMEDCHEM, 4:1292-1301, AUG 2009
abstract,
full text
Bonomi, M., Barducci, A., Parrinello, M.
Reconstructing the Equilibrium Boltzmann Distribution from Well-Tempered Metadynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1615-1621, AUG 2009
abstract,
full text
Oberhofer, H., Dellago, C.
Efficient Extraction of Free Energy Profiles From Nonequilibrium Experiments
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1726-1736, AUG 2009
abstract,
full text
Jasuja, R., Ulloor, J., Yengo, C.M., Choong, K., Istomin, A.Y., Livesay, D.R., Jacobs, D.J., Swerdloff, R.S., Miksovska, J., Larsen, R.W., Bhasin, S.
Kinetic and Thermodynamic Characterization of Dihydrotestosterone-Induced Conformational Perturbations in Androgen Receptor Ligand-Binding Domain
MOLECULAR ENDOCRINOLOGY, 23:1231-1241, AUG 2009
abstract,
full text
Kastner, J., Loeffler, H.H., Roberts, S.K., Martin-Fernandez, M.L., Winn, M.D.
Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics
JOURNAL OF STRUCTURAL BIOLOGY, 167:117-128, AUG 2009
abstract,
full text
Verde, A.V., Acres, J.M., Maranas, J.K.
Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations
BIOMACROMOLECULES, 10:2118-2128, AUG 2009
abstract,
full text
Rodriguez-Ropero, F., Zanuy, D., Assfeld, X., Aleman, C.
Modeling an Electronic Conductor Based on Natural Peptide Sequences
BIOMACROMOLECULES, 10:2338-2343, AUG 2009
abstract,
full text
Gong, L.C., Zhou, X.
Structuring and sampling complex conformation space: Weighted ensemble dynamics simulations
PHYSICAL REVIEW E, 80: Art. No. 026707, AUG 2009
abstract,
full text
Zhu, H., Roder, B., May, V.
Time and frequency resolved spontaneous emission from supramolecular pheophorbide-a complexes: A mixed quantum classical computation
CHEMICAL PHYSICS, 362:19-26, JUL 30 2009
abstract,
full text
Brooks, B.R., Brooks, C.L., Mackerell, A.D., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A.R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R.W., Post, C.B., Pu, J.Z., Schaefer, M., Tidor, B., Venable, R.M., Woodcock, H.L., Wu, X., Yang, W., York, D.M., Karplus, M.
CHARMM: The Biomolecular Simulation Program
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1545-1614, JUL 30 2009
abstract,
full text
Krishnan, M., Smith, J.C.
Response of Small-Scale, Methyl Rotors to Protein-Ligand Association: A Simulation Analysis of Calmodulin-Peptide Binding
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:10083-10091, JUL 29 2009
abstract,
full text
Wei, C.Y., Pohorille, A.
Permeation of Membranes by Ribose and Its Diastereomers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:10237-10245, JUL 29 2009
abstract,
full text
Li, J.L., Geng, C.Y., Bu, Y.X., Zhang, L., Zhang, L.B., Huang, X.R., Sun, C.C.
Decoupling Interactions between EF-hands of Recoverin and Ca(2+): Steered Molecular Dynamics Simulation
ACTA CHIMICA SINICA, 67:1597-1602, JUL 28 2009
abstract,
full text
Varga, A., Lionne, C., Lallemand, P., Szabo, J., Adamek, N., Valentin, C., Vas, M., Barman, T., Chaloin, L.
Direct Kinetic Evidence That Lysine 215 Is Involved in the Phospho-Transfer Step of Human 3-Phosphoglycerate Kinase
BIOCHEMISTRY, 48:6998-7008, JUL 28 2009
abstract,
full text
Mehboob, S., Guo, L., Fu, W.T., Mittal, A., Yau, T., Truong, K., Johlfs, M., Long, F., Fung, L.W.M., Johnson, M.E.
Glutamate Racemase Dimerization Inhibits Dynamic Conformational Flexibility and Reduces Catalytic Rates
BIOCHEMISTRY, 48:7045-7055, JUL 28 2009
abstract,
full text
Bucher, D., Kuyucak, S.
Importance of water polarization for ion permeation in narrow pores
CHEMICAL PHYSICS LETTERS, 477:207-210, JUL 28 2009
abstract,
full text
Yang, L., Song, G., Jernigan, R.L.
Protein elastic network models and the ranges of cooperativity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:12347-12352, JUL 28 2009
abstract,
full text
Zhuang, S.L., Peng, Q., Cao, Y., Li, H.B.
Modulating the Mechanical Stability of Extracellular Matrix Protein Tenascin-C in a Controlled and Reversible Fashion
JOURNAL OF MOLECULAR BIOLOGY, 390:820-829, JUL 24 2009
abstract,
full text
DeMille, R.C., Molinero, V.
Coarse-grained ions without charges: Reproducing the solvation structure of NaCl in water using short-ranged potentials
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 034107, JUL 21 2009
abstract,
full text
Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., Trout, B.L.
Design of therapeutic proteins with enhanced stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:11937-11942, JUL 21 2009
abstract,
full text
Schoen, P.A.E., Michel, B., Curioni, A., Poulikakos, D.
Hydrogen-bond enhanced thermal energy transport at functionalized, hydrophobic and hydrophilic silica-water interfaces
CHEMICAL PHYSICS LETTERS, 476:271-276, JUL 16 2009
abstract,
full text
Talavera, A., Friemann, R., Gomez-Puerta, S., Martinez-Fleites, C., Garrido, G., Rabasa, A., Lopez-Requena, A., Pupo, A., Johansen, R.F., Sanchez, O., Krengel, U., Moreno, E.
Nimotuzumab, an Antitumor Antibody that Targets the Epidermal Growth Factor Receptor, Blocks Ligand Binding while Permitting the Active Receptor Conformation
CANCER RESEARCH, 69:5851-5859, JUL 15 2009
abstract,
full text
Iori, F., Di Felice, R., Molinari, E., Corni, S.
GoIP: An Atomistic Force-Field to Describe the Interaction of Proteins With Au(111) Surfaces in Water
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1465-1476, JUL 15 2009
abstract,
full text
Sun, T.G., Li, C.H., Chen, W.Z., Wang, C.X.
A novel back-door pathway for glutamine release from GlnBP revealed by steered molecular dynamics simulation
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 905:51-58, JUL 15 2009
abstract,
full text
Hodak, M., Chisnell, R., Lu, W.C., Bernholc, J.
Functional implications of multistage copper binding to the prion protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:11576-11581, JUL 14 2009
abstract,
full text
Halling-Brown, M.D., Moss, D.S., Sansom, C.E., Shepherd, A.J.
A computational Grid framework for immunological applications
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 367:2705-2716, JUL 13 2009
abstract,
full text
Zhang, X.F., Bursulaya, B., Lee, C.C., Chen, B.H., Pivaroff, K., Jegla, T.
Divalent Cations Slow Activation of EAG Family K(+) Channels through Direct Binding to S4
BIOPHYSICAL JOURNAL, 97:110-120, JUL 8 2009
abstract,
full text
Hsin, J., Gumbart, J., Trabuco, L.G., Villa, E., Qian, P., Hunter, C.N., Schulten, K.
Protein-Induced Membrane Curvature Investigated through Molecular Dynamics Flexible Fitting
BIOPHYSICAL JOURNAL, 97:321-329, JUL 8 2009
abstract,
full text,
TCBG publications
Chen, Q., Wang, Q., Liu, Y.C., Wu, T., Kang, Y., Moore, J.D., Gubbins, K.E.
Energetics investigation on encapsulation of protein/peptide drugs in carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 131: Art. No. 015101, JUL 7 2009
abstract,
full text
Silva, J.R., Pan, H., Wu, D., Nekouzadeh, A., Decker, K.F., Cui, J.M., Baker, N.A., Sept, D., Rudy, Y.
A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:11102-11106, JUL 7 2009
abstract,
full text
Politi, R., Sapir, L., Harries, D.
The Impact of Polyols on Water Structure in Solution: A Computational Study
JOURNAL OF PHYSICAL CHEMISTRY A, 113:7548-7555, JUL 2 2009
abstract,
full text
Ahn, K.H., Pellegrini, M., Tsomaia, N., Yatawara, A.K., Kendall, D.A., Mierke, D.F.
Structural Analysis of the Human Cannabinoid Receptor One Carboxyl-Terminus Identifies Two Amphipathic Helices
BIOPOLYMERS, 91:565-573, JUL 2009
abstract,
full text
Guixe, V., Merino, F.
The ADP-dependent Sugar Kinase Family: Kinetic and Evolutionary Aspects
IUBMB LIFE, 61:753-761, JUL 2009
abstract,
full text
Hixson, C.A., Wheeler, R.A.
Pressure Annealing as a Complement to Temperature Annealing To Find Low-Energy Structures of Oligomeric Molecules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1883-1894, JUL 2009
abstract,
full text
Pan, Y.P., Nussinov, R.
Cooperativity Dominates the Genomic Organization of p53-Response Elements: A Mechanistic View
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000448, JUL 2009
abstract,
full text
Zanuy, D., Ballano, G., Jimenez, A.I., Casanovas, J., Haspel, N., Cativiela, C., Curco, D., Nussinov, R., Aleman, C.
Protein Segments with Conformationally Restricted Amino Acids Can Control Supramolecular Organization at the Nanoscale
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:1623-1629, JUL 2009
full text
Pearce, B.C., Langley, D.R., Kang, J., Huang, H.W., Kulkarni, A.
E-Novo: An Automated Workflow for Efficient Structure-Based Lead Optimization
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:1797-1809, JUL 2009
abstract,
full text
Beckham, S.A., Piedrafita, D., Phillips, C.I., Samarawickrema, N., Law, R.H.P., Smooker, P.M., Quinsey, N.S., Irving, J.A., Greenwood, D., Verhelst, S.H.L., Bogyo, M., Turk, B., Coetzer, T.H., Wijeyewickrema, L.C., Spithill, T.W., Pike, R.N.
A major cathepsin B protease from the liver fluke Fasciola hepatica has atypical active site features and a potential role in the digestive tract of newly excysted juvenile parasites
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 41:1601-1612, JUL 2009
abstract,
full text
Dorvel, B., Sigalov, G., Zhao, Q., Comer, J., Dimitrov, V., Mirsaidov, U., Aksimentiev, A., Timp, G.
Analyzing the forces binding a restriction endonuclease to DNA using a synthetic nanopore
NUCLEIC ACIDS RESEARCH, 37:4170-4179, JUL 2009
abstract,
full text
Wells, G.A., Muller, I.B., Wrenger, C., Louw, A.I.
The activity of Plasmodium falciparum arginase is mediated by a novel inter-monomer salt-bridge between Glu295-Arg404
FEBS JOURNAL, 276:3517-3530, JUL 2009
abstract,
full text
Cai, B., Ding, Z.C., Zhang, Q., Ni, F.Y., Wang, H., Zheng, Q., Wang, Y., Zhou, G.M., Wang, K.Q., Sun, H.Z., Wu, H.M., Huang, Z.X.
The structural and biological significance of the EAAEAE insert in the alpha-domain of human neuronal growth inhibitory factor
FEBS JOURNAL, 276:3547-3558, JUL 2009
abstract,
full text
Song, C., Corry, B.
Role of acetylcholine receptor domains in ion selectivity
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:1466-1473, JUL 2009
abstract,
full text
Prince-Carter, A., Pfaffinger, P.J.
Multiple intermediate states precede pore block during N-type inactivation of a voltage-gated potassium channel
JOURNAL OF GENERAL PHYSIOLOGY, 134:15-34, JUL 2009
abstract,
full text
Katti, D.R., Matar, M.I., Katti, K.S., Amarasinghe, P.M.
Multiscale modeling of swelling clays: A computational and experimental approach
KSCE JOURNAL OF CIVIL ENGINEERING, 13:243-255, JUL 2009
abstract,
full text
Drikakis, D., Lechuga, J., Pal, S.
Effects of Shock Waves on Biological Membranes: A Molecular Dynamics Study
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 6:1437-1442, JUL 2009
abstract,
full text
Luckow, A., Jha, S., Kim, J., Merzky, A., Schnor, B.
Adaptive distributed replica-exchange simulations
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 367:2595-2606, JUN 28 2009
abstract,
full text
Tralau, T., Lafite, P., Levy, C., Combe, J.P., Scrutton, N.S., Leys, D.
An Internal Reaction Chamber in Dimethylglycine Oxidase Provides Efficient Protection from Exposure to Toxic Formaldehyde
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:17826-17834, JUN 26 2009
abstract,
full text
Traaseth, N.J., Shi, L., Verardi, R., Mullen, D.G., Barany, G., Veglia, G.
Structure and topology of monomeric phospholamban in lipid membranes determined by a hybrid solution and solid-state NMR approach
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:10165-10170, JUN 23 2009
abstract,
full text
Saldias, C., Gargallo, L., Sandoval, C., Leiva, A., Radic, D., Caballero, J., Saavedra, M., Gonzalez-Nilo, F.D.
Inclusion complexes containing poly(epsilon-caprolactone)diol and cyclodextrins. Experimental and theoretical studies
POLYMER, 50:2926-2932, JUN 19 2009
abstract,
full text
Rodriguez-Ropero, F., Preat, J., Zanuy, D., Torras, J., Aleman, C.
Sensing Mechanism of Calix[4]arene-Substituted Poly(thiophene) Ion Receptor: Effects of the Selectivity on the Molecular Rigidity
JOURNAL OF PHYSICAL CHEMISTRY B, 113:8284-8287, JUN 18 2009
abstract,
full text
Bagchi, S., Charnley, A.K., Smith, A.B., Hochstrasser, R.M.
Equilibrium Exchange Processes of the Aqueous Tryptophan Dipeptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:8412-8417, JUN 18 2009
abstract,
full text
Maffeo, C., Aksimentiev, A.
Structure, Dynamics, and Ion Conductance of the Phospholamban Pentamer
BIOPHYSICAL JOURNAL, 96:4853-4865, JUN 17 2009
abstract,
full text
Burke, J.E., Babakhani, A., Gorfe, A.A., Kokotos, G., Li, S., Woods, V.L., McCammon, J.A., Dennis, E.A.
Location of Inhibitors Bound to Group IVA Phospholipase A(2) Determined by Molecular Dynamics and Deuterium Exchange Mass Spectrometry
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:8083-8091, JUN 17 2009
abstract,
full text
Tsai, M.Y., Morozov, A.N., Chu, K.Y., Lin, S.H.
Molecular Dynamics insight into the role of tertiary (foldon) interactions on unfolding in Cytochrome c
CHEMICAL PHYSICS LETTERS, 475:111-115, JUN 16 2009
abstract,
full text
McDonald, S.M., Aguayo, D., Gonzalez-Nilo, F.D., Patton, J.T.
Shared and Group-Specific Features of the Rotavirus RNA Polymerase Reveal Potential Determinants of Gene Reassortment Restriction
JOURNAL OF VIROLOGY, 83:6135-6148, JUN 15 2009
abstract,
full text
Domene, C., Furini, S.
Dynamics, Energetics, and Selectivity of the Low-K(+) KcsA Channel Structure
JOURNAL OF MOLECULAR BIOLOGY, 389:637-645, JUN 12 2009
abstract,
full text
Sen, K., Hackett, J.C.
Molecular Oxygen Activation and Proton Transfer Mechanisms in Lanosterol 14 alpha-Demethylase Catalysis
JOURNAL OF PHYSICAL CHEMISTRY B, 113:8170-8182, JUN 11 2009
abstract,
full text
Yin, Y., Arkhipov, A., Schulten, K.
Simulations of Membrane Tubulation by Lattices of Amphiphysin N-BAR Domains
STRUCTURE, 17:882-892, JUN 10 2009
abstract,
full text,
TCBG publications
Bennett, M.J., Chik, J.K., Slysz, G.W., Luchko, T., Tuszynski, J., Sackett, D.L., Schriemer, D.C.
Structural Mass Spectrometry of the alpha beta-Tubulin Dimer Supports a Revised Model of Microtubule Assembly
BIOCHEMISTRY, 48:4858-4870, JUN 9 2009
abstract,
full text
Choe, S., Grabe, M.
Conformational dynamics of the inner pore helix of voltage-gated potassium channels
JOURNAL OF CHEMICAL PHYSICS, 130: Art. No. 215103, JUN 7 2009
abstract,
full text
Cai, W.S., Sun, T.T., Liu, P., Chipot, C., Shao, X.G.
Inclusion Mechanism of Steroid Drugs into beta-Cyclodextrins. Insights from Free Energy Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7836-7843, JUN 4 2009
abstract,
full text
Zanuy, D., Flores-Ortega, A., Jimenez, A.I., Calaza, M.I., Cativiela, C., Nussinov, R., Ruoslahti, E., Aleman, C.
In Silico Molecular Engineering for a Targeted Replacement in a Tumor-Homing Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7879-7889, JUN 4 2009
abstract,
full text
Cheng, X.L., Ivanov, I., Wang, H.L., Sine, S.M., McCammon, J.A.
Molecular-Dynamics Simulations of ELIC-a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor
BIOPHYSICAL JOURNAL, 96:4502-4513, JUN 3 2009
abstract,
full text
Rivera, E., Straub, J., Thirumalai, D.
Sequence and Crowding Effects in the Aggregation of a 10-Residue Fragment Derived from Islet Amyloid Polypeptide
BIOPHYSICAL JOURNAL, 96:4552-4560, JUN 3 2009
abstract,
full text
Hammoudeh, D.I., Follis, A.V., Prochownik, E.V., Metallo, S.J.
Multiple Independent Binding Sites for Small-Molecule Inhibitors on the Oncoprotein c-Myc
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:7390-7401, JUN 3 2009
abstract,
full text
Shen, J.W., Wu, T., Wang, Q., Kang, Y., Chen, X.
Adsorption of Insulin Peptide on Charged Single-Walled Carbon Nanotubes: Significant Role of Ordered Water Molecules
CHEMPHYSCHEM, 10:1260-1269, JUN 2 2009
abstract,
full text
Butler, T., Goldenfeld, N., Mathew, D., Luthey-Schulten, Z.
Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement
PHYSICAL REVIEW E, 79: Art. No. 060901, JUN 2009
abstract,
full text
Kumar, D., Misra, J.R., Kumar, A., Chugh, J., Sharma, S., Hosur, R.V.
NMR-derived solution structure of SUMO from Drosophila melanogaster [dSmt3]
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:1046-1050, JUN 2009
full text
Le Nours, J., De Maria, L., Welner, D., Jorgensen, C.T., Christensen, L.L.H., Borchert, T.V., Larsen, S., Lo Leggio, L.
Investigating the binding of beta-1,4-galactan to Bacillus licheniformis beta-1,4-galactanase by crystallography and computational modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:977-989, JUN 2009
abstract,
full text
Watanabe, T., Inadomi, Y., Umeda, H., Fukuzawa, K., Tanaka, S., Nakano, T., Nagashima, U.
Fragment Molecular Orbital (FMO) and FMO-MO Calculations of DNA: Accuracy Validation of Energy and Interfragment Interaction Energy
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 6:1328-1337, JUN 2009
abstract,
full text
Harvey, M.J., Giupponi, G., De Fabritiis, G.
ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1632-1639, JUN 2009
abstract,
full text
Ho, M.H., De Vivo, M., Dal Peraro, M., Klein, M.L.
Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1657-1666, JUN 2009
abstract,
full text
Bruno, A., Guadix, A.E., Costantino, G.
Molecular Dynamics Simulation of the Heterodimeric mGluR2/5HT(2A) Complex. An Atomistic Resolution Study of a Potential New Target in Psychiatric Conditions
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:1602-1616, JUN 2009
abstract,
full text
Tatsis, V.A., Tsoulos, I.G., Krinas, C.S., Alexopoulos, C., Stavrakoudis, A.
Insights into the structure of the PmrD protein with molecular dynamics simulations
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 44:393-399, JUN 1 2009
abstract,
full text
Prezhdo, O.V., Pereverzev, Y.V.
Theoretical Aspects of the Biological Catch Bond
ACCOUNTS OF CHEMICAL RESEARCH, 42:693-703, JUN 2009
abstract,
full text
Vistoli, G., Orioli, M., Pedretti, A., Regazzoni, L., Canevotti, R., Negrisoli, G., Carini, M., Aldini, G.
Design, Synthesis, and Evaluation of Carnosine Derivatives as Selective and Efficient Sequestering Agents of Cytotoxic Reactive Carbonyl Species
CHEMMEDCHEM, 4:967-975, JUN 2009
abstract,
full text
Lee, T.S., Potts, S.J., Albitar, M.
Basis for Resistance to Imatinib in 16 BCR-ABL Mutants as Determined Using Molecular Dynamics
RECENT PATENTS ON ANTI-CANCER DRUG DISCOVERY, 4:164-173, JUN 2009
abstract,
full text
Buggert, M., Cadena, C., Mokrushina, L., Smirnova, I., Maginn, E.J., Arlt, W.
COSMO-RS Calculations of Partition Coefficients: Different Tools for Conformational Search
CHEMICAL ENGINEERING & TECHNOLOGY, 32:977-986, JUN 2009
abstract,
full text
Bhardwaj, N., Gerstein, M.
Relating protein conformational changes to packing efficiency and disorder
PROTEIN SCIENCE, 18:1230-1240, JUN 2009
abstract,
full text
Zhang, G.D., Chen, J.A., Tanaka, T.
Deregulation of allosteric response of Lactococcus lactis prolidase and its effects on enzyme activity
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1794:968-975, JUN 2009
abstract,
full text
Mustafa, M., Henderson, D.J., Busath, D.D.
Computational studies of gramicidin permeation: An entryway sulfonate enhances cation occupancy at entry sites
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:1404-1412, JUN 2009
abstract,
full text
Weidemuller, C., Hauser, K.
Ion transport and energy transduction of P-type ATPases: Implications from electrostatic calculations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1787:721-729, JUN 2009
abstract,
full text
Schweiker, S.S., Loughlin, W.A., Brown, C.L., Pierens, G.K.
Synthesis of new modified truncated peptides and inhibition of glycogen phosphorylase
JOURNAL OF PEPTIDE SCIENCE, 15:442-450, JUN 2009
abstract,
full text
Meirovitch, H., Cheluvaraja, S., White, R.P.
Methods for Calculating the Entropy and Free Energy and their Application to Problems Involving Protein Flexibility and Ligand Binding
CURRENT PROTEIN & PEPTIDE SCIENCE, 10:229-243, JUN 2009
abstract,
full text
Maldonado, E., Roth, M.W., Gray, P.A.
Fully Atomistic Molecular Dynamics Simulations of the Behavior of a Simple Model of Crude Oil Confined between Graphene Planes
ACS APPLIED MATERIALS & INTERFACES, 1:1211-1217, JUN 2009
abstract,
full text
Chen, C., Li, W.Z., Song, Y.C., Yang, J.
Hydrogen bonding analysis of glycerol aqueous solutions: A molecular dynamics simulation study
JOURNAL OF MOLECULAR LIQUIDS, 146:23-28, MAY 31 2009
abstract,
full text
Docquier, J.D., Calderone, V., De Luca, F., Benvenuti, M., Giuliani, F., Bellucci, L., Tafi, A., Nordmann, P., Botta, M., Rossolini, G.M., Mangani, S.
Crystal Structure of the OXA-48 beta-Lactamase Reveals Mechanistic Diversity among Class D Carbapenemases
CHEMISTRY & BIOLOGY, 16:540-547, MAY 29 2009
abstract,
full text
Song, C., Corry, B.
Intrinsic Ion Selectivity of Narrow Hydrophobic Pores
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7642-7649, MAY 28 2009
abstract,
full text
Frydenvang, K., Lash, L.L., Naur, P., Postila, P.A., Pickering, D.S., Smith, C.M., Gajhede, M., Sasaki, M., Sakai, R., Pentikainen, O.T., Swanson, G.T., Kastrup, J.S.
Full Domain Closure of the Ligand-binding Core of the Ionotropic Glutamate Receptor iGluR5 Induced by the High Affinity Agonist Dysiherbaine and the Functional Antagonist 8,9-Dideoxyneodysiherbaine
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:14219-14229, MAY 22 2009
abstract,
full text
Logothetit, G.E., Ramos, J., Economou, I.G.
Molecular Modeling of Imidazolium-Based [Tf(2)N(-)] Ionic Liquids: Microscopic Structure, Thermodynamic and Dynamic Properties, and Segmental Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7211-7224, MAY 21 2009
abstract,
full text
Walch, S.P., Komadina, J.D., Prinz, F.B.
A Computational Comparison of Electron Transfer from Reduced Ferredoxin to Flavin Adenine Dinucleotide and a Gold Electrode
JOURNAL OF PHYSICAL CHEMISTRY B, 113:7298-7307, MAY 21 2009
abstract,
full text
Bastug, T., Kuyucak, S.
Importance of the Peptide Backbone Description in Modeling the Selectivity Filter in Potassium Channels
BIOPHYSICAL JOURNAL, 96:4006-4012, MAY 20 2009
abstract,
full text
Zou, H.L., Liu, J., Blasie, J.K.
Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a Cyanophenylalanine Spectroscopic Probe
BIOPHYSICAL JOURNAL, 96:4188-4199, MAY 20 2009
abstract,
full text
Tian, J.H., Garcia, A.E.
An Alpha-Helical Peptide in AOT Micelles Prefers to be Localized at the Water/Headgroup Interface
BIOPHYSICAL JOURNAL, 96:L57-L59, MAY 20 2009
abstract,
full text
Dubey, D.K., Tomar, V.
The effect of tensile and compressive loading on the hierarchical strength of idealized tropocollagen-hydroxyapatite biomaterials as a function of the chemical environment
JOURNAL OF PHYSICS-CONDENSED MATTER, 21: Art. No. 205103, MAY 20 2009
abstract,
full text
Burress, J., Kraus, M., Beckner, M., Cepel, R., Suppes, G., Wexler, C., Pfeifer, P.
Hydrogen storage in engineered carbon nanospaces
NANOTECHNOLOGY, 20: Art. No. 204026, MAY 20 2009
abstract,
full text
Liu, P., Marzahn, M.R., Robbins, A.H., Gutierrez-de-Teran, H., Rodriguez, D., McClung, S.H., Stevens, S.M., Yowell, C.A., Dame, J.B., McKenna, R., Dunn, B.M.
Recombinant Plasmepsin 1 from the Human Malaria Parasite Plasmodium falciparum: Enzymatic Characterization, Active Site Inhibitor Design, and Structural Analysis
BIOCHEMISTRY, 48:4086-4099, MAY 19 2009
abstract,
full text
Peters, G.H.
The effect of Asp54 phosphorylation on the energetics and dynamics in the response regulator protein SpoOF studied by molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:648-658, MAY 15 2009
abstract,
full text
Chen, C., Li, W.Z.
The Relation between the Ratio of Hydrogen Bonding Acceptor Number to Donor Number and Solute Concentration
ACTA CHIMICA SINICA, 67:883-887, MAY 14 2009
abstract,
full text
Dittmer, J., Thogersen, L., Underhaug, J., Bertelsen, K., Vosegaard, T., Pedersen, J.M., Schiott, B., Tajkhorshid, E., Skrydstrup, T., Nielsen, N.C.
Incorporation of Antimicrobial Peptides into Membranes: A Combined Liquid-State NMR and Molecular Dynamics Study of Alamethicin in DMPC/DHPC Bicelles
JOURNAL OF PHYSICAL CHEMISTRY B, 113:6928-6937, MAY 14 2009
abstract,
full text
Henin, J., Shinoda, W., Klein, M.L.
Models for Phosphatidylglycerol Lipids Put to a Structural Test
JOURNAL OF PHYSICAL CHEMISTRY B, 113:6958-6963, MAY 14 2009
abstract,
full text
Cheng, M.H., Xu, Y., Tang, P.
Anionic Lipid and Cholesterol Interactions with alpha 4 beta 2 nAChR: Insights from MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:6964-6970, MAY 14 2009
abstract,
full text
Paul, A., Bezer, S., Venkatramani, R., Kocsis, L., Wierzbinski, E., Balaeff, A., Keinan, S., Beratan, D.N., Achim, C., Waldeck, D.H.
Role of Nucleobase Energetics and Nucleobase Interactions in Single-Stranded Peptide Nucleic Acid Charge Transfer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:6498-6507, MAY 13 2009
abstract,
full text
Wang, H.L., Toghraee, R., Papke, D., Cheng, X.L., McCammon, J.A., Ravaioli, U., Sine, S.M.
Single-Channel Current Through Nicotinic Receptor Produced by Closure of Binding Site C-Loop
BIOPHYSICAL JOURNAL, 96:3582-3590, MAY 6 2009
abstract,
full text
Freddolino, P.L., Park, S., Roux, B., Schulten, K.
Force Field Bias in Protein Folding Simulations
BIOPHYSICAL JOURNAL, 96:3772-3780, MAY 6 2009
abstract,
full text,
TCBG publications
Joshi, M., Ebalunode, J.O., Briggs, J.M.
Computational insights into the interaction of the anthrax lethal factor with the N-terminal region of its substrates
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:323-335, MAY 1 2009
abstract,
full text
Jones, P.M., George, A.M.
Opening of the ADP-bound active site in the ABC transporter ATPase dimer: Evidence for a constant contact, alternating sites model for the catalytic cycle
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:387-396, MAY 1 2009
abstract,
full text
Whitford, P.C., Noel, J.K., Gosavi, S., Schug, A., Sanbonmatsu, K.Y., Onuchic, J.N.
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:430-441, MAY 1 2009
abstract,
full text
Singh, R.P., Brooks, B.R., Klauda, J.B.
Binding and release of cholesterol in the Osh4 protein of yeast
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 75:468-477, MAY 1 2009
abstract,
full text
Blomberg, L.M., Mangold, M., Mitchell, J.B.O., Blumberger, J.
Theoretical Study of the Reaction Mechanism of Streptomyces coelicolor Type II Dehydroquinase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1284-1294, MAY 2009
abstract,
full text
Golji, J., Collins, R., Mofrad, M.R.K.
Molecular Mechanics of the alpha-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000389, MAY 2009
abstract,
full text
Singh, N., Duenas-Gonzalez, A., Lyko, F., Medina-Franco, J.L.
Molecular Modeling and Molecular Dynamics Studies of Hydralazine with Human DNA Methyltransferase 1
CHEMMEDCHEM, 4:792-799, MAY 2009
abstract,
full text
Tanrikulu, Y., Proschak, E., Werner, T., Geppert, T., Todoroff, N., Klenner, A., Kottke, T., Sander, K., Schneider, E., Seifert, R., Stark, H., Clark, T., Schneider, G.
Homology Model Adjustment and Ligand Screening with a Pseudoreceptor of the Human Histamine H(4) Receptor
CHEMMEDCHEM, 4:820-827, MAY 2009
abstract,
full text
Kang, Y., Liu, Y.C., Wang, Q., Shen, J.W., Wu, T., Guan, W.J.
On the spontaneous encapsulation of proteins in carbon nanotubes
BIOMATERIALS, 30:2807-2815, MAY 2009
abstract,
full text
Wan, S.Z., Coveney, P.V.
A Comparative Study of the COX-1 and COX-2 Isozymes Bound to Lipid Membranes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1038-1050, MAY 2009
abstract,
full text
Lin, Y.W., Ying, T.L., Liao, L.F.
Dynamic consequences of mutating the typical HPGG motif of apocytochrome b(5) revealed by computer simulation
CHINESE CHEMICAL LETTERS, 20:631-634, MAY 2009
abstract,
full text
Ekonomiuk, D., Caflisch, A.
Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism
PROTEIN SCIENCE, 18:1003-1011, MAY 2009
abstract,
full text
Xu, J.C., Crowley, M.F., Smith, J.C.
Building a foundation for structure-based cellulosome design for cellulosic ethanol: Insight into cohesin-dockerin complexation from computer simulation
PROTEIN SCIENCE, 18:949-959, MAY 2009
abstract,
full text
Shen, R., Guo, W.L.
Ion binding properties and structure stability of the NaK channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:1024-1032, MAY 2009
abstract,
full text
Pedretti, A., Marconi, C., Bettinelli, I., Vistoli, G.
Comparative modeling of the quaternary structure for the human TRPM8 channel and analysis of its binding features
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:973-982, MAY 2009
abstract,
full text
Fadouloglou, V.E., Bastaki, M.N., Ashcroft, A.E., Phillips, S.E.V., Panopoulos, N.J., Glykos, N.M., Kokkinidis, M.
On the quaternary association of the type III secretion system HrcQ(B)-C protein: Experimental evidence differentiates among the various oligomerization models
JOURNAL OF STRUCTURAL BIOLOGY, 166:214-225, MAY 2009
abstract,
full text
Gutierrez, P.A., Rojano, B.A.
DOCKING OF TYROSINASE CICLOARTANE INHIBITORS
VITAE-REVISTA DE LA FACULTAD DE QUIMICA FARMACEUTICA, 16:245-251, MAY-AUG 2009
abstract,
full text
Bhowmik, R., Katti, K.S., Katti, D.R.
Mechanisms of Load-Deformation Behavior of Molecular Collagen in Hydroxyapatite-Tropocollagen Molecular System: Steered Molecular Dynamics Study
JOURNAL OF ENGINEERING MECHANICS-ASCE, 135:413-421, MAY 2009
abstract,
full text
Pitera, J.W.
Current developments in and importance of high-performance computing in drug discovery
CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT, 12:388-396, MAY 2009
abstract,
full text
Lee, T.S., Giambasu, G.M., Sosa, C.P., Martick, M., Scott, W.G., York, D.M.
Threshold Occupancy and Specific Cation Binding Modes in the Hammerhead Ribozyme Active Site are Required for Active Conformation
JOURNAL OF MOLECULAR BIOLOGY, 388:195-206, APR 24 2009
abstract,
full text
Matsumoto, F., Maeda, K., Chatake, T., Maeda, Y., Fujiwara, S.
Functional aberration of myofibrils by cardiomyopathy-causing mutations in the coiled-coil region of the troponin-core domain
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 382:205-209, APR 24 2009
abstract,
full text
Mandal, P.K., Limbrick, D., Coleman, D.R., Dyer, G.A., Ren, Z.Y., Birtwistle, J.S., Xiong, C.Y., Chen, X.M., Briggs, J.M., McMurray, J.S.
Conformationally Constrained Peptidomimetic Inhibitors of Signal Transducer and Activator of Transcription 3: Evaluation and Molecular Modeling
JOURNAL OF MEDICINAL CHEMISTRY, 52:2429-2442, APR 23 2009
abstract,
full text
Long, H., King, P.W., Ghirardi, M.L., Kim, K.
Hydrogenase/Ferredoxin Charge-Transfer Complexes: Effect of Hydrogenase Mutations on the Complex Association
JOURNAL OF PHYSICAL CHEMISTRY A, 113:4060-4067, APR 23 2009
abstract,
full text
Maruthamuthu, V., Schulten, K., Leckband, D.
Elasticity and Rupture of a Multi-Domain Neural Cell Adhesion Molecule Complex
BIOPHYSICAL JOURNAL, 96:3005-3014, APR 22 2009
abstract,
full text,
TCBG publications
Schulz, R., Kleinekathofer, U.
Transitions between Closed and Open Conformations of ToIC: The Effects of Ions in Simulations
BIOPHYSICAL JOURNAL, 96:3116-3125, APR 22 2009
abstract,
full text
Shim, J.Y.
Transmembrane Helical Domain of the Cannabinoid CB(1) Receptor
BIOPHYSICAL JOURNAL, 96:3251-3262, APR 22 2009
abstract,
full text
Gulla, S.V., Sharma, G., Borbat, P., Freed, J.H., Ghimire, H., Benedikt, M.R., Holt, N.L., Lorigan, G.A., Rege, K., Mavroidis, C., Budil, D.E.
Molecular-Scale Force Measurement in a Coiled-Coil Peptide Dimer by Electron Spin Resonance
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:5374-+, APR 22 2009
abstract,
full text
Dittrich, B., Warren, J.E., Fabbiani, F.P.A., Morgenroth, W., Corry, B.
Temperature dependence of rotational disorder in a non-standard amino acid from X-ray crystallography and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:2601-2609, APR 21 2009
abstract,
full text
Sethi, A., Eargle, J., Black, A.A., Luthey-Schulten, Z.
Dynamical networks in tRNA: protein complexes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:6620-6625, APR 21 2009
abstract,
full text
Karayiannis, N.C., Laso, M., Kroger, M.
Detailed Atomistic Molecular Dynamics Simulations of alpha-Conotoxin AuIB in Water
JOURNAL OF PHYSICAL CHEMISTRY B, 113:5016-5024, APR 16 2009
abstract,
full text
Khandelia, H., Jensen, M.O., Mouritsen, O.G.
To Gate or Not To Gate: Using Molecular Dynamics Simulations To Morph Gated Plant Aquaporins into Constitutively Open Conformations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:5239-5244, APR 16 2009
abstract,
full text
Swift, R.V., McCammon, J.A.
Substrate Induced Population Shifts and Stochastic Gating in the PBCV-1 mRNA Capping Enzyme
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:5126-5133, APR 15 2009
abstract,
full text
Lee, T.S., Ma, W.L., Zhang, X., Giles, F., Kantarjian, H., Albitar, M.
Mechanisms of Constitutive Activation of Janus Kinase 2-V617F Revealed at the Atomic Level Through Molecular Dynamics Simulations
CANCER, 115:1692-1700, APR 15 2009
abstract,
full text
Roberts, B.P., Scanlon, M.J., Krippner, G.Y., Chalmers, D.K.
Molecular Dynamics of Poly(L-lysine) Dendrimers with Naphthalene Disulfonate Caps
MACROMOLECULES, 42:2775-2783, APR 14 2009
abstract,
full text
Roberts, B.P., Krippner, G.Y., Scanlon, M.J., Chalmers, D.K.
Molecular Dynamics of Variegated Polyamide Dendrimers
MACROMOLECULES, 42:2784-2794, APR 14 2009
abstract,
full text
Bellesia, G., Shea, J.E.
Effect of beta-sheet propensity on peptide aggregation
JOURNAL OF CHEMICAL PHYSICS, 130: Art. No. 145103, APR 14 2009
abstract,
full text
Calderon, C.P., Janosi, L., Kosztin, I.
Using stochastic models calibrated from nanosecond nonequilibrium simulations to approximate mesoscale information
JOURNAL OF CHEMICAL PHYSICS, 130: Art. No. 144908, APR 14 2009
abstract,
full text
Masetti, M., Cavalli, A., Recanatini, M., Gervasio, F.L.
Exploring Complex Protein-Ligand Recognition Mechanisms with Coarse Metadynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:4807-4816, APR 9 2009
abstract,
full text
Jardon-Valadez, E., Bondar, A.N., Tobias, D.J.
Dynamics of the Internal Water Molecules in Squid Rhodopsin
BIOPHYSICAL JOURNAL, 96:2572-2576, APR 8 2009
abstract,
full text
Chen, P.C., Kuyucak, S.
Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 96:2577-2588, APR 8 2009
abstract,
full text
Khandelia, H., Mouritsen, O.G.
Lipid Gymnastics: Evidence of Complete Acyl Chain Reversal in Oxidized Phospholipids from Molecular Simulations
BIOPHYSICAL JOURNAL, 96:2734-2743, APR 8 2009
abstract,
full text
Cheng, Y., Pei, Q.X., Gao, H.J.
Molecular-dynamics studies of competitive replacement in peptide-nanotube assembly for control of drug release
NANOTECHNOLOGY, 20: Art. No. 145101, APR 8 2009
abstract,
full text
Park, S., Bardhan, J.P., Roux, B., Makowski, L.
Simulated x-ray scattering of protein solutions using explicit-solvent models
JOURNAL OF CHEMICAL PHYSICS, 130: Art. No. 134114, APR 7 2009
abstract,
full text
Quick, M., Winther, A.M.L., Shi, L., Nissen, P., Weinstein, H., Javitch, J.A.
Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:5563-5568, APR 7 2009
abstract,
full text
Nyblom, M., Frick, A., Wang, Y., Ekvall, M., Hallgren, K., Hedfalk, K., Neutze, R., Tajkhorshid, E., Tornroth-Horsefield, S.
Structural and Functional Analysis of SoPIP2;1 Mutants Adds Insight into Plant Aquaporin Gating
JOURNAL OF MOLECULAR BIOLOGY, 387:653-668, APR 3 2009
abstract,
full text
Xie, B.B., Bian, F., Chen, X.L., He, H.L., Guo, J., Gao, X., Zeng, Y.X., Chen, B., Zhou, B.C., Zhang, Y.Z.
Cold Adaptation of Zinc Metalloproteases in the Thermolysin Family from Deep Sea and Arctic Sea Ice Bacteria Revealed by Catalytic and Structural Properties and Molecular Dynamics NEW INSIGHTS INTO RELATIONSHIP BETWEEN CONFORMATIONAL FLEXIBILITY AND HYDROGEN BONDING
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:9257-9269, APR 3 2009
abstract,
full text
Szori, M., Tobias, D.J., Roeselova, M.
Microscopic Wetting of Mixed Self-assembled Monolayers: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 113:4161-4169, APR 2 2009
abstract,
full text
Liu, B., Li, X.Y., Li, B.L., Xu, B.Q., Zhao, Y.L.
Carbon Nanotube Based Artificial Water Channel Protein: Membrane Perturbation and Water Transportation
NANO LETTERS, 9:1386-1394, APR 2009
abstract,
full text
Kang, Y.K., Lee, O.S., Deria, P., Kim, S.H., Park, T.H., Bonnell, D.A., Saven, J.G., Therien, M.J.
Helical Wrapping of Single-Walled Carbon Nanotubes by Water Soluble Poly(p-phenyleneethynylene)
NANO LETTERS, 9:1414-1418, APR 2009
abstract,
full text
Jetton, N., Rothberg, K.G., Hubbard, J.G., Wise, J., Li, Y., Ball, H.L., Ruben, L.
The cell cycle as a therapeutic target against Trypanosoma brucei: Hesperadin inhibits Aurora kinase-1 and blocks mitotic progression in bloodstream forms
MOLECULAR MICROBIOLOGY, 72:442-458, APR 2009
abstract,
full text
Carvajal-Diaz, J.A., Liu, L.J., Cagin, T.
Structure and Dynamics of Water Within Single Wall Carbon Nanotubes and Self-Assembled Cyclic Peptide Nanotubes
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 6:894-902, APR 2009
abstract,
full text
Wiley, A.P., Williams, S.L., Essex, J.W.
Conformational Motions of HIV-1 Protease Identified Using Reversible Digitally Filtered Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1117-1128, APR 2009
abstract,
full text
Chang, C.H., Kim, K.
Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:1137-1145, APR 2009
abstract,
full text
Sharma, G., Mavroidis, C., Rege, K., Yarmush, M.L., Budil, D.
Computational Studies of a Protein-based Nanoactuator for Nanogripping Applications
INTERNATIONAL JOURNAL OF ROBOTICS RESEARCH, 28:421-435, APR 2009
abstract,
full text
Cai, K.C., Wang, J.P.
Molecular Dynamical Structures of Glycolaldehyde
ACTA PHYSICO-CHIMICA SINICA, 25:677-683, APR 2009
abstract,
full text
Klepeis, J.L., Lindorff-Larsen, K., Dror, R.O., Shaw, D.E.
Long-timescale molecular dynamics simulations of protein structure and function
CURRENT OPINION IN STRUCTURAL BIOLOGY, 19:120-127, APR 2009
abstract,
full text
Upadhayaya, R.S., Vandavasi, J.K., Vasireddy, N.R., Sharma, V., Dixit, S.S., Chattopadhyaya, J.
Design, synthesis, biological evaluation and molecular modelling studies of novel quinoline derivatives against Mycobacterium tuberculosis
BIOORGANIC & MEDICINAL CHEMISTRY, 17:2830-2841, APR 1 2009
abstract,
full text
Czub, J., Neumann, A., Borowski, E., Baginski, M.
Influence of a lipid bilayer on the conformational behavior of amphotericin B derivatives - A molecular dynamics study
BIOPHYSICAL CHEMISTRY, 141:105-116, APR 2009
abstract,
full text
Su, Z.Y., Wang, Y.T.
A Molecular Dynamics Simulation of the Human Lysozyme Camelid VHH HL6 Antibody System
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 10:1719-1727, APR 2009
abstract,
full text
Skjaerven, L., Hollup, S.M., Reuter, N.
Normal mode analysis for proteins
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 898:42-48, MAR 30 2009
abstract,
full text
Lin, Y.W., Ni, F.Y., Ying, T.L.
Early events in thermal unfolding of apocytochrome b(562) and its double-cysteine mutant as revealed by molecular dynamics simulation
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 898:82-89, MAR 30 2009
abstract,
full text
Khalfa, A., Treptow, W., Maigret, B., Tarek, M.
Self assembly of peptides near or within membranes using coarse grained MD simulations
CHEMICAL PHYSICS, 358:161-170, MAR 30 2009
abstract,
full text
Matsunaga, Y., Fuchigami, S., Kidera, A.
Multivariate frequency domain analysis of protein dynamics
JOURNAL OF CHEMICAL PHYSICS, 130: Art. No. 124104, MAR 28 2009
abstract,
full text
Xu, D., Newhouse, E.I., Amaro, R.E., Pao, H.C., Cheng, L.S., Markwick, P.R.L., McCammon, J.A., Li, W.W., Arzberger, P.W.
Distinct Glycan Topology for Avian and Human Sialopentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective
JOURNAL OF MOLECULAR BIOLOGY, 387:465-491, MAR 27 2009
abstract,
full text
Vakhrushev, A.V., Suyetin, M.V.
Methane storage in bottle-like nanocapsules
NANOTECHNOLOGY, 20: Art. No. 125602, MAR 25 2009
abstract,
full text
Coskuner, O., Bergeron, D.E., Rincon, L., Hudgens, J.W., Gonzalez, C.A.
Identification of Active Sites of Biomolecules II: Saccharide and Transition Metal Ion in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY A, 113:2491-2499, MAR 19 2009
abstract,
full text
Dixit, P.D., Merchant, S., Asthagiri, D.
Ion Selectivity in the KcsA Potassium Channel from the Perspective of the Ion Binding Site
BIOPHYSICAL JOURNAL, 96:2138-2145, MAR 18 2009
abstract,
full text
Telesco, S.E., Radhakrishnan, R.
Atomistic Insights into Regulatory Mechanisms of the HER2 Tyrosine Kinase Domain: A Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 96:2321-2334, MAR 18 2009
abstract,
full text
Bardhan, J.P., Knepley, M.G., Anitescu, M.
Bounding the electrostatic free energies associated with linear continuum models of molecular solvation
JOURNAL OF CHEMICAL PHYSICS, 130: Art. No. 104108, MAR 14 2009
abstract,
full text
Peng, Q., Zhuang, S.L., Wang, M.J., Cao, Y., Khor, Y.A., Li, H.B.
Mechanical Design of the Third FnIII Domain of Tenascin-C
JOURNAL OF MOLECULAR BIOLOGY, 386:1327-1342, MAR 13 2009
abstract,
full text
Ridge, C.D., Shaka, A.J.
"Ersatz" and "Hybrid" NMR Spectral Estimates Using the Filter Diagonalization Method
JOURNAL OF PHYSICAL CHEMISTRY A, 113:2036-2052, MAR 12 2009
abstract,
full text
Moussa, S.G., McIntire, T.M., Szori, M., Roeselova, M., Tobias, D.J., Grimm, R.L., Hemminger, J.C., Finlayson-Pitts, B.J.
Experimental and Theoretical Characterization of Adsorbed Water on Self-Assembled Monolayers: Understanding the Interaction of Water with Atmospherically Relevant Surfaces
JOURNAL OF PHYSICAL CHEMISTRY A, 113:2060-2069, MAR 12 2009
abstract,
full text
Bondar, A.N., del Val, C., White, S.H.
Rhomboid Protease Dynamics and Lipid Interactions
STRUCTURE, 17:395-405, MAR 11 2009
abstract,
full text
Miao, L.L., Schulten, K.
Transport-Related Structures and Processes of the Nuclear Pore Complex Studied through Molecular Dynamics
STRUCTURE, 17:449-459, MAR 11 2009
abstract,
full text,
TCBG publications
Yang, S., Banavali, N.K., Roux, B.
Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:3776-3781, MAR 10 2009
abstract,
full text
Xia, Z., Zhu, Z.H., Zhu, J., Zhou, R.H.
Recognition Mechanism of siRNA by Viral p19 Suppressor of RNA Silencing: A Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 96:1761-1769, MAR 4 2009
abstract,
full text
Guptaroy, B., Zhang, M.J., Bowton, E., Binda, F., Shi, L., Weinstein, H., Galli, A., Javitch, J.A., Neubig, R.R., Gnegy, M.E.
A Juxtamembrane Mutation in the N Terminus of the Dopamine Transporter Induces Preference for an Inward-Facing Conformation
MOLECULAR PHARMACOLOGY, 75:514-524, MAR 2009
abstract,
full text
Leone, V., Lattanzi, G., Molteni, C., Carloni, P.
Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000309, MAR 2009
abstract,
full text
Hashem, Y., Auffinger, P.
A short guide for molecular dynamics simulations of RNA systems
METHODS, 47:187-197, MAR 2009
abstract,
full text
Mascayano, C., Rezende, M.C., Mendez, C., Nunez, G., Chiang, V.
Solute-Solvent Interactions in Solutions of Solvatochromic Phenoxides: A Dynamics Simulation Study
JOURNAL OF SOLUTION CHEMISTRY, 38:363-371, MAR 2009
abstract,
full text
Hardy, D.J., Stone, J.E., Schulten, K.
Multilevel summation of electrostatic potentials using graphics processing units
PARALLEL COMPUTING, 35:164-177, MAR 2009
abstract,
full text,
TCBG publications
Nandi, T.K., Bairagya, H.R., Mukhopadhyay, B.P., Sekar, K., Sukul, D., Bera, A.K.
Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease
JOURNAL OF BIOSCIENCES, 34:27-34, MAR 2009
abstract,
full text
Slater, G.W., Holm, C., Chubynsky, M.V., de Haan, H.W., Dube, A., Grass, K., Hickey, O.A., Kingsburry, C., Sean, D., Shendruk, T.N., Nhan, L.X.
Modeling the separation of macromolecules: A review of current computer simulation methods
ELECTROPHORESIS, 30:792-818, MAR 2009
abstract,
full text
Djajamuliadi, J., Kagawa, T.F., Ohgo, K., Kumashiro, K.K.
Insights into a putative hinge region in elastin using molecular dynamics simulations
MATRIX BIOLOGY, 28:92-100, MAR 2009
abstract,
full text
Chen, C., Li, W.Z.
Molecular Dynamics Simulation of Hydrogen Bonding Characteristics in Aqueous Glycerol Solutions
ACTA PHYSICO-CHIMICA SINICA, 25:507-512, MAR 2009
abstract,
full text
Chen, W., Lou, J.Z., Zhu, C.
Molecular Dynamics Simulated Unfolding of von Willebrand Factor A Domains by Force
CELLULAR AND MOLECULAR BIOENGINEERING, 2:75-86, MAR 2009
abstract,
full text
Cideciyan, A.V., Swider, M., Aleman, T.S., Tsybovsky, Y., Schwartz, S.B., Windsor, E.A.M., Roman, A.J., Sumaroka, A., Steinberg, J.D., Jacobson, S.G., Stone, E.M., Palczewski, K.
ABCA4 disease progression and a proposed strategy for gene therapy
HUMAN MOLECULAR GENETICS, 18:931-941, MAR 1 2009
abstract,
full text
Taylor, J., Whiteford, N.E., Bradley, G., Watson, G.W.
Validation of all-atom phosphatidylcholine lipid force fields in the tensionless NPT ensemble
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:638-649, MAR 2009
abstract,
full text
Tatsis, V.A., Tsoulos, I.G., Stavrakoudis, A.
Molecular Dynamics Simulations of the TSSPSAD Peptide Antigen in Free and Bound with CAMPATH-1H Fab Antibody States: The Importance of the beta-Turn Conformation
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 15:1-9, MAR 2009
abstract,
full text
Panek, J.J., Ward, T.R., Jezierska, A., Novic, M.
Effects of tryptophan residue fluorination on streptavidin stability and biotin-streptavidin interactions via molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 15:257-266, MAR 2009
abstract,
full text
Kagawa, T.F., O'Connell, M.R., Mouat, P., Paoli, M., O'Toole, P.W., Cooney, J.C.
Model for Substrate Interactions in C5a Peptidase from Streptococcus pyogenes: A 1.9 angstrom Crystal Structure of the Active Form of ScpA
JOURNAL OF MOLECULAR BIOLOGY, 386:754-772, FEB 27 2009
abstract,
full text
Salcedo, E., Farrell, D.M., Zheng, L.J., Phistry, M., Bagg, E.E., Britt, S.G.
The Green-absorbing Drosophila Rh6 Visual Pigment Contains a Blue-shifting Amino Acid Substitution That Is Conserved in Vertebrates
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:5717-5722, FEB 27 2009
abstract,
full text
Cabeca, L.F., Pickholz, M., de Paula, E., Marsaioli, A.J.
Liposome-Prilocaine Interaction Mapping Evaluated through STD NMR and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 113:2365-2370, FEB 26 2009
abstract,
full text
Sener, M., Hsin, J., Trabuco, L.G., Villa, E., Qian, P., Hunter, C.N., Schulten, K.
Structural model and excitonic properties of the dimeric RC-LH1-Pufx complex from Rhodobacter sphaeroides
CHEMICAL PHYSICS, 357:188-197, FEB 23 2009
abstract,
full text,
TCBG publications
Gunnerson, K.N., Pereverzev, Y.V., Prezhdo, O.V.
Atomistic Simulation Combined with Analytic Theory To Study the Response of the P-Selectin/PSGL-1 Complex to an External Force
JOURNAL OF PHYSICAL CHEMISTRY B, 113:2090-2100, FEB 19 2009
abstract,
full text
Szep, S., Park, S., Boder, E.T., Van Duyne, G.D., Saven, J.G.
Structural coupling between FKBP12 and buried water
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:603-611, FEB 15 2009
abstract,
full text
Skjot, M., De Maria, L., Chatterjee, R., Svendsen, A., Patkar, S.A., Ostergaard, P.R., Brask, J.
Understanding the Plasticity of the alpha/beta Hydrolase Fold: Lid Swapping on the Candida antarctica Lipase B Results in Chimeras with Interesting Biocatalytic Properties
CHEMBIOCHEM, 10:520-527, FEB 13 2009
abstract,
full text
Radi, M., Maga, G., Alongi, M., Angeli, L., Samuele, A., Zanoli, S., Bellucci, L., Tafi, A., Casaluce, G., Giorgi, G., Armand-Ugon, M., Gonzalez, E., Este, J.A., Baltzinger, M., Bec, G., Dumas, P., Ennifar, E., Botta, M.
Discovery of Chiral Cyclopropyl Dihydro-Alkylthio-Benzyl-Oxopyrimidine (S-DABO) Derivatives as Potent HIV-1 Reverse Transcriptase Inhibitors with High Activity Against Clinically Relevant Mutants
JOURNAL OF MEDICINAL CHEMISTRY, 52:840-851, FEB 12 2009
abstract,
full text
Cai, K.C., Wang, J.P.
Multiple Anharmonic Vibrational Probes of Sugar Structure and Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1681-1692, FEB 12 2009
abstract,
full text
Lee, O.S., Schatz, G.C.
Molecular Dynamics Simulation of DNA-Functionalized Gold Nanoparticles
JOURNAL OF PHYSICAL CHEMISTRY C, 113:2316-2321, FEB 12 2009
abstract,
full text
Khavrutskii, I.V., Gorfe, A.A., Lu, B.Z., McCammon, J.A.
Free Energy for the Permeation of Na(+) and Cl(-) Ions and Their Ion-Pair through a Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:1706-1716, FEB 11 2009
abstract,
full text
Rodriguez, J., Semino, R., Laria, D.
Building up Nanotubes: Docking of "Janus" Cyclodextrins in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1241-1244, FEB 5 2009
abstract,
full text
Poghosyan, A.H., Arsenyan, L.H., Gharabekyan, H.H., Koetz, J., Shahinyan, A.A.
Molecular Dynamics Study of Poly(diallyldimethylammonium chloride) (PDADMAC)/Sodium Dodecyl Sulfate (SDS)/Decanol/Water Systems
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1303-1310, FEB 5 2009
abstract,
full text
Rodriguez, J., Elola, M.D.
Encapsulation of Small Ionic Molecules within alpha-Cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1423-1428, FEB 5 2009
abstract,
full text
Cruz-Chu, E.R., Aksimentiev, A., Schulten, K.
Ionic Current Rectification through Silica Nanopores
JOURNAL OF PHYSICAL CHEMISTRY C, 113:1850-1862, FEB 5 2009
abstract,
full text,
TCBG publications
Fuson, K.L., Ma, L., Sutton, R.B., Oberhauser, A.F.
The C2 Domains of Human Synaptotagmin 1 Have Distinct Mechanical Properties
BIOPHYSICAL JOURNAL, 96:1083-1090, FEB 4 2009
abstract,
full text
Dixit, A., Torkamani, A., Schork, N.J., Verkhivker, G.
Computational Modeling of Structurally Conserved Cancer Mutations in the RET and MET Kinases: The Impact on Protein Structure, Dynamics, and Stability
BIOPHYSICAL JOURNAL, 96:858-874, FEB 4 2009
abstract,
full text
Bellesia, G., Shea, J.E.
What Determines the Structure and Stability of KFFE Monomers, Dimers, and Protofibrils?
BIOPHYSICAL JOURNAL, 96:875-886, FEB 4 2009
abstract,
full text
Espinoza-Fonseca, L.M.
Leucine-rich hydrophobic clusters promote folding of the N-terminus of the intrinsically disordered transactivation domain of p53
FEBS LETTERS, 583:556-560, FEB 4 2009
abstract,
full text
Swift, R.V., Durrant, J., Amaro, R.E., McCammont, J.A.
Toward Understanding the Conformational Dynamics of RNA Ligation
BIOCHEMISTRY, 48:709-719, FEB 3 2009
abstract,
full text
Huang, Q., Korte, T., Rachakonda, P.S., Knapp, E.W., Herrmann, A.
Energetics of the loop-to-helix transition leading to the coiled-coil structure of influenza virus hemagglutinin HA2 subunits
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:291-303, FEB 1 2009
abstract,
full text
Banavali, N.K., Roux, B.
Flexibility and charge asymmetry in the activation loop of Src tyrosine kinases
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:378-389, FEB 1 2009
abstract,
full text
Furini, S., Beckstein, O., Domene, C.
Permeation of water through the KcsA K(+) channel
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 74:437-448, FEB 1 2009
abstract,
full text
Williams, S.L., Essex, J.W.
Study of the Conformational Dynamics of the Catalytic Loop of WT and G140A/G149A HIV-1 Integrase Core Domain Using Reversible Digitally Filtered Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:411-421, FEB 2009
abstract,
full text
Wong, S., Amaro, R.E., McCammon, J.A.
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:422-429, FEB 2009
abstract,
full text
Verdone, G., Corazza, A., Colebrooke, S.A., Cicero, D., Eliseo, T., Boyd, J., Doliana, R., Fogolari, F., Viglino, P., Colombatti, A., Campbell, I.D., Esposito, G.
NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1
JOURNAL OF BIOMOLECULAR NMR, 43:79-96, FEB 2009
abstract,
full text
Barria, M.I., Gonzalez, A., Vera-Otarola, J., Leon, U., Vollrath, V., Marsac, D., Monasterio, O., Perez-Acle, T., Soza, A., Lopez-Lastra, M.
Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation
NUCLEIC ACIDS RESEARCH, 37:957-971, FEB 2009
abstract,
full text
Miao, Y.L., Ortoleva, P.J.
Molecular Dynamics/Order Parameter Extrapolation for Bionanosystem Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:423-437, FEB 2009
abstract,
full text
Petridis, L., Smith, J.C.
A Molecular Mechanics Force Field for Lignin
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:457-467, FEB 2009
abstract,
full text
Sharma, M., Khanna, S., Bulusu, G., Mitra, A.
Comparative modeling of thioredoxin glutathione reductase from Schistosoma mansoni: A multifunctional target for antischistosomal therapy
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 27:665-675, FEB 2009
abstract,
full text
Bairagya, H.R., Mukhopadhyay, B.P., Sekarz, K.
Conserved Water Mediated H-bonding Dynamics of Inhibitor, Cofactor, Asp 364 and Asn 303 in Human IMPDH II
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 26:497-507, FEB 2009
abstract,
full text
Clark, L.A., Boriack-Sjodin, P.A., Day, E., Eldredge, J., Fitch, C., Jarpe, M., Miller, S., Li, Y., Simon, K., van Vlijmen, H.W.T.
An antibody loop replacement design feasibility study and a loop-swapped dimer structure
PROTEIN ENGINEERING DESIGN & SELECTION, 22:93-101, FEB 2009
abstract,
full text
Russel, D., Lasker, K., Phillips, J., Schneidman-Duhovny, D., Velazquez-Muriel, J.A., Sali, A.
The structural dynamics of macromolecular processes
CURRENT OPINION IN CELL BIOLOGY, 21:97-108, FEB 2009
abstract,
full text
Poghosyan, A.H., Shahinyan, A.A.
A new parameter for validation molecular dynamics simulation (MD) data
COMPUTER PHYSICS COMMUNICATIONS, 180:238-240, FEB 2009
abstract,
full text
Stavrakoudis, A.
A disulfide linked model of the complement protein C8 gamma complexed with C8 alpha indel peptide
JOURNAL OF MOLECULAR MODELING, 15:165-171, FEB 2009
abstract,
full text
Pagadala, N.S., Arha, M., Reddy, P.S., Kumar, R., Sirisha, V.L., Prashant, S., Reddy, K.J., Khan, B., Rawal, S.K., Kishor, P.B.K.
Phylogenetic analysis, homology modelling, molecular dynamics and docking studies of caffeoyl-CoA-O- methyl transferase (CCoAOMT 1 and 2) isoforms isolated from subabul (Leucaena leucocephala)
JOURNAL OF MOLECULAR MODELING, 15:203-221, FEB 2009
abstract,
full text
Yu, X., Wang, Q.M., Yang, J.C., Buch, I., Tsai, C.J., Ma, B.Y., Cheng, S.Z.D., Nussinov, R., Zheng, J.
Mutational Analysis and Allosteric Effects in the HIV-1 Capsid Protein Carboxyl-Terminal Dimerization Domain
BIOMACROMOLECULES, 10:390-399, FEB 2009
abstract,
full text
Reddy, G., Straub, J.E., Thirumalai, D.
Influence of Preformed Asp23-Lys28 Salt Bridge on the Conformational Fluctuations of Monomers and Dimers of A beta Peptides with Implications for Rates of Fibril Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1162-1172, JAN 29 2009
abstract,
full text
Kaminski, S., Daminelli, G., Mroginski, M.A.
Molecular Dynamics Simulations of the Chromophore Binding Site of Deinococcus radiodurans Bacteriophytochrome Using New Force Field Parameters for the Phytochromobilin Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 113:945-958, JAN 29 2009
abstract,
full text
Khurana, E., Dal Peraro, M., DeVane, R., Vemparala, S., DeGrado, W.F., Klein, M.L.
Molecular dynamics calculations suggest a conduction mechanism for the M2 proton channel from influenza A virus
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 106:1069-1074, JAN 27 2009
abstract,
full text
Zhu, Y.D., Wei, M.J., Shao, Q., Lu, L.H., Lu, X.H., Shen, W.F.
Molecular Dynamics Study of Pore Inner Wall Modification Effect in Structure of Water Molecules Confined in Single-Walled Carbon Nanotubes
Journal of Physical Chemistry C, 113:882-889, JAN 22 2009
abstract,
full text
Jones, M.K., Catte, A., Patterson, J.C., Gu, F.F., Chen, J.G., Li, L., Segrest, J.P.
Thermal Stability of Apolipoprotein A-I in High-Density Lipoproteins by Molecular Dynamics
BIOPHYSICAL JOURNAL, 96:354-371, JAN 21 2009
abstract,
full text
Tayefeh, S., Kloss, T., Kreim, M., Gebhardt, M., Baumeister, D., Hertel, B., Richter, C., Schwalbe, H., Moroni, A., Thiel, G., Kast, S.M.
Model Development for the Viral Kcv Potassium Channel
BIOPHYSICAL JOURNAL, 96:485-498, JAN 21 2009
abstract,
full text
Comer, J., Dimitrov, V., Zhao, Q., Timp, G., Aksimentiev, A.
Microscopic Mechanics of Hairpin DNA Translocation through Synthetic Nanopores
BIOPHYSICAL JOURNAL, 96:593-608, JAN 21 2009
abstract,
full text
Chen, Y., Chen, C.G., Kotsikorou, E., Lynch, D.L., Reggio, P.H., Liu-Chen, L.Y.
GEC1-kappa Opioid Receptor Binding Involves Hydrophobic Interactions
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:1673-1685, JAN 16 2009
abstract,
full text
Berteotti, A., Cavalli, A., Branduardi, D., Gervasio, F.L., Recanatini, M., Parrinello, M.
Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:244-250, JAN 14 2009
abstract,
full text
Tiberio, G., Muccioli, L., Berardi, R., Zannoni, C.
Towards in Silico Liquid Crystals. Realistic Transition Temperatures and Physical Properties for n-Cyanobiphenyls via Molecular Dynamics Simulations
CHEMPHYSCHEM, 10:125-136, JAN 12 2009
abstract,
full text
Ju, P.C., Pages, G., Riek, R.P., Chen, P.C., Torres, A.M., Bansal, P.S., Kuyucak, S., Kuchel, P.W., Vandenberg, J.I.
The Pore Domain Outer Helix Contributes to Both Activation and Inactivation of the hERG K(+) Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 284:1000-1008, JAN 9 2009
abstract,
full text
Calderon, C.P., Harris, N.C., Kiang, C.H., Cox, D.D.
Quantifying Multiscale Noise Sources in Single-Molecule Time Series
JOURNAL OF PHYSICAL CHEMISTRY B, 113:138-148, JAN 8 2009
abstract,
full text
Toschi, F., Lugli, F., Biscarini, F., Zerbetto, F.
Effects of Electric Field Stress on a beta-Amyloid Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 113:369-376, JAN 8 2009
abstract,
full text
Peters, G.H., Hansen, F.Y., Moller, M.S., Westh, P.
Effects of Fatty Acid Inclusion in a DMPC Bilayer Membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 113:92-102, JAN 8 2009
abstract,
full text
Zhu, H., May, V.
Mixed Quantum Classical Simulations of Electronic Excitation Energy Transfer and Related Optical Spectra: Supramolecular Pheophorbide-a Complexes in Solution
ENERGY TRANSFER DYNAMICS IN BIOMATERIAL SYSTEMS, 93:35-71, 2009
abstract,
full text
Stavrakoudis, A., Tsoulos, I.G., Shenkarev, Z.O., Ovchinnikova, T.V.
Molecular Dynamics Simulation of Antimicrobial Peptide Arenicin-2: beta-Hairpin Stabilization by Noncovalent Interactions
BIOPOLYMERS, 92:143-155, 2009
abstract,
full text
Chiu, C.C., Dieckmann, G.R., Nielsen, S.O.
Role of Peptide-Peptide Interactions in Stabilizing Peptide-Wrapped Single-Walled Carbon Nanotubes: A Molecular Dynamics Study
BIOPOLYMERS, 92:156-163, 2009
abstract,
full text
Zanuy, D., Curco, D., Nussinov, R., Aleman, C.
Influence of the Dye Presence on the Conformational Preferences of CREKA, a Tumor Homing Linear Pentapeptide
BIOPOLYMERS, 92:83-93, 2009
abstract,
full text
Vasilyeva, A., Clodfelter, J.E., Rector, B., Hollis, T., Scarpinato, K.D., Salsbury, F.R.
Small molecule induction of MSH2-dependent cell death suggests a vital role of mismatch repair proteins in cell death
DNA REPAIR, 8:103-113, JAN 1 2009
abstract,
full text
Sinicropi, A., Bernini, C., Basosi, R., Olivucci, M.
A novel biomimetic photochemical switch at work: design of a photomodulable peptide
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 8:1639-1649, 2009
abstract,
full text
Flenner, E., Das, J., Rheinstadter, M.C., Kosztin, I.
Subdiffusion and lateral diffusion coefficient of lipid atoms and molecules in phospholipid bilayers
PHYSICAL REVIEW E, 79: Art. No. 011907, JAN 2009
abstract,
full text
Baskin, I.I., Palyulin, V.A., Zefirov, N.S.
Molecular modelling of receptors of physiologically active compounds for medicinal chemistry purposes
RUSSIAN CHEMICAL REVIEWS, 78:495-511, 2009
abstract,
full text
Williams, S.L., Andrew McCammon, J.
Conformational Dynamics of the Flexible Catalytic Loop in Mycobacterium tuberculosis 1-Deoxy-d-xylulose 5-Phosphate Reductoisomerase
CHEMICAL BIOLOGY & DRUG DESIGN, 73:26-38, JAN 2009
abstract,
full text
Olsson, J.D.M., Landstrom, J., Ronnols, J., Oscarson, S., Widmalm, G.
Synthesis of and molecular dynamics simulations on a tetrasaccharide corresponding to the repeating unit of the capsular polysaccharide from Salmonella enteritidis
ORGANIC & BIOMOLECULAR CHEMISTRY, 7:1612-1618, 2009
abstract,
full text
Calleja, V., Laguerre, M., Parker, P.J., Larijani, B.
Role of a Novel PH-Kinase Domain Interface in PKB/Akt Regulation: Structural Mechanism for Allosteric Inhibition
PLOS BIOLOGY, 7:189-200, JAN 2009
abstract,
full text
Vistoli, G., Pedretti, A., Mazzolari, A., Bolchi, C., Testa, B.
Influence of Ionization State on the Activation of Temocapril by hCES1: A Molecular-Dynamics Study
CHEMISTRY & BIODIVERSITY, 6:2092-2100, 2009
abstract,
full text
Bhowmik, R., Katti, K.S., Katti, D.R.
Molecular interactions of degradable and non-degradable polymers with hydroxyapatite influence mechanics of polymer-hydroxyapatite nanocomposite biomaterials
INTERNATIONAL JOURNAL OF NANOTECHNOLOGY, 6:511-529, 2009
abstract,
full text
Alizadeh, A., Parsafar, G.A., Ejtehadi, M.R.
Mechanism of water permeation through modified carbon nanotubes as a model for peptide nanotube channels
INTERNATIONAL JOURNAL OF NANOTECHNOLOGY, 6:926-941, 2009
abstract,
full text
Yakubovich, A.V., Solov'yov, I.A., Solov'yov, A.V., Greiner, W.
Phase transitions in polypeptides: analysis of energy fluctuations
EUROPEAN PHYSICAL JOURNAL D, 51:25-32, JAN 2009
abstract,
full text
Wang, J.H., Cao, Z.X., Li, S.Q.
Molecular Dynamics Simulations of Intrinsically Disordered Proteins in Human Diseases
CURRENT COMPUTER-AIDED DRUG DESIGN, 5:280-287, 2009
abstract,
full text
Lundberg, M., Kawatsu, T., Vreven, T., Frisch, M.J., Morokuma, K.
Transition States in a Protein Environment - ONIOM QM:MM Modeling of Isopenicillin N Synthesis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 5:222-234, JAN 2009
abstract,
full text
Zhuang, W., Hayashi, T., Mukamel, S.
Coherent Multidimensional Vibrational Spectroscopy of Biomolecules: Concepts, Simulations, and Challenges
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 48:3750-3781, 2009
full text
Vaidehi, N., Pease, J.E., Horuk, R.
MODELING SMALL MOLECULE-COMPOUND BINDING To G-PROTEIN-COUPLED RECEPTORS
CHEMOKINES, PT A, 460:263-+, 2009
abstract,
full text
Garate, J.A., English, N.J., MacElroy, J.M.D.
Carbon nanotube assisted water self-diffusion across lipid membranes in the absence and presence of electric fields
MOLECULAR SIMULATION, 35:3-12, 2009
abstract,
full text
Gallo, M.T., Grant, B.J., Teodoro, M.L., Melton, J., Cieplak, P., Phillips, G.N., Stec, B.
Novel procedure for thermal equilibration in molecular dynamics simulation
MOLECULAR SIMULATION, 35:349-357, 2009
abstract,
full text
Choi, H.J., Kim, J.Y., Hong, S.D., Ha, M.Y., Jang, J.
Molecular simulation of the nanoscale water confined between an atomic force microscope tip and a surface
MOLECULAR SIMULATION, 35:466-472, 2009
abstract,
full text
Mulheran, P., Kubiak, K.
Protein adsorption mechanisms on solid surfaces: lysozyme-on-mica
MOLECULAR SIMULATION, 35:561-566, 2009
abstract,
full text
Zhao, X.C.
Motions of ions in a nanoscale Paul trap from molecular dynamics
MOLECULAR SIMULATION, 35:812-821, 2009
abstract,
full text
Yang, Q., Du, L.P., Tsai, K.C., Wang, X.J., Li, M.Y., You, Q.D.
Pharmacophore Mapping for Kv1.5 Potassium Channel Blockers
QSAR & COMBINATORIAL SCIENCE, 28:59-71, JAN 2009
abstract,
full text
Broer, A., Balkrishna, S., Kottra, G., Davis, S., Oakley, A., Broer, S.
Sodium translocation by the iminoglycinuria associated imino transporter (SLC6A20)
MOLECULAR MEMBRANE BIOLOGY, 26:333-346, 2009
abstract,
full text
Artali, R., Beretta, G., Morazzoni, P., Bombardelli, E., Meneghetti, F.
Green tea catechins in chemoprevention of cancer: A molecular docking investigation into their interaction with glutathione S-transferase (GST P1-1)
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 24:287-295, 2009
abstract,
full text
Suter, J.L., Anderson, R.L., Greenwell, H.C., Coveney, P.V.
Recent advances in large-scale atomistic and coarse-grained molecular dynamics simulation of clay minerals
JOURNAL OF MATERIALS CHEMISTRY, 19:2482-2493, 2009
abstract,
full text
Gajdanowicz, P., Garcia-Mata, C., Gonzalez, W., Morales-Navarro, S.E., Sharma, T., Gonzalez-Nilo, F.D., Gutowicz, J., Mueller-Roeber, B., Blatt, M.R., Dreyer, I.
Distinct roles of the last transmembrane domain in controlling Arabidopsis K(+) channel activity
NEW PHYTOLOGIST, 182:380-391, 2009
abstract,
full text
Shi, G.C., Kindratenko, V.V., Ufimtsev, I.S., Martinez, T.J., Phillips, J.C., Gottlieb, S.A.
Implementation of scientific computing applications on the Cell Broadband Engine
SCIENTIFIC PROGRAMMING, 17:135-151, 2009
abstract,
full text
Jia, L.L., Nguyen, D., Halley, J.W., Pham, P., Lamanna, W., Hamrock, S.
Proton Transport in HTFSI-TFSI-EMI Mixtures: Experiment and Theory
JOURNAL OF THE ELECTROCHEMICAL SOCIETY, 156:B136-B151, 2009
abstract,
full text
Monti, M.C., Casapullo, A., Cavasotto, C.N., Tosco, A., Dal Piaz, F., Ziemys, A., Margarucci, L., Riccio, R.
The Binding Mode of Petrosaspongiolide M to the Human Group HA Phospholipase A(2): Exploring the Role of Covalent and Noncovalent Interactions in the Inhibition Process
CHEMISTRY-A EUROPEAN JOURNAL, 15:1155-1163, 2009
abstract,
full text
Casanovas, J., Preat, J., Zanuy, D., Aleman, C.
Sensing Abilities of Crown Ether Functionalized Polythiophenes
CHEMISTRY-A EUROPEAN JOURNAL, 15:4676-4684, 2009
abstract,
full text
Cruz-Chu, E.R., Ritz, T., Siwy, Z.S., Schulten, K.
Molecular control of ionic conduction in polymer nanopores
FARADAY DISCUSSIONS, 143:47-62, 2009
abstract,
full text,
TCBG publications
Tobias, D.J., Sengupta, N., Tarek, N.
Hydration dynamics of purple membranes
FARADAY DISCUSSIONS, 141:99-116, 2009
abstract,
full text
Ponomarev, S.Y., Putkaradze, V., Bishop, T.C.
Relaxation dynamics of nucleosomal DNA
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:10633-10643, 2009
abstract,
full text
Zakrzewska, K., Bouvier, B., Michon, A., Blanchet, C., Lavery, R.
Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:10712-10721, 2009
abstract,
full text
Murtola, T., Bunker, A., Vattulainen, I., Deserno, M., Karttunen, M.
Multiscale modeling of emergent materials: biological and soft matter
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:1869-1892, 2009
abstract,
full text
Zegarra, F.C., Peralta, G.N., Coronado, A.M., Gao, Y.Q.
Free energies and forces in helix-coil transition of homopolypeptides under stretching
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:4019-4024, 2009
abstract,
full text
Goldsmith, J., Martens, C.C.
Pressure-induced water flow through model nanopores
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:528-533, 2009
abstract,
full text
Sezer, D., Prandolini, M.J., Prisner, T.F.
Dynamic nuclear polarization coupling factors calculated from molecular dynamics simulations of a nitroxide radical in water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:6626-6637, 2009
abstract,
full text
Sezer, D., Gafurov, M., Prandolini, M.J., Denysenkov, V.P., Prisner, T.F.
Dynamic nuclear polarization of water by a nitroxide radical: rigorous treatment of the electron spin saturation and comparison with experiments at 9.2 Tesla
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:6638-6653, 2009
abstract,
full text
Cai, K.C., Han, C., Wang, J.P.
Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:9149-9159, 2009
abstract,
full text
Cruzeiro, L., Lopes, P.A.
Are the native states of proteins kinetic traps?
MOLECULAR PHYSICS, 107:1485-1493, 2009
abstract,
full text
Nevidimov, A.V., Razumov, V.F.
Molecular dynamics simulations of AOT reverse micelles' self-assembly
MOLECULAR PHYSICS, 107:2169-2180, 2009
abstract,
full text
Chen, C., Li, W.Z., Song, Y.C., Yang, J.
Molecular dynamics simulation studies of cryoprotective agent solutions: the relation between melting temperature and the ratio of hydrogen bonding acceptor to donor number
MOLECULAR PHYSICS, 107:673-684, 2009
abstract,
full text
Zhmakin, A.I.
Fundamentals of Cryobiology Physical Phenomena and Mathematical Models Introduction
FUNDAMENTALS OF CRYOBIOLOGY: PHYSICAL PHENOMENA AND MATHEMATICAL MODELS, , 2009
full text
Rikvold, P.A., Abou Hamad, I., Juwono, T., Robb, D.T., Novotny, M.A.
Applications of Computer Simulations and Statistical Mechanics in Surface Electrochemistry
MODERN ASPECTS OF ELECTROCHEMISTRY, NO 44: MODELLING AND NUMERICAL SIMULATIONS II, Issue 44, 131-149, 2009
abstract,
full text
Marchese, F.T.
Interactive Molecular Visualization at the Interface
TRENDS IN INTERACTIVE VISUALIZATION: STATE-OF-THE-ART SURVEY, DOI 10.1007/978-1-84800-269-2_11, 2009
abstract,
full text
Benitez, B.A.S., Arora, K., Balistreri, L., Schlick, T.
Mismatched Base-Pair Simulations for ASFV Pol x/DNA Complexes Help Interpret Frequent G.G Misincorporation
JOURNAL OF MOLECULAR BIOLOGY, 384:1086-1097, DEC 31 2008
abstract,
full text
Pomata, M.H.H., Laria, D., Skaf, M.S., Elola, M.D.
Molecular dynamics simulations of AOT-water/formamide reverse micelles: Structural and dynamical properties
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 244503, DEC 28 2008
abstract,
full text
Zhu, J.H., Luo, B.H., Xiao, T., Zhang, C.Z., Nishida, N., Springer, T.A.
Structure of a Complete Integrin Ectodomain in a Physiologic Resting State and Activation and Deactivation by Applied Forces
MOLECULAR CELL, 32:849-861, DEC 26 2008
abstract,
full text
Chiu, C.C., Dieckmann, G.R., Nielsen, S.O.
Molecular Dynamics Study of a Nanotube-Binding Amphiphilic Helical Peptide at Different Water/Hydrophobic Interfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 112:16326-16333, DEC 25 2008
abstract,
full text
Peters, B., Zimmermann, N.E.R., Beckham, G.T., Tester, J.W., Trout, B.L.
Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:17342-17350, DEC 24 2008
abstract,
full text
Rodriguez, Y., Mezei, M., Osman, R.
The PT1-Ca(2+) Gla Domain Binds to a Membrane through Two Dipalmitoylphosphatidylserines. A Computational Study
BIOCHEMISTRY, 47:13267-13278, DEC 16 2008
abstract,
full text
Wu, S., Zhuravlev, P.I., Papoian, G.A.
High Resolution Approach to the Native State Ensemble Kinetics and Thermodynamics
BIOPHYSICAL JOURNAL, 95:5524-5532, DEC 15 2008
abstract,
full text
Peplowski, L., Kubiak, K., Nowak, W.
Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095
CHEMICAL PHYSICS LETTERS, 467:144-149, DEC 15 2008
abstract,
full text
Rheinstadter, M.C., Das, J., Flenner, E.J., Bruning, B., Seydel, T., Kosztin, I.
Motional Coherence in Fluid Phospholipid Membranes
PHYSICAL REVIEW LETTERS, 101: Art. No. 248106, DEC 12 2008
abstract,
full text
Sint, K., Wang, B., Kral, P.
Selective Ion Passage through Functionalized Graphene Nanopores
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:16448-+, DEC 10 2008
abstract,
full text
van der Kamp, M.W., Shaw, K.E., Woods, C.J., Mulholland, A.J.
Biomolecular simulation and modelling: status, progress and prospects
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 5:S173-S190, DEC 6 2008
abstract,
full text
Kelkar, M.S., Shi, W., Maginn, E.J.
Determining the Accuracy of Classical Force Fields for Ionic Liquids: Atomistic Simulation of the Thermodynamic and Transport Properties of 1-Ethyl-3-methylimidazolium Ethylsulfate ([emim][EtSO(4)]) and Its Mixtures with Water
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 47:9115-9126, DEC 3 2008
abstract,
full text
Heo, J., Ja, W.W., Benzer, S., Goddard, W.A.
The Predicted Binding Site and Dynamics of Peptide Inhibitors to the Methuselah GPCR from Drosophila melanogaster
BIOCHEMISTRY, 47:12740-12749, DEC 2 2008
abstract,
full text
Fowler, P.W., Tai, K.H., Sansom, M.S.P.
The Selectivity of K+ Ion Channels: Testing the Hypotheses
BIOPHYSICAL JOURNAL, 95:5062-5072, DEC 1 2008
abstract,
full text
Zhang, Z.Y., Lu, L.Y., Noid, W.G., Krishna, V., Pfaendtner, J., Voth, G.A.
A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules
BIOPHYSICAL JOURNAL, 95:5073-5083, DEC 1 2008
abstract,
full text
Wen, P.C., Tajkhorshid, E.
Dimer Opening of the Nucleotide Binding Domains of ABC Transporters after ATP Hydrolysis
BIOPHYSICAL JOURNAL, 95:5100-5110, DEC 1 2008
abstract,
full text
Shaikh, S.A., Tajkhorshid, E.
Potential Cation and H+ Binding Sites in Acid Sensing Ion Channel-1
BIOPHYSICAL JOURNAL, 95:5153-5164, DEC 1 2008
abstract,
full text
Sengupta, N., Jaud, S., Tobias, D.J.
Hydration Dynamics in a Partially Denatured Ensemble of the Globular Protein Human alpha-Lactalbumin Investigated with Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 95:5257-5267, DEC 1 2008
abstract,
full text
Pfaendtner, J., Voth, G.A.
Molecular Dynamics Simulation and Coarse-Grained Analysis of the Arp2/3 Complex
BIOPHYSICAL JOURNAL, 95:5324-5333, DEC 1 2008
abstract,
full text
Orlowski, S., Nowak, W.
Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin
BIOSYSTEMS, 94:263-266, DEC 2008
abstract,
full text
Singh, N., Briggs, J.M.
Molecular Dynamics Simulations of Factor Xa: Insight into Conformational Transition of Its Binding Subsites
BIOPOLYMERS, 89:1104-1113, DEC 2008
abstract,
full text
Kim, S.N., Kuang, Z.F., Grote, J.G., Farmer, B.L., Naik, R.R.
Enrichment of (6,5) Single Wall Carbon Nanotubes Using Genomic DNA
NANO LETTERS, 8:4415-4420, DEC 2008
abstract,
full text
Liu, F., Ye, X.S., Wu, T., Wang, C.T., Shen, J.W., Kang, Y.
Conformational Mobility of GOx Coenzyme Complex on Single-Wall Carbon Nanotubes
SENSORS, 8:8453-8462, DEC 2008
abstract,
full text
Raimondo, D., Giorgetti, A., Bernassola, F., Melino, G., Tramontano, A.
Modelling and molecular dynamics of the interaction between the E3 ubiquitin ligase itch and the E2 UbcH7
BIOCHEMICAL PHARMACOLOGY, 76:1620-1627, DEC 1 2008
abstract,
full text
Laio, A., Gervasio, F.L.
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
REPORTS ON PROGRESS IN PHYSICS, 71: Art. No. 126601, DEC 2008
abstract,
full text
Lee, T.S., Ma, W.L., Zhang, X., Giles, F., Cortes, J., Kantarjian, H., Albitar, M.
BCR-ABL alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations
MOLECULAR CANCER THERAPEUTICS, 7:3834-3841, DEC 2008
abstract,
full text
Colizzi, F., Recanatini, M., Cavalli, A.
Mechanical Features of Plasmodium falciparum Acyl Carrier Protein in the Delivery of Substrates
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2289-2293, DEC 2008
abstract,
full text
Verstraelen, T., Van Houteghem, M., Van Speybroeck, V., Waroquier, M.
MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2414-2424, DEC 2008
abstract,
full text
Emperador, A., Meyer, T., Orozco, M.
United-Atom Discrete Molecular Dynamics of Proteins Using Physics-Based Potentials
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:2001-2010, DEC 2008
abstract,
full text
Chipot, C.
Milestones in the Activation of a G Protein-Coupled Receptor. Insights from Molecular-Dynamics Simulations into the Human Cholecystokinin Receptor-1
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:2150-2159, DEC 2008
abstract,
full text
Tsigelny, I.F., Sharikov, Y., Miller, M.A., Masliah, E.
Mechanism of alpha-synuclein oligomerization and membrane interaction: theoretical approach to unstructured proteins studies
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE, 4:350-357, DEC 2008
abstract,
full text
Pedretti, A., De Luca, L., Marconi, C., Negrisoli, G., Aldini, G., Vistoli, G.
Modeling of the Intestinal Peptide Transporter hPepT1 and Analysis of Its Transport Capacities by Docking and Pharmacophore Mapping
CHEMMEDCHEM, 3:1913-1921, DEC 2008
abstract,
full text
Grigorenko, B.L., Shadrina, M.S., Topol, I.A., Collins, J.R., Nemukhin, A.V.
Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1784:1908-1917, DEC 2008
abstract,
full text
Shen, H.B., Xu, F., Hu, H.R., Wang, F.F., Wu, Q., Huang, Q., Wang, H.H.
Coevolving residues of (beta/alpha)(8)-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics
JOURNAL OF STRUCTURAL BIOLOGY, 164:281-292, DEC 2008
abstract,
full text
Labro, A.J., Raes, A.L., Grottesi, A., Van Hoorick, D., Sansom, M.S.P., Snyders, D.J.
Kv Channel Gating Requires a Compatible S4-S5 Linker and Bottom Part of S6, Constrained by Non-interacting Residues
JOURNAL OF GENERAL PHYSIOLOGY, 132:667-680, DEC 2008
abstract,
full text
Gumbart, J., Schulten, K.
The Roles of Pore Ring and Plug in the SecY Protein-conducting Channel
JOURNAL OF GENERAL PHYSIOLOGY, 132:709-719, DEC 2008
abstract,
full text,
TCBG publications
Giupponi, G., Harvey, M.J., De Fabritiis, G.
The impact of accelerator processors for high-throughput molecular modeling and simulation
DRUG DISCOVERY TODAY, 13:1052-1058, DEC 2008
abstract,
full text
Alexiadis, A., Kassinos, S.
Molecular Simulation of Water in Carbon Nanotubes
CHEMICAL REVIEWS, 108:5014-5034, DEC 2008
full text
Feng, J.J., Murgida, D.H., Kuhlmann, U., Utesch, T., Mroginski, M.A., Hildebrandt, P., Weidinger, I.M.
Gated Electron Transfer of Yeast Iso-1 Cytochrome c on Self-Assembled Monolayer-Coated Electrodes
JOURNAL OF PHYSICAL CHEMISTRY B, 112:15202-15211, NOV 27 2008
abstract,
full text
Romanowska, J., Setny, P., Trylska, J.
Molecular Dynamics Study of the Ribosomal A-Site
JOURNAL OF PHYSICAL CHEMISTRY B, 112:15227-15243, NOV 27 2008
abstract,
full text
Wedberg, R., Peters, G.H., Abildskov, J.
Total correlation function integrals and isothermal compressibilities from molecular simulations
FLUID PHASE EQUILIBRIA, 273:1-10, NOV 25 2008
abstract,
full text
Vladimirov, E., Ivanova, A., Rosch, N.
Effect of solvent polarization on the reorganization energy of electron transfer from molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 194515, NOV 21 2008
abstract,
full text
Vaitheeswaran, S., Thirumalai, D.
Interactions between amino acid side chains in cylindrical hydrophobic nanopores with applications to peptide stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:17636-17641, NOV 18 2008
abstract,
full text
Jang, H., Ma, B., Lal, R., Nussinov, R.
Models of Toxic beta-Sheet Channels of Protegrin-1 Suggest a Common Subunit Organization Motif Shared with Toxic Alzheimer beta-Amyloid Ion Channels
BIOPHYSICAL JOURNAL, 95:4631-4642, NOV 15 2008
abstract,
full text
Hogberg, C.J., Nikitin, A.M., Lyubartsev, A.P.
Modification of the CHARMM force field for DMPC lipid bilayer
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:2359-2369, NOV 15 2008
abstract,
full text
Haddadian, E.J., Cheng, M.H.Y., Coalson, R.D., Xu, Y., Tang, P.
In Silico Models for the Human alpha 4 beta 2 Nicotinic Acetylcholine Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 112:13981-13990, NOV 6 2008
abstract,
full text
Gutowski, K.E., Maginn, E.J.
Amine-Functionalized Task-Specific Ionic Liquids: A Mechanistic Explanation for the Dramatic Increase in Viscosity upon Complexation with CO2 from Molecular Simulation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:14690-14704, NOV 5 2008
abstract,
full text
Pickholz, M., Fraceto, L.F., de Paula, E.
Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 108:2386-2391, NOV 5 2008
abstract,
full text
Firlej, L., Kuchta, B., Roth, M.W., Connolly, M.J., Wexler, C.
Structural and Phase Properties of Tetracosane (C24H50) Monolayers Adsorbed on Graphite: An Explicit Hydrogen Molecular Dynamics Study
LANGMUIR, 24:12392-12397, NOV 4 2008
abstract,
full text
Hua, L., Zhou, R.H., Thirumalai, D., Berne, B.J.
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:16928-16933, NOV 4 2008
abstract,
full text
McDaniel, A., Fuchs, E., Liu, Y., Ford, C.
Directed evolution of Aspergillus niger glucoamylase to increase thermostability
MICROBIAL BIOTECHNOLOGY, 1:523-531, NOV 2008
abstract,
full text
Lyman, E., Pfaendtner, J., Voth, G.A.
Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins
BIOPHYSICAL JOURNAL, 95:4183-4192, NOV 1 2008
abstract,
full text
Vashisth, H., Abrams, C.F.
Ligand Escape Pathways and (Un)Binding Free Energy Calculations for the Hexameric Insulin-Phenol Complex
BIOPHYSICAL JOURNAL, 95:4193-4204, NOV 1 2008
abstract,
full text
Thogersen, L., Schiott, B., Vosegaard, T., Nielsen, N.C., Tajkhorshid, E.
Peptide Aggregation and Pore Formation in a Lipid Bilayer: A Combined Coarse-Grained and All Atom Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 95:4337-4347, NOV 1 2008
abstract,
full text
Trzaskowski, B., Leonarski, F., Les, A., Adamowicz, L.
Altering the Orientation of Proteins on Self-Assembled Monolayers: A Computational Study
BIOMACROMOLECULES, 9:3239-3245, NOV 2008
abstract,
full text
Forney, M.W., Janosi, L., Kosztin, I.
Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes
PHYSICAL REVIEW E, 78: Art. No. 051913, NOV 2008
abstract,
full text
Miguel, V., Monti, M.R., Argarana, C.E.
The role of MutS oligomers on Pseudomonas aeruginosa Mismatch Repair System activity
DNA REPAIR, 7:1799-1808, NOV 1 2008
abstract,
full text
Buehler, M.J., Keten, S., Ackbarow, T.
Theoretical and computational hierarchical nanomechanics of protein materials: Deformation and fracture
PROGRESS IN MATERIALS SCIENCE, 53:1101-1241, NOV 2008
abstract,
full text
Tintori, C., Corradi, V., Magnani, M., Manetti, F., Botta, M.
Targets Looking for Drugs: A Multistep Computational Protocol for the Development of Structure-Based Pharmacophores and Their Applications for Hit Discovery
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2166-2179, NOV 2008
abstract,
full text
Chimerel, C., Movileanu, L., Pezeshki, S., Winterhalter, M., Kleinekathofer, U.
Transport at the nanoscale: temperature dependence of ion conductance
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 38:121-125, NOV 2008
abstract,
full text
Alam, S.R., Agarwal, P.K., Vetter, J.S.
Performance characteristics of biomolecular simulations on high-end systems with multi-core processors
PARALLEL COMPUTING, 34:640-651, NOV 2008
abstract,
full text
Wang, L.G., Ounjai, P., Sigworth, F.J.
Streptavidin crystals as nanostructured supports and image-calibration references for cryo-EM data collection
JOURNAL OF STRUCTURAL BIOLOGY, 164:190-198, NOV 2008
abstract,
full text
Liu, M., Su, J.G., Kong, R., Sun, T.G., Tan, J.J., Chen, W.Z., Wang, C.X.
Molecular dynamics simulations of the bacterial periplasmic heme binding proteins ShuT and PhuT
BIOPHYSICAL CHEMISTRY, 138:42-49, NOV 2008
abstract,
full text
Harding, J.H., Duffy, D.M., Sushko, M.L., Rodger, P.M., Quigley, D., Elliott, J.A.
Computational Techniques at the Organic-Inorganic Interface in Biomineralization
CHEMICAL REVIEWS, 108:4823-4854, NOV 2008
full text
Wang, B.Y., Vukovic, L., Kral, P.
Nanoscale Rotary Motors Driven by Electron Tunneling
PHYSICAL REVIEW LETTERS, 101: Art. No. 186808, OCT 31 2008
abstract,
full text
Cooke, B., Schmidler, S.C.
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 164112, OCT 28 2008
abstract,
full text
Halverson, J.D., Maldarelli, C., Couzis, A., Koplik, J.
A molecular dynamics study of the motion of a nanodroplet of pure liquid on a wetting gradient
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 164708, OCT 28 2008
abstract,
full text
Cozzini, P., Kellogg, G.E., Spyrakis, F., Abraham, D.J., Costantino, G., Emerson, A., Fanelli, F., Gohlke, H., Kuhn, L.A., Morris, G.M., Orozco, M., Pertinhez, T.A., Rizzi, M., Sotriffer, C.A.
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
JOURNAL OF MEDICINAL CHEMISTRY, 51:6237-6255, OCT 23 2008
full text
Bonomi, M., Branduardi, D., Gervasio, F.L., Parrinello, M.
The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:13938-13944, OCT 22 2008
abstract,
full text
Huber, T., Menon, S., Sakmar, T.P.
Structural basis for ligand binding and specificity in adrenergic receptors: Implications for GPCR-targeted drug discovery
BIOCHEMISTRY, 47:11013-11023, OCT 21 2008
abstract,
full text
Rodinger, T., Howell, P.L., Pomes, R.
Calculation of absolute protein-ligand binding free energy using distributed replica sampling
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 155102, OCT 21 2008
abstract,
full text
Joshi, M.C., Sharma, A., Kant, S., Birah, A., Gupta, G.P., Khan, S.R., Bhatnagar, R., Banerjee, N.
An insecticidal GroEL protein with chitin binding activity from Xenorhabdus nematophila
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:28287-28296, OCT 17 2008
abstract,
full text
Tsukazaki, T., Mori, H., Fukai, S., Ishitani, R., Mori, T., Dohmae, N., Perederina, A., Sugita, Y., Vassylyev, D.G., Ito, K., Nureki, O.
Conformational transition of Sec machinery inferred from bacterial SecYE structures
NATURE, 455:988-U72, OCT 16 2008
abstract,
full text
Ballano, G., Zanuy, D., Jimenez, A.I., Cativiela, C., Nussinov, R., Aleman, C.
Structural Analysis of a beta-Helical Protein Motif Stabilized by Targeted Replacements with Conformationally Constrained Amino Acids
JOURNAL OF PHYSICAL CHEMISTRY B, 112:13101-13115, OCT 16 2008
abstract,
full text
Zeiger, A.S., Layton, B.E.
Molecular Modeling of the Axial and Circumferential Elastic Moduli of Tubulin
BIOPHYSICAL JOURNAL, 95:3606-3618, OCT 15 2008
abstract,
full text
Tuncel, A., Kavakli, I.H., Keskin, O.
Insights into subunit interactions in the heterotetrameric structure of potato ADP-glucose pyrophosphorylase
BIOPHYSICAL JOURNAL, 95:3628-3639, OCT 15 2008
abstract,
full text
Long, H., Chang, C.H., King, P.W., Ghirardi, M.L., Kim, K.
Brownian dynamics and molecular dynamics study of the association between hydrogenase and ferredoxin from Chlamydomonas reinhardtii
BIOPHYSICAL JOURNAL, 95:3753-3766, OCT 15 2008
abstract,
full text
Sharma, D., Feng, G., Khor, D., Genchev, G.Z., Lu, H., Li, H.B.
Stabilization provided by neighboring strands is critical for the mechanical stability of proteins
BIOPHYSICAL JOURNAL, 95:3935-3942, OCT 15 2008
abstract,
full text
Zhong, W.Y., Guo, W.L., Ma, S.J.
Intrinsic aqueduct orifices facilitate K+ channel gating
FEBS LETTERS, 582:3320-3324, OCT 15 2008
abstract,
full text
Herrera, F.E., Chesi, A., Paleologou, K.E., Schmid, A., Munoz, A., Vendruscolo, M., Gustincich, S., Lashuel, H.A., Carloni, P.
Inhibition of alpha-Synuclein Fibrillization by Dopamine Is Mediated by Interactions with Five C-Terminal Residues and with E83 in the NAC Region
PLOS ONE, 3: Art. No. e3394, OCT 14 2008
abstract,
full text
Chen, L.Y.
Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 144113, OCT 14 2008
abstract,
full text
Park, S., Lau, A.Y., Roux, B.
Computing conformational free energy by deactivated morphing
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 134102, OCT 7 2008
abstract,
full text
Ishitani, R., Sugita, Y., Dohmae, N., Furuya, N., Hattori, M., Nureki, O.
Mg2+-sensing mechanism of Mg2+ transporter MgtE probed by molecular dynamics study
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:15393-15398, OCT 7 2008
abstract,
full text
Karachevtsev, V.A., Gladchenko, G.O., Karachevtsev, M.V., Valeev, V.A., Leontiev, V.S., Lytvyn, O.S.
Adsorption of poly(rA) on the carbon nanotube surface and its hybridization with poly(rU)
CHEMPHYSCHEM, 9:2010-2018, OCT 6 2008
abstract,
full text
Bhattacharya, S., Hall, S.E., Vaidehi, N.
Agonist-induced conformational changes in bovine rhodopsin: Insight into activation of G-protein-coupled receptors
JOURNAL OF MOLECULAR BIOLOGY, 382:539-555, OCT 3 2008
abstract,
full text
Falvo, C., Hayashi, T., Zhuang, W., Mukamel, S.
Coherent two dimensional infrared spectroscopy of a cyclic decapeptide Antamanide. A simulation study of the amide-I and A bands
JOURNAL OF PHYSICAL CHEMISTRY B, 112:12479-12490, OCT 2 2008
abstract,
full text
Mitra, A., Sept, D.
Taxol allosterically alters the dynamics of the tubulin dimer and increases the flexibility of microtubules
BIOPHYSICAL JOURNAL, 95:3252-3258, OCT 1 2008
abstract,
full text
Gorfe, A.A., Baron, R., McCammon, J.A.
Water-membrane partition thermodynamics of an amphiphilic lipopeptide: An enthalpy-driven hydrophobic effect
BIOPHYSICAL JOURNAL, 95:3269-3277, OCT 1 2008
abstract,
full text
Koyama, Y.M., Kobayashi, T.J., Tomoda, S., Ueda, H.R.
Perturbational formulation of principal component analysis in molecular dynamics simulation
PHYSICAL REVIEW E, 78: Art. No. 046702, OCT 2008
abstract,
full text
De Fabritiis, G., Coveney, P.V., Villa-Freixa, J.
Energetics of K(+) permeability through Gramicidin A by forward-reverse steered molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 73:185-194, OCT 2008
abstract,
full text
Liu, M.S., Todd, B.D., Yao, S.G., Feng, Z.P., Norton, R.S., Sadus, R.J.
Coarse-grained dynamics of the receiver domain of NtrC: Fluctuations, correlations and implications for allosteric cooperativity
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 73:218-227, OCT 2008
abstract,
full text
Damjanovic, A., Miller, B.T., Wenaus, T.J., Maksimovic, P., Garcia-Moreno, B., Brooks, B.R.
Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2021-2029, OCT 2008
abstract,
full text
Streiff, J.H., Jones, K.A.
Volatile Anesthetic Binding to Proteins Is Influenced by Solvent and Aliphatic Residues
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:2066-2073, OCT 2008
abstract,
full text
Floquet, N., Dedieu, S., Martiny, L., Dallchez, M., Perahia, D.
Human thrombospondin's (TSP-1) C-terminal domain opens to interact with the CD-47 receptor: A molecular modeling study
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 478:103-109, OCT 1 2008
abstract,
full text
Cerutti, D.S., Duke, R., Freddolino, P.L., Fan, H., Lybrand, T.P.
A Vulnerability in Popular Molecular Dynamics Packages Concerning Langevin and Andersen Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:1669-1680, OCT 2008
abstract,
full text
Hong, R., Magistrato, A., Carloni, P.
Anthrax Lethal Factor Investigated by Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:1745-1756, OCT 2008
abstract,
full text
Levoin, N., Calmels, T., Poupardin-Olivier, O., Labeeuw, O., Danvy, D., Robert, P., Berrebi-Bertrand, I., Ganellin, C.R., Schunack, W., Stark, H., Capet, M.
Refined Docking as a Valuable Tool for Lead Optimization: Application to Histamine H(3) Receptor Antagonists
ARCHIV DER PHARMAZIE, 341:610-623, OCT 2008
abstract,
full text
Shen, J.W., Wu, T., Wang, Q., Kang, Y.
Induced stepwise conformational change of human serum albumin on carbon nanotube surfaces
BIOMATERIALS, 29:3847-3855, OCT 2008
abstract,
full text
Pei, Q.X., Lim, C.G., Cheng, Y., Gao, H.J.
Molecular dynamics study on DNA oligonucleotide translocation through carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 125101, SEP 28 2008
abstract,
full text
Zlatev, I., Dutartre, H., Barvik, I., Neyts, J., Canard, B., Vasseur, J.J., Alvarez, K., Morvan, F.
Phosphoramidate dinucleosides as hepatitis C virus polymerase inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 51:5745-5757, SEP 25 2008
abstract,
full text
Xiao, B., Dubin, A.E., Bursulaya, B., Viswanath, V., Jegla, T.J., Patapoutian, A.
Identification of transmembrane domain 5 as a critical molecular determinant of menthol sensitivity in mammalian TRPA1 channels
JOURNAL OF NEUROSCIENCE, 28:9640-9651, SEP 24 2008
abstract,
full text
Dehez, F., Pebay-Peyroula, E., Chipot, C.
Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:12725-12733, SEP 24 2008
abstract,
full text
Brannigan, G., Henin, J., Law, R., Eckenhoff, R., Klein, M.L.
Embedded cholesterol in the nicotinic acetylcholine receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:14418-14423, SEP 23 2008
abstract,
full text
Glosser, C.J., Hill, R.C.
Dielectric screening in a spherical cavity
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL, 41: Art. No. 375402, SEP 19 2008
abstract,
full text
Manna, D., Bhardwaj, N., Vora, M.S., Stahelin, R.V., Lu, H., Cho, W.H.
Differential roles of phosphatidylserine, PtdIns(4,5)P(2), and PtdIns(3,4,5)P(3) in plasma membrane targeting of C2 domains - Molecular dynamics simulation, membrane binding, and cell translocation studies of the PKC alpha C2 domain
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:26047-26058, SEP 19 2008
abstract,
full text
Espinoza-Fonseca, L.M., Kast, D., Thomas, D.D.
Thermodynamic and structural basis of phosphorylation-induced disorder-to-order transition in the regulatory light chain of smooth muscle myosin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:12208-+, SEP 17 2008
abstract,
full text
Lou, J.Z., Zhu, C.
Flow induces loop-to-beta-hairpin transition on the beta-switch of platelet glycoprotein Ib alpha
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:13847-13852, SEP 16 2008
abstract,
full text
Roberts, E., Sethi, A., Montoya, J., Woese, C.R., Luthey-Schulten, Z.
Molecular signatures of ribosomal evolution
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:13953-13958, SEP 16 2008
abstract,
full text
Corry, B., Jayatilaka, D.
Simulation of structure, orientation, and energy transfer between AlexaFluor molecules attached to MscL
BIOPHYSICAL JOURNAL, 95:2711-2721, SEP 15 2008
abstract,
full text
Law, R.J., Munson, K., Sachs, G., Lightstone, F.C.
An ion gating mechanism of gastric H,K-ATPase based on molecular dynamics simulations
BIOPHYSICAL JOURNAL, 95:2739-2749, SEP 15 2008
abstract,
full text
Arkhipov, A., Yin, Y., Schulten, K.
Four-scale description of membrane sculpting by BAR domains
BIOPHYSICAL JOURNAL, 95:2806-2821, SEP 15 2008
abstract,
full text,
TCBG publications
Chandler, D.E., Hsin, J., Harrison, C.B., Gumbart, J., Schulten, K.
Intrinsic curvature properties of photosynthetic proteins in chromatophores
BIOPHYSICAL JOURNAL, 95:2822-2836, SEP 15 2008
abstract,
full text,
TCBG publications
Stancanelli, R., Crupi, V., De Luca, L., Ficarra, P., Ficarra, R., Gitto, R., Guardo, M., Iraci, N., Majolino, D., Tommasini, S., Venuti, V.
Improvement of water solubility of non-competitive AMPA receptor antagonists by complexation with beta-cyclodextrin
BIOORGANIC & MEDICINAL CHEMISTRY, 16:8706-8712, SEP 15 2008
abstract,
full text
Luan, B., Aksimentiev, A.
Strain softening in stretched DNA
PHYSICAL REVIEW LETTERS, 101: Art. No. 118101, SEP 12 2008
abstract,
full text
Neres, J., Labello, N.P., Somu, R.V., Boshoff, H.I., Wilson, D.J., Vannada, J., Chen, L., Barry, C.E., Bennett, E.M., Aldrich, C.C.
Inhibition of siderophore biosynthesis in Mycobacterium tuberculosis with nucleoside bisubstrate analogues: Structure-activity relationships of the nucleobase domain of 5 '-O-[N-(salicyl)sulfamoyl]adenosine
JOURNAL OF MEDICINAL CHEMISTRY, 51:5349-5370, SEP 11 2008
abstract,
full text
McAllister, K.A., Zou, H.L., Cochran, F.V., Bender, G.M., Senes, A., Fry, H.C., Nanda, V., Keenan, P.A., Lear, J.D., Saven, J.G., Therien, M.J., Blasie, J.K., DeGrado, W.F.
Using alpha-helical coiled-coils to design nanostructured metalloporphyrin arrays
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:11921-11927, SEP 10 2008
abstract,
full text
Tsigelny, I.F., Crews, L., Desplats, P., Shaked, G.M., Sharikov, Y., Mizuno, H., Spencer, B., Rockenstein, E., Trejo, M., Platoshyn, O., Yuan, J.X.J., Masliah, E.
Mechanisms of Hybrid Oligomer Formation in the Pathogenesis of Combined Alzheimer's and Parkinson's Diseases
PLOS ONE, 3: Art. No. e3135, SEP 4 2008
abstract,
full text
Emperador, A., Carrillo, O., Rueda, M., Orozco, M.
Exploring the suitability of coarse-grained techniques for the representation of protein dynamics
BIOPHYSICAL JOURNAL, 95:2127-2138, SEP 1 2008
abstract,
full text
Priya, M.H., Shah, J.K., Asthagiri, D., Paulaitis, M.E.
Distinguishing thermodynamic and kinetic views of the preferential hydration of protein surfaces
BIOPHYSICAL JOURNAL, 95:2219-2225, SEP 1 2008
abstract,
full text
Furini, S., Domene, C., Rossi, M., Tartagni, M., Cavalcanti, S.
Model-based prediction of the alpha-hemolysin structure in the hexameric state
BIOPHYSICAL JOURNAL, 95:2265-2274, SEP 1 2008
abstract,
full text
Huang, Z.J., Tajkhorshid, E.
Dynamics of the extracellular gate and ion-substrate coupling in the glutamate transporter
BIOPHYSICAL JOURNAL, 95:2292-2300, SEP 1 2008
abstract,
full text
De Fabritiis, G., Geroult, S., Coveney, P.V., Waksman, G.
Insights from the energetics binding at the domain-ligand of the Src SH2 domain of water interface
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:1290-1297, SEP 2008
abstract,
full text
Sadiq, S.K., Wright, D., Watson, S.J., Zasada, S.J., Stoica, I., Coveney, P.V.
Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1909-1919, SEP 2008
abstract,
full text
Miller, B.T., Singh, R.P., Klauda, J.B., Hodoscek, M., Brooks, B.R., Woodcock, H.L.
CHARMMing: A new, flexible web portal for CHARMM
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1920-1929, SEP 2008
abstract,
full text
Tantar, A.A., Conilleau, S., Parent, B., Melab, N., Brillet, L., Roy, S., Talbi, E.G., Horvath, D.
Docking and biomolecular simulations on computer grids: Status and trends
CURRENT COMPUTER-AIDED DRUG DESIGN, 4:235-249, SEP 2008
abstract,
full text
Snyder, S.E., Rotkin, S.V.
Optical identification of a DNA-wrapped carbon nanotube: Signs of helically broken symmetry
SMALL, 4:1284-1286, SEP 2008
full text
Mura, C., McCammon, J.A.
Molecular dynamics of a kappa B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation
NUCLEIC ACIDS RESEARCH, 36:4941-4955, SEP 2008
abstract,
full text
Yang, Q., Du, L.P., Wang, X.J., Li, M.Y., You, Q.D.
Modeling the binding modes of Kv1.5 potassium channel and blockers
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 27:178-187, SEP 2008
abstract,
full text
Amaro, R.E., Baron, R., McCammon, J.A.
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 22:693-705, SEP 2008
abstract,
full text
Yago, T., Lou, J., Wu, T., Yang, J., Miner, J.J., Coburn, L., Lopez, J.A., Cruz, M.A., Dong, J.F., McIntire, L.V., McEver, R.P., Zhu, C.
Platelet glycoprotein lb alpha forms catch bonds with human WT vWF but not with type 2B von Willebrand disease vWF
JOURNAL OF CLINICAL INVESTIGATION, 118:3195-3207, SEP 2008
abstract,
full text
Martinez, L., Polikarpov, I., Skaf, M.S.
Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered molecular dynamics approach
JOURNAL OF PHYSICAL CHEMISTRY B, 112:10741-10751, AUG 28 2008
abstract,
full text
Guzman, D.L., Roland, J.T., Keer, H., Kong, Y.P., Ritz, T., Yee, A., Guan, Z.B.
Using steered molecular dynamics simulations and single-molecule force spectroscopy to guide the rational design of biomimetic modular polymeric materials
POLYMER, 49:3892-3901, AUG 26 2008
abstract,
full text
Caballero, J., Zamora, C., Aguayo, D., Yanez, C., Gonzalez-Nilo, F.D.
Study of the interaction between progesterone and beta-cyclodextrin by electrochemical techniques and steered molecular dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 112:10194-10201, AUG 21 2008
abstract,
full text
Stavrakoudis, A.
Molecular dynamics simulations of an apoliprotein A-I derived peptide in explicit water
CHEMICAL PHYSICS LETTERS, 461:294-299, AUG 20 2008
abstract,
full text
De Vivo, M., Dal Peraro, M., Klein, M.L.
Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:10955-10962, AUG 20 2008
abstract,
full text
Homouz, D., Perham, M., Samiotakis, A., Cheung, M.S., Wittung-Stafshede, P.
Crowded, cell-like environment induces shape changes in aspherical protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:11754-11759, AUG 19 2008
abstract,
full text
Moritsugu, K., Smith, J.C.
REACH coarse-grained biomolecular simulation: Transferability between different protein structural classes
BIOPHYSICAL JOURNAL, 95:1639-1648, AUG 15 2008
abstract,
full text
Blood, P.D., Swenson, R.D., Voth, G.A.
Factors influencing local membrane curvature induction by N-BAR domains as revealed by molecular dynamics simulations
BIOPHYSICAL JOURNAL, 95:1866-1876, AUG 15 2008
abstract,
full text
Beautrait, A., Karaboga, A.S., Souchet, M., Maigret, B.
Induced fit in liver X receptor beta: A molecular dynamics-based investigation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:873-882, AUG 15 2008
abstract,
full text
Dynowski, M., Schaaf, G., Loque, D., Moran, O., Ludewig, U.
Plant plasma membrane water channels conduct the signalling molecule H2O2
BIOCHEMICAL JOURNAL, 414:53-61, AUG 15 2008
abstract,
full text
Vanacore, R.M., Ham, A.J.L., Cartailler, J.P., Sundaramoorthy, M., Todd, P., Pedchenko, V., Sado, Y., Borza, D.B., Hudson, B.G.
A role for collagen IV cross-links in conferring immune privilege to the Goodpasture autoantigen - Structural basis for the crypticity of B cell epitopes
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:22737-22748, AUG 15 2008
abstract,
full text
Anzini, M., Braile, C., Valenti, S., Cappelli, A., Vomero, S., Marinelli, L., Limongelli, V., Novellino, E., Betti, L., Giannaccini, G., Lucacchini, A., Ghelardini, C., Norcini, M., Makovec, F., Giorgi, G., Fryer, R.I.
Ethyl 8-fluoro-6-(3-nitrophenyl)-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carbox ylate as novel, highly potent, and safe antianxiety agent
JOURNAL OF MEDICINAL CHEMISTRY, 51:4730-4743, AUG 14 2008
abstract,
full text
Coluci, V.R., Sato, F., Braga, S.F., Skaf, M.S., Galvao, D.S.
Rotational dynamics and polymerization of C(60) in C(60)-cubane crystals: A molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 064506, AUG 14 2008
abstract,
full text
Ding, Z.C., Chen, D., Ni, F.Y., Zheng, Q., Cai, B., Yao, W.H., Wang, Y., Zhou, G.M., Huang, Z.X.
Incorporation of a glycine within the conserved TCPCP motif of human neuronal growth inhibitory factor significantly reduces its bioactivity
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 372:779-784, AUG 8 2008
abstract,
full text
Yao, Y., Harrison, C.B., Freddolino, P.L., Schulten, K., Mayer, M.L.
Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors
EMBO JOURNAL, 27:2158-2170, AUG 6 2008
abstract,
full text,
TCBG publications
Murphy, D.L., Kosa, J., Jaeger, J., Sweasy, J.B.
The Asp285 variant of DNA polymerase beta extends mispaired primer termini via increased nucleotide binding
BIOCHEMISTRY, 47:8048-8057, AUG 5 2008
abstract,
full text
Materese, C.K., Goldmon, C.C., Papoian, G.A.
Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:10659-10664, AUG 5 2008
abstract,
full text
Lin, J.P., Seeman, N.C., Vaidehi, N.
Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface
BIOPHYSICAL JOURNAL, 95:1099-1107, AUG 1 2008
abstract,
full text
Chen, Z.Z., Lou, J.H., Zhu, C., Schulten, K.
Flow-induced structural transition in the beta-switch region of glycoprotein Ib
BIOPHYSICAL JOURNAL, 95:1303-1313, AUG 1 2008
abstract,
full text,
TCBG publications
Greene, D.N., Garcia, T., Sutton, R.B., Gernert, K.M., Benian, G.M., Oberhauser, A.F.
Single-molecule force spectroscopy reveals a stepwise unfolding of Caenorhabditis elegans giant protein kinase domains
BIOPHYSICAL JOURNAL, 95:1360-1370, AUG 1 2008
abstract,
full text
Artigas, R.A., Gonzalez, A., Riquelme, E., Carvajal, C.A., Cattani, A., Martinez-Aguayo, A., Kalergis, A.M., Perez-Acle, T., Fardella, C.E.
A novel adrenocorticotropin receptor mutation alters its structure and function, causing familial glucocorticoid deficiency
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 93:3097-3105, AUG 2008
abstract,
full text
Luan, B.Q., Aksimentiev, A.
Electro-osmotic screening of the DNA charge in a nanopore
PHYSICAL REVIEW E, 78: Art. No. 021912, AUG 2008
abstract,
full text
Pedretti, A., Bocci, E., Maggi, R., Vistoli, G.
Homology modelling of human DHCR24 (seladin-1) and analysis of its binding properties through molecular docking and dynamics simulations
STEROIDS, 73:708-719, AUG 2008
abstract,
full text
Buku, A., Keselman, I., Lupyan, D., Mezei, M., Price, J.A.
Effective mast cell degranulating peptide inhibitors of the IgE/Fc epsilon RI receptor interaction
CHEMICAL BIOLOGY & DRUG DESIGN, 72:133-139, AUG 2008
abstract,
full text
Jo, S., Kim, T., Iyer, V.G., Im, W.
Software news and updates - CHARNIM-GUI: A web-based grraphical user interface for CHARMM
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1859-1865, AUG 2008
abstract,
full text
Merino, F., Guixe, V.
Specificity evolution of the ADP-dependent sugar kinase family - in silico studies of the glucokinase/phosphofructokinase bifunctional enzyme from Methanocaldococcus jannaschii
FEBS JOURNAL, 275:4033-4044, AUG 2008
abstract,
full text
Bray, J.K., Goddard, W.A.
The structure of human serotonin 2c G-protein-coupled receptor bound to agonists and antagonists
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 27:66-81, AUG 2008
abstract,
full text
Joung, I.S., Cheatham, T.E.
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:9020-9041, JUL 31 2008
abstract,
full text
Alexiadis, A., Kassinos, S.
Molecular dynamic simulations of carbon nanotubes in CO(2) atmosphere
CHEMICAL PHYSICS LETTERS, 460:512-516, JUL 30 2008
abstract,
full text
Iori, F., Corni, S.
Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1656-1666, JUL 30 2008
abstract,
full text
Coskuner, O., Bergeron, D.E., Rincon, L., Hudgens, J.W., Gonzalez, C.A.
Glycosidic linkage conformation of methyl-alpha-mannopyranoside
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 045102, JUL 28 2008
abstract,
full text
Hu, X.H., Murata, L.B., Weichsel, A., Brailey, J.L., Roberts, S.A., Nighorn, A., Montfort, W.R.
Allostery in recombinant soluble guanylyl cyclase from Manduca sexta
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:20968-20977, JUL 25 2008
abstract,
full text
Wang, B.Y., Kral, P.
Dragging of polarizable nanodroplets by distantly solvated ions
PHYSICAL REVIEW LETTERS, 101: Art. No. 046103, JUL 25 2008
abstract,
full text
Lugli, F., Zerbetto, F.
Atomistic simulation of "drop-on-demand" inkjet dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 112:10616-10621, JUL 24 2008
abstract,
full text
Domene, C., Klein, M.L., Branduardi, D., Gervasio, F.L., Parrinello, M.
Conformational changes and gating at the selectivity filter of potassium channels
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:9474-9480, JUL 23 2008
abstract,
full text
Zhao, X., Rignall, T.R., McCabe, C., Adney, W.S., Himmel, M.E.
Molecular simulation evidence for processive motion of Trichoderma reesei Cel7A during cellulose depolymerization
CHEMICAL PHYSICS LETTERS, 460:284-288, JUL 20 2008
abstract,
full text
Mao, Y., Tero, R., Imai, Y., Hoshino, T., Urisu, T.
The morphology of GM1(x)/SM(0.6-x)/Chol(0.4) planar bilayers supported on SiO(2) surfaces
CHEMICAL PHYSICS LETTERS, 460:289-294, JUL 20 2008
abstract,
full text
Verkhivker, G., Tiana, G., Camilloni, C., Provasi, D., Broglia, R.A.
Atomistic simulations of the HIV-1 protease folding inhibition
BIOPHYSICAL JOURNAL, 95:550-562, JUL 15 2008
abstract,
full text
Isin, B., Schulten, K., Tajkhorshid, E., Bahar, I.
Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodopsin restrained by normal modes
BIOPHYSICAL JOURNAL, 95:789-803, JUL 15 2008
abstract,
full text,
TCBG publications
Voltz, K., Trylska, J., Tozzini, V., Kurkal-Siebert, V., Langowski, J., Smith, J.
Coarse-grained force field for the nucleosome from self-consistent multiscaling
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1429-1439, JUL 15 2008
abstract,
full text
Wang, Y., Tajkhorshid, E.
Electrostatic funneling of substrate in mitochondrial inner membrane carriers
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:9598-9603, JUL 15 2008
abstract,
full text
Eshet, H., Bruneval, F., Parrinello, M.
New Lennard-Jones metastable phase
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 026101, JUL 14 2008
full text
Kim, K.Y., Nascimento, A.S., Golubev, A.M., Polikarpov, I., Kim, C.S., Kang, S.I., Kim, S.I.
Catalytic mechanism of inulinase from Arthrobacter sp S37
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 371:600-605, JUL 11 2008
abstract,
full text
Cheng, L.S., Amaro, R.E., Xu, D., Li, W.W., Arzberger, P.W., McCammon, J.A.
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
JOURNAL OF MEDICINAL CHEMISTRY, 51:3878-3894, JUL 10 2008
abstract,
full text
Dynowski, M., Mayer, M., Moran, O., Ludewig, U.
Molecular determinants of ammonia and urea conductance in plant aquaporin homologs
FEBS LETTERS, 582:2458-2462, JUL 9 2008
abstract,
full text
Brazdova, V., Bowler, D.R.
Automatic data distribution and load balancing with space-filling curves: implementation in CONQUEST
JOURNAL OF PHYSICS-CONDENSED MATTER, 20: Art. No. 275223, JUL 9 2008
abstract,
full text
Zhu, H., May, V., Roder, B.
Mixed quantum classical simulations of electronic excitation energy transfer: The pheophorbide-a DAB dendrimer P(4) in solution
CHEMICAL PHYSICS, 351:117-128, JUL 3 2008
abstract,
full text
Budi, A., Legge, F.S., Treutlein, H., Yarovsky, I.
Comparative study of insulin chain-b in isolated and monomeric environments under external stress
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7916-7924, JUL 3 2008
abstract,
full text
Diao, J., Tajkhorshid, E.
Indirect role of Ca2+ in the assembly of extracellular matrix proteins
BIOPHYSICAL JOURNAL, 95:120-127, JUL 1 2008
abstract,
full text
Iskandarsyah, Tejo, B.A., Tambunan, U.S.F., Verkhivker, G., Siahaan, T.J.
Structural modifications of ICAM-1 cyclic peptides to improve the activity to inhibit heterotypic adhesion of T cells
CHEMICAL BIOLOGY & DRUG DESIGN, 72:27-33, JUL 2008
abstract,
full text
Jang, H., Michaud-Agrawal, N., Johnston, J.M., Woolf, T.B.
How to lose a kink and gain a helix: pH independent conformational changes of the fusion domains from influenza hemagglutinin in heterogeneous lipid bilayers
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:299-312, JUL 2008
abstract,
full text
Zou, J., Wang, Y.D., Ma, F.X., Xiang, M.L., Shi, B., Wei, Y.Q., Yang, S.Y.
Detailed conformational dynamics of juxtamembrane region and activation loop in c-Kit kinase activation process
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 72:323-332, JUL 2008
abstract,
full text
Shaw, D.E., Deneroff, M.M., Dror, R.O., Kuskin, J.S., Larson, R.H., Salmon, J.K., Young, C., Batson, B., Bowers, K.J., Chao, J.C., Eastwood, M.P., Gagliardo, J., Grossman, J.P., Ho, C.R., Ierardi, D.J., Kolossvary, I., Klepeis, J.L., Layman, T., Mcleavey, C., Moraes, M.A., Mueller, R., Priest, E.C., Shan, Y.B., Spengler, J., Theobald, M., Towles, B., Wang, S.C.
Anton, a special-purpose machine for molecular dynamics simulation
COMMUNICATIONS OF THE ACM, 51:91-97, JUL 2008
abstract,
full text
Blanchette, C.D., Law, R., Benner, W.H., Pesavento, J.B., Cappuccio, J.A., Walsworth, V., Kuhn, E.A., Corzett, M., Chromy, B.A., Segelke, B.W., Coleman, M.A., Bench, G., Hoeprich, P.D., Sulchek, T.A.
Quantifying size distributions of nanolipoprotein particles with single-particle analysis and molecular dynamic simulations
JOURNAL OF LIPID RESEARCH, 49:1420-1430, JUL 2008
abstract,
full text
Verstraelen, T., Van Speybroeck, V., Waroquier, M.
ZEOBUILDER: A GUI toolkit for the construction of complex molecular structures on the nanoscale with building blocks
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1530-1541, JUL 2008
abstract,
full text
Jo, S., Vargyas, M., Vasko-Szedlar, J., Roux, B., Im, W.
PBEQ-Solver for online visualization of electrostatic potential of biomolecules
NUCLEIC ACIDS RESEARCH, 36:W270-W275, JUL 2008
abstract,
full text
Andreozzi, F., Formoso, G., Prudente, S., Hribal, M.L., Pandolfi, A., Bellacchio, E., Di Silvestre, S., Trischitta, V., Consoli, A., Sesti, G.
TRIB3 r84 variant is associated with impaired insulin-mediated nitric oxide production in human endothelial cells
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 28:1355-1360, JUL 2008
abstract,
full text
Sonoda, M.T., Martinez, L., Webb, P., Skaf, M.S., Polikarpov, I.
Ligand dissociation from estrogen receptor is mediated by receptor dimerization: Evidence from molecular dynamics simulations
MOLECULAR ENDOCRINOLOGY, 22:1565-1578, JUL 2008
abstract,
full text
Cruzeiro, L.
Proteins multi-funnel energy landscape and misfolding diseases
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 21:549-554, JUL-AUG 2008
abstract,
full text
Marksteiner, M., Haslinger, P., Ulbricht, H., Sclafani, M., Oberhofer, H., Dellago, C., Arndt, M.
Gas-phase formation of large neutral alkaline-earth metal tryptophan complexes
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 19:1021-1026, JUL 2008
abstract,
full text
Nilsson, L.M., Thomas, W.E., Sokurenko, E.V., Vogel, V.
Beyond induced-fit receptor-ligand interactions: Structural changes that can significantly extend bond lifetimes
STRUCTURE, 16:1047-1058, JUL 2008
abstract,
full text
Anishkin, A., Kamaraju, K., Sukharev, S.
Mechanosensitive channel MscS in the open state: Modeling of the transition, explicit simulations, and experimental measurements of conductance
JOURNAL OF GENERAL PHYSIOLOGY, 132:67-83, JUL 2008
abstract,
full text
Nalian, A., Iakhiaev, A.V.
Possible mechanisms contributing to oxidative inactivation of activated protein C: Molecular dynamics study
THROMBOSIS AND HAEMOSTASIS, 100:18-25, JUL 2008
abstract,
full text
Noid, W.G., Chu, J.W., Ayton, G.S., Krishna, V., Izvekov, S., Voth, G.A., Das, A., Andersen, H.C.
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 244114, JUN 28 2008
abstract,
full text
Beckham, G.T., Peters, B., Trout, B.L.
Evidence for a size dependent nucleation mechanism in solid state polymorph transformations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7460-7466, JUN 26 2008
abstract,
full text
Rodriguez, J., Rico, D.H., Domenianni, L., Laria, D.
Confinement of polar solvents within beta-cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7522-7529, JUN 26 2008
abstract,
full text
Lechuga, J., Drikakis, D., Pal, S.
Molecular dynamics study of the interaction of a shock wave with a biological membrane
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN FLUIDS, 57:677-692, JUN 20 2008
abstract,
full text
Shi, L., Quick, M., Zhao, Y.F., Weinstein, H., Javitch, J.A.
The mechanism of a neurotransmitter : sodium symporter - Inward release of Na+ and substrate is triggered by substrate in a second binding site
MOLECULAR CELL, 30:667-677, JUN 20 2008
abstract,
full text
Kniazeff, J., Shi, L., Loland, C.J., Javitch, J.A., Weinstein, H., Gether, U.
An intracellular interaction network regulates conformational transitions in the dopamine transporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:17691-17701, JUN 20 2008
abstract,
full text
Zhao, X.C.
Interaction of C-60 derivatives and ssDNA from simulations
JOURNAL OF PHYSICAL CHEMISTRY C, 112:8898-8906, JUN 19 2008
abstract,
full text
Sotomayor, M., Schulten, K.
The allosteric role of the Ca(2+) switch in adhesion and elasticity of C-cadherin
BIOPHYSICAL JOURNAL, 94:4621-4633, JUN 15 2008
abstract,
full text,
TCBG publications
Wise, J.G., Vogel, P.D.
Subunit b-dimer of the Escherichia coli ATP synthase can form left-handed coiled-coils
BIOPHYSICAL JOURNAL, 94:5040-5052, JUN 15 2008
abstract,
full text
Shih, A.Y., Sligar, S.G., Schulten, K.
Molecular models need to be tested: The case of a solar flares discoidal HDL model
BIOPHYSICAL JOURNAL, 94:L87-L89, JUN 15 2008
abstract,
full text,
TCBG publications
Krippner-Heidenreich, A., Grunwald, I., Zimmermann, G., Kuhnle, M., Gerspach, J., Sterns, T., Shnyder, S.D., Gill, J.H., Mannel, D.N., Pfizenmaier, K., Scheurich, P.
Single-chain TNF, a TNF derivative with enhanced stability and antitumoral activity
JOURNAL OF IMMUNOLOGY, 180:8176-8183, JUN 15 2008
abstract,
full text
Prentiss, M.C., Wales, D.J., Wolynes, P.G.
Protein structure prediction using basin-hopping
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 225106, JUN 14 2008
abstract,
full text
Espinoza-Fonseca, L.M., Garcia-Machorro, J.
Aromatic-aromatic interactions in the formation of the MDM2-p53 complex
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 370:547-551, JUN 13 2008
abstract,
full text
Henin, J., Shinoda, W., Klein, M.L.
United-atom acyl chains for CHARMM phospholipids
JOURNAL OF PHYSICAL CHEMISTRY B, 112:7008-7015, JUN 12 2008
abstract,
full text
Lee, T.S., York, D.M.
Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:7168-+, JUN 11 2008
abstract,
full text
Pincus, D.L., Hyeon, C., Thirumalai, D.
Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:7364-7372, JUN 11 2008
abstract,
full text
Casanovas, J., Zanuy, D., Aleman, C.
Structural and electronic properties of crown ether functionalized oligothiophenes
MACROMOLECULES, 41:3919-3924, JUN 10 2008
abstract,
full text
Zheng, J., Jang, H., Ma, B., Nussinov, R.
Annular structures as intermediates in fibril formation of Alzheimer A beta(17-42)
JOURNAL OF PHYSICAL CHEMISTRY B, 112:6856-6865, JUN 5 2008
abstract,
full text
Vemparala, S., Domene, C., Kleinz, M.L.
Interaction of anesthetics with open and closed conformations of a potassium channel studied via molecular dynamics and normal mode analysis
BIOPHYSICAL JOURNAL, 94:4260-4269, JUN 1 2008
abstract,
full text
Kimura, S.R., Tebben, A.J., Langley, D.R.
Expanding GPCR homology model binding sites via a balloon potential: A molecular dynamics refinement approach
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:1919-1929, JUN 2008
abstract,
full text
Murtola, T., Vattulainen, I., Falck, E.
Insights into activation and RNA binding of trp RNA-binding attenuation protein (TRAP) through all-atom simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:1995-2011, JUN 2008
abstract,
full text
Jojart, B., Kiss, R., Viskolcz, B., Keseru, G.M.
Activation mechanism of the human histamine H4 receptor - An explicit membrane molecular dynamics simulation study
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:1199-1210, JUN 2008
abstract,
full text
Rodriguez-Ropero, F., Zanuy, D., Aleman, C.
Molecular dynamics of a calix[4]arene-containing polymer in dichloromethane solution: Ability of the solvent molecules to fill the cavity of the macrocycle
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1233-1241, JUN 2008
abstract,
full text
Witt, M., Slusarz, M.J., Ciarkowski, J.
Molecular modeling of Vasopressin V2 Receptor tetramer in hydrated lipid membrane
QSAR & COMBINATORIAL SCIENCE, 27:684-693, JUN 2008
abstract,
full text
Fernandez-Ballester, G., Ferrer-Montiel, A.
Molecular modeling of the full-length human TRPV1 channel in closed and desensitized states
JOURNAL OF MEMBRANE BIOLOGY, 223:161-172, JUN 2008
abstract,
full text
Ding, S.Y., Xu, Q., Crowley, M., Zeng, Y., Nimlos, M., Lamed, R., Bayer, E.A., Himmel, M.E.
A biophysical perspective on the cellulosome: new opportunities for biomass conversion
CURRENT OPINION IN BIOTECHNOLOGY, 19:218-227, JUN 2008
abstract,
full text
Scrofano, R., Gokhale, M.B., Trouw, F., Prasanna, V.K.
Accelerating molecular dynamics simulations with reconfigurable computers
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 19:764-778, JUN 2008
abstract,
full text
DeMarco, M.L., Woods, R.J.
Structural glycobiology: A game of snakes and ladders
GLYCOBIOLOGY, 18:426-440, JUN 2008
abstract,
full text
Gorfe, A.A., Grant, B.J., McCammon, J.A.
Mapping the nucleotide and isoform-dependent structural and dynamical features of ras proteins
STRUCTURE, 16:885-896, JUN 2008
abstract,
full text
Liu, M., Sun, T., Hu, J., Chen, W., Wang, C.
Study on the mechanism of the BtuF periplasmic-binding protein for vitamin B-12
BIOPHYSICAL CHEMISTRY, 135:19-24, JUN 2008
abstract,
full text
Di Rocco, G., Battistuzzi, G., Borsari, M., De Rienzo, F., Ranieri, A., Tutino, M.L., Sola, M.
Cloning, expression and physicochemical characterization of a di-heme cytochrome c(4) from the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC 125
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 13:789-799, JUN 2008
abstract,
full text
Pan, Y.P., Nussinov, R.
P53-induced DNA bending: The interplay between p53-ONA and p53-p53 interactions
JOURNAL OF PHYSICAL CHEMISTRY B, 112:6716-6724, MAY 29 2008
abstract,
full text
Chang, C.E.A., McLaughlin, W.A., Baron, R., Wang, W., McCammon, J.A.
Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:7456-7461, MAY 27 2008
abstract,
full text
Sikdar, D., Pradhan, S.M., Katti, D.R., Katti, K.S., Mohanty, B.
Altered phase model for polymer clay nanocomposites
LANGMUIR, 24:5599-5607, MAY 20 2008
abstract,
full text
Freddolino, P.L., Liu, F., Gruebele, M., Schulten, K.
Ten-microsecond molecular dynamics simulation of a fast-folding WW domain
BIOPHYSICAL JOURNAL, 94:L75-L77, MAY 15 2008
abstract,
full text,
TCBG publications
Venkatramani, R., Radhakrishnan, R.
Effect of oxidatively damaged DNA on the active site preorganization during nucleotide incorporation in a high fidelity polymerase from Bacillus stearothermaphilus
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:1360-1372, MAY 15 2008
abstract,
full text
Zanuy, D., Aleman, C.
Simulation of the self-assembly of poly(alpha-glutamate) and dodecyltrimethylammonium: Diffusive role of the surfactant cations
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 46:917-924, MAY 15 2008
abstract,
full text
Lim, M.C.G., Pei, Q., Zhong, Z.W.
Translocation of DNA oligonucleotide through carbon nanotube channels under induced pressure difference
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 387:3111-3120, MAY 15 2008
abstract,
full text
Minh, D.D.L., McCammon, J.A.
Springs and speeds in free energy reconstruction from irreversible single-molecule pulling experiments
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5892-5897, MAY 15 2008
abstract,
full text
Klauda, J.B., Eldho, N.V., Gawrisch, K., Brooks, B.R., Pastor, R.W.
Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5924-5929, MAY 15 2008
abstract,
full text
Wang, J.P., Zhuang, W., Mukamel, S., Hochstrasser, R.
Two-dimensional infrared spectroscopy as a probe of the solvent electrostatic field for a twelve residue peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5930-5937, MAY 15 2008
abstract,
full text
Lopez, C.F., Darst, R.K., Rossky, P.J.
Mechanistic elements of protein cold denaturation
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5961-5967, MAY 15 2008
abstract,
full text
Oliveira, L.C., Schug, A., Onuchic, J.N.
Geometrical features of the protein folding mechanism are a robust property of the energy landscape: A detailed investigation of several reduced models
JOURNAL OF PHYSICAL CHEMISTRY B, 112:6131-6136, MAY 15 2008
abstract,
full text
Krishnan, A., Giuliani, A., Zbilut, J.P., Tomita, M.
Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations
PLOS ONE, 3: Art. No. e2149, MAY 14 2008
abstract,
full text
Zhao, X., Krstic, P.S.
A molecular dynamics simulation study on trapping ions in a nanoscale Paul trap
NANOTECHNOLOGY, 19: Art. No. 195702, MAY 14 2008
abstract,
full text
Bellesia, G., Fedorov, M.V., Timoshenko, E.G.
Structural transitions in model beta-sheet tapes
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 195105, MAY 12 2008
abstract,
full text
Veluraja, K., Seethalakshmi, A.N.
Dynamics of sialyl Lewis(a) in aqueous solution and prediction of the structure of the sialyl Lewis(a)-SelectinE complex
JOURNAL OF THEORETICAL BIOLOGY, 252:15-23, MAY 7 2008
abstract,
full text
Shushkov, P.G., Tzvetanov, S.A., Ivanova, A.N., Tadjer, A.V.
Dielectric properties tangential to the interface in model insoluble monolayers: Theoretical assessment
LANGMUIR, 24:4615-4624, MAY 6 2008
abstract,
full text
Fushinobu, S., Mertz, B., Hill, A.D., Hidaka, M., Kitaoka, M., Reilly, P.J.
Computational analyses of the conformational itinerary along the reaction pathway of GH94 cellobiose phosphorylase
CARBOHYDRATE RESEARCH, 343:1023-1033, MAY 5 2008
abstract,
full text
Canagarajah, B.J., Hummer, G., Prinz, W.A., Hurley, J.H.
Dynamics of cholesterol exchange in the oxysterol binding protein family
JOURNAL OF MOLECULAR BIOLOGY, 378:737-748, MAY 2 2008
abstract,
full text
Pedretti, A., Marconi, C., Bolchi, C., Fumagalli, L., Ferrara, R., Pallavicini, M., Valoti, E., Vistoli, G.
Modelling of full-length human alpha 4 beta 2 nicotinic receptor by fragmental approach and analysis of its binding modes
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 369:648-653, MAY 2 2008
abstract,
full text
Owens, J.D., Houston, M., Luebke, D., Green, S., Stone, J.E., Phillips, J.C.
GPU computing
PROCEEDINGS OF THE IEEE, 96:879-899, MAY 2008
abstract,
full text
Yogurtcu, O.N., Erdemli, S.B., Nussinov, R., Turkay, M., Keskin, O.
Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations
BIOPHYSICAL JOURNAL, 94:3475-3485, MAY 1 2008
abstract,
full text
Bebenek, K., Garcia-Diaz, M., Foley, M.C., Pedersen, L.C., Schlick, T., Kunkel, T.A.
Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda
EMBO REPORTS, 9:459-464, MAY 2008
abstract,
full text
Cheng, M.H., Coalson, R.D., Cascio, M.
Molecular dynamics simulations of ethanol binding to the transmembrane domain of the glycine receptor: Implications for the channel potentiation mechanism
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:972-981, MAY 1 2008
abstract,
full text
Mathew, D.C., Luthey-Schulten, Z.
On the physical basis of the amino acid polar requirement
JOURNAL OF MOLECULAR EVOLUTION, 66:519-528, MAY 2008
abstract,
full text
Alexiadis, A., Kassinos, S.
Influence of water model and nanotube rigidity on the density of water in carbon nanotubes
CHEMICAL ENGINEERING SCIENCE, 63:2793-2797, MAY 2008
abstract,
full text
Economou, I.G., Karakatsani, E.K., Logotheti, G.E., Ramos, J., Vanin, A.A.
Multi-scale modeling of structure, dynamic and thermodynamic properties of imidazolium-based ionic liquids: Ab initio DFT calculations, molecular simulation and equation of state predictions
OIL & GAS SCIENCE AND TECHNOLOGY-REVUE DE L INSTITUT FRANCAIS DU PETROLE, 63:283-293, MAY-JUN 2008
abstract,
full text
Gu, Y.F., VanCourt, T., Herbordt, M.C.
Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations
PARALLEL COMPUTING, 34:261-277, MAY 2008
abstract,
full text
Chen, X., Wu, T., Wang, Q., Shen, J.W.
Shield effect of silicate on adsorption of proteins onto silicon-doped hydroxyapatite (100) surface
BIOMATERIALS, 29:2423-2432, MAY 2008
abstract,
full text
Project, E., Nachliel, E., Gutman, M.
Parameterization of Ca+2-protein interactions for molecular dynamics simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1163-1169, MAY 2008
abstract,
full text
Gentilucci, L., Squassabia, F., Demarco, R., Artali, R., Cardillo, G., Tolomelli, A., Spampinato, S., Bedini, A.
Investigation of the interaction between the atypical agonist c[YpwFG] and MOR
FEBS JOURNAL, 275:2315-2337, MAY 2008
abstract,
full text
Anderson, J.A., Lorenz, C.D., Travesset, A.
General purpose molecular dynamics simulations fully implemented on graphics processing units
JOURNAL OF COMPUTATIONAL PHYSICS, 227:5342-5359, MAY 1 2008
abstract,
full text
Delgado-Buscalioni, R., Coveney, P.V., De Fabritiis, G.
Towards multi-scale modelling of complex liquids using hybrid particle-continuum schemes
PROCEEDINGS OF THE INSTITUTION OF MECHANICAL ENGINEERS PART C-JOURNAL OF MECHANICAL ENGINEERING SCIENCE, 222:769-776, MAY 2008
abstract,
full text
Harms, M.J., Schlessman, J.L., Chimenti, M.S., Sue, G.R., Damjanovic, A., Garcia-Moreno, B.
A buried lysine that titrates with a normal pK(a): Role of conformational flexibility at the protein-water interface as a determinant of pK(a)values
PROTEIN SCIENCE, 17:833-845, MAY 2008
abstract,
full text
Wang, X., Bansal, S., Jiang, M., Prestegard, J.H.
RDC-assisted modeling of symmetric protein homo-oligomers
PROTEIN SCIENCE, 17:899-907, MAY 2008
abstract,
full text
Trabuco, L.G., Villa, E., Mitra, K., Frank, J., Schulten, K.
Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
STRUCTURE, 16:673-683, MAY 2008
abstract,
full text,
TCBG publications
Zheng, J., Ma, B.Y., Chang, Y., Nussinov, R.
Molecular dynamics simulations of Alzheimer A beta(40) elongation and lateral association
FRONTIERS IN BIOSCIENCE, 13:3919-3930, MAY 2008
abstract,
full text
Bellesia, G., Shea, J.E.
Structure and stability of amyloid fibrils formed from synthetic beta-peptides
FRONTIERS IN BIOSCIENCE, 13:6957-6965, MAY 2008
abstract,
full text
Yu, Y.M., Cai, W.S., Chipot, C., Sun, T.T., Shao, X.G.
Spatial arrangement of alpha-cyclodextrins in a rotaxane. Insights from free-energy calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:5268-5271, MAY 1 2008
abstract,
full text
Jacob, C.R., Neugebauer, J., Visscher, L.
Software news and update a flexible implementation of frozen-density embedding for use in multilevel Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:1011-1018, APR 30 2008
abstract,
full text
Kaila, V.R.I., Verkhovsky, M.I., Hummer, G., Wikstrom, M.
Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:6255-6259, APR 29 2008
abstract,
full text
Qvist, J., Davidovic, M., Hamelberg, D., Halle, B.
A dry ligand-binding cavity in a solvated protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:6296-6301, APR 29 2008
abstract,
full text
Zhang, C., Wu, W.B., Lu, Y.J., Gu, L.Q., Huang, Z.S.
Molecular modeling studies of interactions between quindoline derivatives and G-quadruplex
ACTA CHIMICA SINICA, 66:953-958, APR 28 2008
abstract,
full text
Bastug, T., Chen, P.C., Patra, S.M., Kuyucak, S.
Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 155104, APR 21 2008
abstract,
full text
Zhu, H., May, V., Roder, B., Renger, T.
Linear absorbance of the pheophorbide-a butanediamine dendrimer P(4) in solution: Computational studies using a mixed quantum classical methodology
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 154905, APR 21 2008
abstract,
full text
Tornatore, L., Marasco, D., Dathan, N., Vitale, R.M., Benedetti, E., Papa, S., Franzoso, G., Ruvo, M., Monti, S.M.
Gadd45 beta forms a homodimeric complex that binds tightly to MKK7
JOURNAL OF MOLECULAR BIOLOGY, 378:97-111, APR 18 2008
abstract,
full text
Dong, X.L., Zhou, H.L., Wu, T., Wang, Q.
Behavior regulation of adsorbed proteins via hydroxyapatite surface texture control
JOURNAL OF PHYSICAL CHEMISTRY B, 112:4751-4759, APR 17 2008
abstract,
full text
Kang, Y., Wang, Q., Liu, Y.C., Wu, T., Chen, Q., Guan, W.J.
Dynamic mechanism of collagen-like peptide encapsulated into carbon nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 112:4801-4807, APR 17 2008
abstract,
full text
Klauda, J.B., Roberts, M.F., Redfield, A.G., Brooks, B.R., Pastor, R.W.
Rotation of lipids in membranes: Molecular dynamics simulation, P-31 spin-lattice relaxation, and rigid-body dynamics
BIOPHYSICAL JOURNAL, 94:3074-3083, APR 15 2008
abstract,
full text
Gonzalez, A., Duran, L.S., Araya-Secchi, R., Garate, J.A., Pessoa-Mahana, C.D., Lagos, C.F., Perez-Acle, T.
Computational modeling study of functional microdomains in cannabinoid receptor type 1
BIOORGANIC & MEDICINAL CHEMISTRY, 16:4378-4389, APR 15 2008
abstract,
full text
Lee, T.S., Potts, S.J., Kantarjian, H., Cortes, J., Giles, F., Albitar, M.
Molecular basis explanation for imatinib resistance of BCR-ABL due to T3151 and P-loop mutations from molecular dynamics simulations
CANCER, 112:1744-1753, APR 15 2008
abstract,
full text
Grohmann, D., Corradi, V., Elbasyouny, M., Baude, A., Horenkamp, F., Laufer, S.D., Manetti, F., Botta, M., Restle, T.
Small molecule inhibitors targeting HIV-1 reverse transcriptase dimerization
CHEMBIOCHEM, 9:916-922, APR 14 2008
abstract,
full text
Darve, E., Rodriguez-Gomez, D., Pohorille, A.
Adaptive biasing force method for scalar and vector free energy calculations
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 144120, APR 14 2008
abstract,
full text
Eargle, J., Black, A.A., Sethi, A., Trabuco, L.G., Luthey-Schulten, Z.
Dynamics of recognition between tRNA and elongation factor Tu
JOURNAL OF MOLECULAR BIOLOGY, 377:1382-1405, APR 11 2008
abstract,
full text
Castro-Camus, E., Johnston, M.B.
Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy
CHEMICAL PHYSICS LETTERS, 455:289-292, APR 10 2008
abstract,
full text
Sharma, V., Wikstrom, M., Laakkonen, L.
Modeling the active-site structure of the cbb(3)-type oxidase from Rhodobacter sphaeroides
BIOCHEMISTRY, 47:4221-4227, APR 8 2008
abstract,
full text
Coskuner, O., Bergeron, D.E., Rincon, L., Hudgens, J.W., Gonzalez, C.A.
Identification of active sites of biomolecules. 1. Methyl-alpha-mannopyranoside and Fe-III
JOURNAL OF PHYSICAL CHEMISTRY A, 112:2940-2947, APR 3 2008
abstract,
full text
Langham, A.A., Ahmad, A.S., Kaznessis, Y.N.
On the nature of antimicrobial activity: A model for protegrin-1 pores
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:4338-4346, APR 2 2008
abstract,
full text
Sikdar, D., Katti, K.S., Katti, D.R.
Molecular interactions alter clay and polymer structure in polymer clay nanocomposites
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 8:1638-1657, APR 2008
abstract,
full text
Cherezov, V., Liu, W., Derrick, J.P., Luan, B., Aksimentiev, A., Katritch, V., Caffrey, M.
In meso crystal structure and docking simulations suggest an alternative proteoglycan binding site in the OpcA outer membrane adhesin
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 71:24-34, APR 2008
abstract,
full text
Alexiadis, A., Kassinos, S.
The density of water in carbon nanotubes
CHEMICAL ENGINEERING SCIENCE, 63:2047-2056, APR 2008
abstract,
full text
Perez, A., Lankas, F., Luque, F.J., Orozco, M.
Towards a molecular dynamics consensus view of B-DNA flexibility
NUCLEIC ACIDS RESEARCH, 36:2379-2394, APR 2008
abstract,
full text
Potoff, J.J., Issa, Z., Manke, C.W., Jena, B.P.
Ca2+-dimethylphosphate complex formation: Providing insight into Ca2+-mediated local dehydration and membrane fusion in cells
CELL BIOLOGY INTERNATIONAL, 32:361-366, APR 2008
abstract,
full text
Parr, C.L., Tanaka, T., Xiao, H.G., Yada, R.Y.
The catalytic significance of the proposed active site residues in Plasmodium falciparum histoaspartic protease
FEBS JOURNAL, 275:1698-1707, APR 2008
abstract,
full text
Lin, Y.W., Wang, Z.H., Ni, F.Y., Huang, Z.X.
Forced unfolding of apocytochrome b(5) by steered molecular dynamics simulation
PROTEIN JOURNAL, 27:197-203, APR 2008
abstract,
full text
Mukhopadhyay, B.P., Ghosh, B., Bairagya, H.R., Nandi, T.K., Chakrabarti, B., Bera, A.K.
Molecular modeling of the ternary complex of rusticyanin-cytochrome c(4)-cytochrome oxidase: An insight to possible H-bond mediated recognition and electron transfer reaction in T. ferrooxidans
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 25:543-551, APR 2008
abstract,
full text
Connolly, A.J., Roth, M.W., Gray, P.A., Wexler, C.
Explicit hydrogen molecular dynamics simulations of hexane deposited onto graphite at various coverages
LANGMUIR, 24:3228-3234, APR 1 2008
abstract,
full text
Aldini, G., Vistoli, G., Regazzoni, L., Gamberoni, L., Facino, R.M., Yamaguchi, S., Uchida, K., Carini, M.
Albumin is the main nucleophilic target of human plasma: A protective role against pro-atherogenic electrophilic reactive carbonyl species?
CHEMICAL RESEARCH IN TOXICOLOGY, 21:824-835, APR 2008
abstract,
full text
MacKerell, A.D., Nilsson, L.
Molecular dynamics simulations of nucleic acid-protein complexes
CURRENT OPINION IN STRUCTURAL BIOLOGY, 18:194-199, APR 2008
abstract,
full text
Martick, M., Lee, T.S., York, D.M., Scott, W.G.
Solvent structure and hammerhead ribozyme catalysis
CHEMISTRY & BIOLOGY, 15:332-342, APR 2008
abstract,
full text
Shreif, Z., Adhangale, P., Cheluvaraja, S., Perera, R., Kuhn, R., Ortoleva, P.
Enveloped viruses understood via multiscale simulation: computer-aided vaccine design
SCIENTIFIC MODELING AND SIMULATIONS, 15:363-380, APR 2008
abstract,
full text
Singh, A., Kushwaha, H.R., Sharma, P.
Molecular modelling and comparative structural account of aspartyl beta-semialdehyde dehydrogenase of Mycobacterium tuberculosis (H37Rv)
JOURNAL OF MOLECULAR MODELING, 14:249-263, APR 2008
abstract,
full text
Bulo, R.E., Jacob, C.R., Visscher, L.
NMR solvent shifts of acetonitrile from frozen density embedding calculations
JOURNAL OF PHYSICAL CHEMISTRY A, 112:2640-2647, MAR 27 2008
abstract,
full text
Foley, M.C., Schlick, T.
Simulations of DNA Pol lambda R517 mutants indicate 517's crucial role in ternary complex stability and suggest DNA slippage origin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:3967-3977, MAR 26 2008
abstract,
full text
Treptow, W., Marrink, S.J., Tarek, M.
Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 112:3277-3282, MAR 20 2008
abstract,
full text
Pereverzev, Y.V., Gunnerson, K.N., Prezhdo, O.V., Sullivan, P.A., Liao, Y., Olbricht, B.C., Akelaitis, A.J.P., Jen, A.K.Y., Dalton, L.R.
Guest-host cooperativity in organic materials greatly enhances the nonlinear optical response
JOURNAL OF PHYSICAL CHEMISTRY C, 112:4355-4363, MAR 20 2008
abstract,
full text
Domene, C., Vemparala, S., Furini, S., Sharp, K., Klein, M.L.
The role of conformation in ion permeation in a K+ channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:3389-3398, MAR 19 2008
abstract,
full text
Bhattacharya, S., Hall, S.E., Li, H., Vaidehi, N.
Ligand-stabilized conformational states of human beta(2) adrenergic receptor: Insight into G-protein-coupled receptor activation
BIOPHYSICAL JOURNAL, 94:2027-2042, MAR 15 2008
abstract,
full text
Catte, A., Patterson, J.C., Bashtovyy, D., Jones, M.K., Gu, F., Li, L., Rampioni, A., Sengupta, D., Vuorela, T., Niemela, P., Karttunen, M., Marrink, S.J., Vattulainen, I., Segrest, J.P.
Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations
BIOPHYSICAL JOURNAL, 94:2306-2319, MAR 15 2008
abstract,
full text
Eriksson, M., Lindhorst, T.K., Hartke, B.
Differential effects of oligosaccharides on the hydration of simple cations
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 105105, MAR 14 2008
abstract,
full text
Anselmi, C., Centini, M., Maggiore, M., Gaggelli, N., Andreassi, M., Buonocore, A., Beretta, G., Facino, R.M.
Non-covalent inclusion of ferulic acid with alpha-cyclodextrin improves photo-stability and delivery: NMR and modeling studies
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 46:645-652, MAR 13 2008
abstract,
full text
Zhou, Y.G., Guan, L., Freites, J.A., Kaback, H.R.
Opening and closing of the periplasmic gate in lactose permease
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:3774-3778, MAR 11 2008
abstract,
full text
Artali, R., Del Pra, A., Foresti, E., Lesci, I.G., Roveri, N., Sabatino, P.
Adsorption of human serum albumin on the chrysotile surface: a molecular dynamics and spectroscopic investigation
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 5:273-283, MAR 6 2008
abstract,
full text
Sikdar, D., Katti, D.R., Katti, K.S.
The role of interfacial interactions on the crystallinity and nanomechanical properties of clay-polymer nanocomposites: A molecular dynamics study
JOURNAL OF APPLIED POLYMER SCIENCE, 107:3137-3148, MAR 5 2008
abstract,
full text
Celik, L., Schiott, B., Tajkhorshid, E.
Substrate binding and formation of an occluded state in the leucine transporter
BIOPHYSICAL JOURNAL, 94:1600-1612, MAR 1 2008
abstract,
full text
Jolley, C.C., Wells, S.A., Frornme, P., Thorpe, M.F.
Fitting low-resolution cryo-EM maps of proteins using constrained geometric simulations
BIOPHYSICAL JOURNAL, 94:1613-1621, MAR 1 2008
abstract,
full text
Huang, H.C., Jupiter, D., Qiu, M., Briggs, J.M., VanBuren, V.
Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2-ns MD simulation
BIOPOLYMERS, 89:210-219, MAR 2008
abstract,
full text
Ko, Y.J., Huh, J., Jo, W.H.
Ion exclusion mechanism in aquaporin at an atomistic level
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 70:1442-1450, MAR 2008
abstract,
full text
Zhmakin, A.I.
Physical aspects of cryobiology
PHYSICS-USPEKHI, 51:231-252, MAR 2008
abstract,
full text
Henriques, E.S., Solov'yov, A.V.
A rational method for probing macromolecules dissociation: the antibody-hapten system
EUROPEAN PHYSICAL JOURNAL D, 46:471-481, MAR 2008
abstract,
full text
Wan, S., Flower, D.R., Coveney, P.V.
Toward an atomistic understanding of the immune synapse: Large-scale molecular dynamics simulation of a membrane-embedded TCR-pMHC-CD4 complex
MOLECULAR IMMUNOLOGY, 45:1221-1230, MAR 2008
abstract,
full text
Hess, B., Kutzner, C., van der Spoel, D., Lindahl, E.
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 4:435-447, MAR 2008
abstract,
full text
Yang, S., Roux, B.
Src kinase conformational activation: Thermodynamics, pathways, and mechanisms
PLOS COMPUTATIONAL BIOLOGY, 4: Art. No. e1000047, MAR 2008
abstract,
full text
Jouanna, P., Pedesseau, L., Pepe, G., Mainprice, D.
Mass and momentum interface equilibrium by molecular modeling. Simulating AFM adhesion between (120) gypsum faces in a saturated solution and consequences on gypsum cohesion
CEMENT AND CONCRETE RESEARCH, 38:290-299, MAR 2008
abstract,
full text
Zhao, Q., Comer, J., Dimitrov, V., Yemenicioglu, S., Aksimentiev, A., Timp, G.
Stretching and unzipping nucleic acid hairpins using a synthetic nanopore
NUCLEIC ACIDS RESEARCH, 36:1532-1541, MAR 2008
abstract,
full text
Nakano, A., Kalia, R.K., Nomura, K.I., Sharma, A., Vashishta, P., Shimojo, F., Van Duin, A.C.T., Goddard, W.A., Biswas, R., Srivastava, D., Yang, L.H.
De novo ultrascale atomistic simulations on high-end parallel supercomputers
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 22:113-128, SPR 2008
abstract,
full text
Lim, B.B.C., Lee, E.H., Sotomayor, M., Schulten, K.
Molecular basis of fibrin clot elasticity
STRUCTURE, 16:449-459, MAR 2008
abstract,
full text,
TCBG publications
Weronski, P., Jiang, Y., Rasmussen, S.
Application of molecular dynamics computer simulations in the design of a minimal self-replicating molecular machine
COMPLEXITY, 13:10-17, MAR-APR 2008
abstract,
full text
Venkatramani, R., Radhakrishnan, R.
Computational study of the force dependence of phosphoryl transfer during DNA synthesis by a high fidelity polymerase
PHYSICAL REVIEW LETTERS, 100: Art. No. 088102, FEB 29 2008
abstract,
full text
Stoica, I., Sadiq, S.K., Coveney, P.V.
Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:2639-2648, FEB 27 2008
abstract,
full text
Zheng, J., Jang, H., Nussinov, R.
beta(2)-microglobulin amyloid fragment organization and morphology and its comparison to A beta suggests that amyloid aggregation pathways are sequence specific
BIOCHEMISTRY, 47:2497-2509, FEB 26 2008
abstract,
full text
Perumal, S., Antipova, O., Orgel, J.P.R.O.
Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105:2824-2829, FEB 26 2008
abstract,
full text
Gorfe, A.A., Chang, C.E.A., Ivanov, I., McCammon, J.A.
Dynamics of the acetylcholinesterase tetramer
BIOPHYSICAL JOURNAL, 94:1144-1154, FEB 15 2008
abstract,
full text
Qamar, S., Williams, P.M., Lindsay, S.M.
Can an atomic force microscope sequence DNA using a nanopore?
BIOPHYSICAL JOURNAL, 94:1233-1240, FEB 15 2008
abstract,
full text
Anishkin, A., Akitake, B., Sukharev, S.
Characterization of the resting MscS: Modeling and analysis of the closed bacterial mechanosensitive channel of small conductance
BIOPHYSICAL JOURNAL, 94:1252-1266, FEB 15 2008
abstract,
full text
Wu, L.N.Y., Genge, B.R., Wuthier, R.E.
Analysis and molecular modeling of the formation, structure, and activity of the phosphatidylserine-calcium-phosphate complex associated with biomineralization
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:3827-3838, FEB 15 2008
abstract,
full text
Horejs, C., Pum, D., Sleytr, U.B., Tscheliessnig, R.
Structure prediction of an S-layer protein by the mean force method
JOURNAL OF CHEMICAL PHYSICS, 128: Art. No. 065106, FEB 14 2008
abstract,
full text
Dalhaimer, P., Pollard, T.D., Nolen, B.J.
Nucleotide-mediated conformational changes of monomeric actin and Arp3 studied by molecular dynamics simulations
JOURNAL OF MOLECULAR BIOLOGY, 376:166-183, FEB 8 2008
abstract,
full text
Zou, H.L., Therien, M.J., Blasie, J.K.
Structure and dynamics of an extended conjugated NLO chromophore within an amphiphilic 4-helix bundle peptide by molecular dynamics simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 112:1350-1357, FEB 7 2008
abstract,
full text
Corry, B.
Designing carbon nanotube membranes for efficient water desalination
JOURNAL OF PHYSICAL CHEMISTRY B, 112:1427-1434, FEB 7 2008
abstract,
full text
Li, Z.Y., Yu, H.B., Zhuang, W., Mukamel, S.
Geometry and excitation energy fluctuations of NMA in aqueous solution with CHARMM, AMBER, OPLS, and GROMOS force fields: Implications for protein ultraviolet spectra simulation
CHEMICAL PHYSICS LETTERS, 452:78-83, FEB 4 2008
abstract,
full text
Henin, J., Tajkhorshid, E., Schulten, K., Chipot, C.
Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF
BIOPHYSICAL JOURNAL, 94:832-839, FEB 1 2008
abstract,
full text,
TCBG publications
Landon, M.R., Amaro, R.E., Baron, R., Ngan, C.H., Ozonoff, D., McCammon, J.A., Vajda, S.
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
CHEMICAL BIOLOGY & DRUG DESIGN, 71:106-116, FEB 2008
abstract,
full text
Pentikainen, U., Pentikainen, O.T., Mulholland, A.J.
Cooperative symmetric to asymmetric conformational transition of the apo-form of scavenger decapping enzyme revealed by simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 70:498-508, FEB 1 2008
abstract,
full text
Rodriguez-Ropero, F., Zanuy, D., Casanovas, J., Nussinov, R., Aleman, C.
Application of 1-aminocyclohexane carboxylic acid to protein nanostructure computer design
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 48:333-343, FEB 2008
abstract,
full text
Solov'yov, I.A., Yakubovich, A.V., Solov'yov, A.V., Greiner, W.
alpha-helix <-> random coil phase transition: analysis of ab initio theory predictions
EUROPEAN PHYSICAL JOURNAL D, 46:227-240, FEB 2008
abstract,
full text
El-Ghazawi, T., El-Araby, E., Huang, M.Q., Gaj, K., Kindratenko, V., Buell, D.
The promise of high-performance reconfigurable computing
COMPUTER, 41:69-+, FEB 2008
abstract,
full text
Hytonen, V.P., Vogel, V.
How force might activate talin's vinculin binding sites: SMD reveals a structural mechanism
PLOS COMPUTATIONAL BIOLOGY, 4: Art. No. e24, FEB 2008
abstract,
full text
Wang, H.L., Cheng, X.L., Taylor, P., McCammon, J.A., Sine, S.M.
Control of cation permeation through the nicotinic receptor channel
PLOS COMPUTATIONAL BIOLOGY, 4: Art. No. e41, FEB 2008
abstract,
full text
Dalal, S., Chikova, A., Jaeger, J., Sweasy, J.B.
The Leu22Pro tumor-associated variant of DNA polymerase beta is dRP lyase deficient
NUCLEIC ACIDS RESEARCH, 36:411-422, FEB 2008
abstract,
full text
Lash, L.L., Sanders, J.M., Akiyama, N., Shoji, M., Postila, P., Pentikainen, O.T., Sasaki, M., Sakai, R., Swanson, G.T.
Novel analogs and stereoisomers of the marine toxin neodysiherbaine with specificity for kainate receptors
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS, 324:484-496, FEB 2008
abstract,
full text
Shen, J.W., Wu, T., Wang, Q., Pan, H.H.
Molecular simulation of protein adsorption and desorption on hydroxyapatite surfaces
BIOMATERIALS, 29:513-532, FEB 2008
abstract,
full text
Todman, S.J., Halling-Brown, M.D., Davies, M.N., Flower, D.R., Kayikci, M., Moss, D.S.
Toward the atomistic simulation of T cell epitopes Automated construction of MHC: Peptide structures for free energy calculations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 26:957-961, FEB 2008
abstract,
full text
Landstroem, J., Nordmark, E.L., Eklund, R., Weintraub, A., Seckler, R., Widmalm, G.
Interaction of a Salmonella enteritidis O-antigen octasaccharide with the phage P22 tailspike protein by NMR spectroscopy and docking studies
GLYCOCONJUGATE JOURNAL, 25:137-143, FEB 2008
abstract,
full text
Yang, L., Song, G., Carriquiry, A., Jernigan, R.L.
Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes
STRUCTURE, 16:321-330, FEB 2008
abstract,
full text
Beautrait, A., Leroux, V., Chavent, M., Ghemtio, L., Devignes, M.D., Smaiel-Tabbone, M., Cai, W., Shao, X., Moreau, G., Bladon, P., Yao, J., Maigret, B.
Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment
JOURNAL OF MOLECULAR MODELING, 14:135-148, FEB 2008
abstract,
full text
Carvacho, I., Gonzalez, W., Torres, Y.P., Brauchi, S., Alvarez, O., Gonzalez-Nilo, F.D., Latorre, R.
Intrinsic electrostatic potential in the BK channel pore: Role in determining single channel conductance and block
JOURNAL OF GENERAL PHYSIOLOGY, 131:147-161, FEB 2008
abstract,
full text
Bleicher, L., Aparicio, R., Nunes, F.M., Martinez, L., Dias, S.M.G., Figueira, A.C.M., Santos, M.A.M., Venturelli, W.H., da Silva, R., Donate, P.M., Neves, F.A.R., Simeoni, L.A., Baxter, J.D., Webb, P., Skaf, M.S., Polikarpov, I.
Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms
BMC STRUCTURAL BIOLOGY, 8: Art. No. 8, JAN 31 2008
abstract,
full text
Interlandi, G., Wetzel, S.K., Settanni, G., Pluckthun, A., Caflisch, A.
Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments
JOURNAL OF MOLECULAR BIOLOGY, 375:837-854, JAN 18 2008
abstract,
full text
Spiegel, K., Magistrato, A., Maurer, P., Ruggerone, P., Rothlisberger, U., Carloni, P., Reedijk, J., Klein, M.L.
Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure
JOURNAL OF COMPUTATIONAL CHEMISTRY, 29:38-49, JAN 15 2008
abstract,
full text
Shen, M.Q., Reitman, Z.J., Zhao, Y., Moustafa, I., Wang, Q.X., Arnold, J.J., Pathak, H.B., Cameron, C.E.
Picornavirus genome replication - Identification of the surface of the poliovirus (PV) 3C dimer that interacts with PV 3Dpol during VPg uridylylation and construction of a structural model for the PV3C(2)-3Dpol complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 283:875-888, JAN 11 2008
abstract,
full text
Zhao, X., Payne, C.M., Cummings, P.T.
Controlled translocation of DNA segments through nanoelectrode gaps from molecular dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 112:8-12, JAN 10 2008
abstract,
full text
Southern, J., Pitt-Francis, J., Whiteley, J., Stokeley, D., Kobashi, H., Nobes, R., Kadooka, Y., Gavaghan, D.
Multi-scale computational modelling in biology and physiology
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 96:60-89, JAN-APR 2008
abstract,
full text
Linderoth, L., Andresen, T.L., Jorgensen, K., Madsen, R., Peters, G.H.
Molecular basis of phospholipase A(2) activity toward phospholipids with sn-1 substitutions
BIOPHYSICAL JOURNAL, 94:14-26, JAN 1 2008
abstract,
full text
Atilgan, C., Aykut, A.O., Atilgan, A.R.
How a vicinal layer of solvent modulates the dynamics of proteins
BIOPHYSICAL JOURNAL, 94:79-89, JAN 1 2008
abstract,
full text
Torras, J., Zanuy, D., Crisma, M., Toniolo, C., Betran, O., Aleman, C.
Correlation between symmetry breaker position and the preferences of conformationally constrained homopeptides: A molecular dynamics investigation
BIOPOLYMERS, 90:695-706, 2008
abstract,
full text
Jena, B.P.
Understanding Membrane Fusion: Combining Experimental and Simulation Studies
METHODS IN NANO CELL BIOLOGY, 90:183-+, 2008
abstract,
full text
Flenner, E., Marga, F., Neagu, A., Kosztin, L., Forgacs, G.
Relating biophysical properties across scales
MULTISCALE MODELING OF DEVELOPMENTAL SYSTEMS, 81:461-483, 2008
abstract,
full text
Sigalov, G., Comer, J., Timp, G., Aksimentiev, A.
Detection of DNA sequences using an alternating electric field in a nanopore capacitor
NANO LETTERS, 8:56-63, JAN 2008
abstract,
full text
Fitch, B.G., Rayshubskiy, A., Eleftheriou, M., Ward, T.J.C., Giampapa, M., Pitman, M.C., Pitera, J., Swope, W.C., Germain, R.S.
Blue Matter: Scaling of N-body simulations to one atom per node
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:159-180, 2008
abstract,
full text
Shih, A.Y., Freddolino, P.L., Arkhipov, A., Sligar, S.G., Schulten, K.
Molecular modeling of the structural properties and formation of high-density lipoprotein particles
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:313-342, 2008
full text,
TCBG publications
Wang, Y., Ohkubo, Y.Z., Tajkhorshid, E.
Gas conduction of lipid bilayers and membrane channels
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:343-367, 2008
abstract,
full text
Karttunen, M., Rottler, J., Vattulainen, I., Sagui, C.
Electrostatics in biomolecular simulations: Where are we now and where are we heading?
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:49-89, 2008
abstract,
full text
Kozakiewicz, A., Neurnann, P., Banach, M., Komoszyiski, M., Wojtczak, A.
Modeling studies of potato nucleoside triphosphate diphosphohydrolase NTPDase1: an insight into the catalytic mechanism
ACTA BIOCHIMICA POLONICA, 55:141-150, 2008
abstract,
full text
Fitch, B.G., Rayshubskiy, A., Eleftheriou, M., Ward, T.J.C., Giampapa, M.E., Pitman, M.C., Pitera, J.W., Swope, W.C., Germain, R.S.
Blue Matter: Scaling of N-body simulations to one atom per node
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 52:145-158, JAN-MAR 2008
abstract,
full text
Kumar, S., Huang, C., Zheng, G., Bohm, E., Bhatele, A., Phillips, J.C., Yu, H., Kale, L.V.
Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 52:177-188, JAN-MAR 2008
abstract,
full text
Zhou, R., Eleftheriou, M., Hon, C.C., Germain, R.S., Royyuru, A.K., Berne, B.J.
Massively parallel molecular dynamics simulations of lysozyme unfolding
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 52:19-30, JAN-MAR 2008
abstract,
full text
Searles, D.J., Evans, D.J.
Fluctuation relations, free energy calculations and irreversibility
CHEMICAL MODELLING: APPLICATIONS AND THEORY, VOL 5: A REVIEW OF THE LITERATURE PUBLISHED BETWEEN JUNE 2005 AND MAY 2007, 5:182-207, 2008
full text
Karachevtsev, V.A., Gladchenko, G.O., Karachevtsev, M.V., Glamazda, A.Y., Leontiev, V.S., Lytvyn, O.S., Dettlaff-Weglikowska, U.
RNA-Wrapped Carbon Nanotubes Aggregation Induced by Polymer Hybridization
MOLECULAR CRYSTALS AND LIQUID CRYSTALS, 497:339-351, 2008
abstract,
full text
Raiteri, P., Bussi, G., Cucinotta, C.S., Credi, A., Stoddart, J.F., Parrinello, M.
Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 47:3536-3539, 2008
full text
Espinoza-Fonseca, L.M., Pedretti, A., Vistoli, G.
Structure and dynamics of the full-length M-1 muscarinic acetylcholine receptor studied by molecular dynamics simulations
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 469:142-150, JAN 1 2008
abstract,
full text
Cohen, J., Olsen, K.W., Schulten, K.
Finding gas migration pathways in proteins using implicit ligand sampling
GLOBINS AND OTHER NITRIC OXIDE-REACTIVE PROTEINS, PART B, 437:439-457, 2008
abstract,
full text,
TCBG publications
Golden, S.D., Olsen, K.W.
Identification of ligand-binding pathways in truncated hemoglobins using locally enhanced sampling molecular dynamics
GLOBINS AND OTHER NITRIC OXIDE-REACTIVE PROTEINS, PART B, 437:459-475, 2008
abstract,
full text
White, S.H., von Heijne, G.
How translocons select transmembrane helices
ANNUAL REVIEW OF BIOPHYSICS, 37:23-42, 2008
abstract,
full text
Dubey, D.K., Tomar, V.
Microstructure dependent dynamic fracture analyses of trabecular bone based on nascent bone atomistic simulations
MECHANICS RESEARCH COMMUNICATIONS, 35:24-31, JAN-MAR 2008
abstract,
full text
Alexiadis, A., Kassinos, S.
Self-diffusivity, hydrogen bonding and density of different water models in carbon nanotubes
MOLECULAR SIMULATION, 34:671-678, 2008
abstract,
full text
Pedretti, A., De Luca, L., Sciarrillo, C., Vistoli, G.
Fragmental modeling of human glutamate transporter EAAT1 and analysis of its binding modes by docking and pharmacophore mapping
CHEMMEDCHEM, 3:79-90, JAN 2008
abstract,
full text
Sharma, G., Rege, K., Budil, D.E., Yarmush, M.L., Mavroidis, C.
Reversible pH-controlled DNA-binding peptide nanotweezers: An in-silico study
INTERNATIONAL JOURNAL OF NANOMEDICINE, 3:505-521, 2008
abstract,
full text
Yang, S.I., Tanaka, T.
Characterization of recombinant prolidase from Lactococcus lactis - changes in substrate specificity by metal cations, and allosteric behavior of the peptidase
FEBS JOURNAL, 275:271-280, JAN 2008
abstract,
full text
Kottakis, F., Papadopoulos, G., Pappa, E.V., Cordopatis, P., Pentas, S., Choli-Papadopoulou, T.
Helicobacter pylori neutrophil-activating protein activates neutrophils by its C-terminal region even without dodecamer formation, which is a prerequisite for DNA protection - novel approaches against Helicobacter pylori inflammation
FEBS JOURNAL, 275:302-317, JAN 2008
abstract,
full text
Colombres, M., Garate, J.A., Lagos, C.F., Araya-Secchi, R., Norambuena, P., Quiroz, S., Larrondo, L., Perez-Acle, T., Eyzaguirre, J.
An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 22:19-28, JAN 2008
abstract,
full text
Ceraudo, E., Murail, S., Tan, Y.V., Lacapere, J.J., Neumann, J.M., Couvineau, A., Laburthe, M.
The vasoactive intestinal peptide (VIP) alpha-helix up to C terminus interacts with the N-terminal ectodomain of the human VIP/Pituitary adenylate cyclase-activating peptide 1 receptor: Photoaffinity, molecular modeling, and dynamics
MOLECULAR ENDOCRINOLOGY, 22:147-155, JAN 2008
abstract,
full text
Weidemuller, C., Hauser, K.
Impact of an electric field on P-type ATPases
SPECTROSCOPY-AN INTERNATIONAL JOURNAL, 22:319-325, 2008
abstract,
full text
Keten, S., Buehler, M.J.
Large deformation and fracture mechanics of a beta-helical protein nanotube: Atomistic and continuum modeling
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, 197:3203-3214, 2008
abstract,
full text
Solares, S.D.
Characterization of deep nanoscale surface trenches with AFM using thin carbon nanotube probes in amplitude-modulation and frequency-force-modulation modes
MEASUREMENT SCIENCE & TECHNOLOGY, 19: Art. No. 015503, JAN 2008
abstract,
full text
Negi, S.S., Carol, A.A., Pandya, S., Braun, W., Anderson, L.E.
Co-localization of glyceraldehyde-3-phosphate dehydrogenase with ferredoxin-NADP reductase in pea leaf chloroplasts
JOURNAL OF STRUCTURAL BIOLOGY, 161:18-30, JAN 2008
abstract,
full text
Zheng, X.J., Wintrode, P.L., Chance, M.R.
Complementary structural mass spectrometry techniques reveal local dynamics in functionally important regions of a metastable serpin
STRUCTURE, 16:38-51, JAN 2008
abstract,
full text
Ohkubo, Y.Z., Tajkhorshid, E.
Distinct structural and adhesive roles of Ca2+ in membrane binding of blood coagulation factors
STRUCTURE, 16:72-81, JAN 2008
abstract,
full text
Zhang, A., Rodriguez-Ropero, F., Zanuy, D., Aleman, C., Meijer, E.W., Schluter, A.D.
A rigid, chiral, dendronized polymer with a thermally stable, right-handed helical conformation
CHEMISTRY-A EUROPEAN JOURNAL, 14:6924-6934, 2008
abstract,
full text
Frangeul, A., Bussetta, C., Deval, J., Barral, K., Alvarez, K., Canard, B.
Gln151 of HIV-1 reverse transcriptase acts as a steric gate towards clinically relevant acyclic phosphonate nucleotide analogues
ANTIVIRAL THERAPY, 13:115-124, 2008
abstract,
full text
Jalkanen, K.J., Gale, J.D., Jalkanen, G.J., McIntosh, D.F., El-Azhary, A.A., Jensen, G.M.
trans-1,2-dicyano-cyclopropane and other cyano-cyclopropane derivatives
THEORETICAL CHEMISTRY ACCOUNTS, 119:211-229, JAN 2008
abstract,
full text
Cai, W., Sun, T., Shao, X., Chipot, C.
Can the anomalous aqueous solubility of beta-cyclodextrin be explained by its hydration free energy alone?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10:3236-3243, 2008
abstract,
full text
Ivanova, A., Jezierski, G., Rosch, N.
Electronic coupling between base pair dimers of LNA : DNA oligomers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10:414-421, 2008
abstract,
full text
Blumberger, J.
Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 10:5651-5667, 2008
abstract,
full text
Tian, P.
Molecular dynamics simulations of nanoparticles
ANNUAL REPORTS ON THE PROGRESS OF CHEMISTRY 2008, VOL 104, SECTION C: PHYSICAL CHEMISTRY, DOI 10.1039/b7030897f, 2008
abstract,
full text
Ghosh, P., Katti, D.R., Katti, K.S.
Mineral and protein-bound water and latching action control mechanical behavior at protein-mineral interfaces in biological nanocomposites
JOURNAL OF NANOMATERIALS, Art. No. 582973, 2008
abstract,
full text
Schulten, K., Phillips, J.C., Kale, L.V., Bhatele, A.
Biomolecular Modeling in the Era of Petascale Computing
PETASCALE COMPUTING: ALGORITHMS AND APPLICATIONS, , 2008
full text,
TCBG publications
Agarwal, P.K., Alam, S.P., Geist, A.
Simulating Biomolecules on the Petascale Supercomputers
PETASCALE COMPUTING: ALGORITHMS AND APPLICATIONS, , 2008
full text
Mugnaini, C., Alongi, M., Togninelli, A., Gevariya, H., Brizzi, A., Manetti, F., Bernardini, C., Angeli, L., Tafi, A., Bellucci, L., Corelli, F., Massa, S., Maga, G., Samuele, A., Facchim, M., Clotet-Codina, I., Armand-Ugon, M., Este, J.A., Botta, M.
Dihydro-alkylthio-benzyl-oxopyrimidines as inhibitors of reverse transcriptase: Synthesis and rationalization of the biological data on both wild-type enzyme and relevant clinical mutants
JOURNAL OF MEDICINAL CHEMISTRY, 50:6580-6595, DEC 27 2007
abstract,
full text
Cheng, M.H.Y., Liu, L.T., Saladino, A.C., Xu, Y., Tang, P.
Molecular dynamics simulations of ternary membrane mixture: Phosphatidylcholine, phosphatidic acid, and cholesterol
JOURNAL OF PHYSICAL CHEMISTRY B, 111:14186-14192, DEC 27 2007
abstract,
full text
Sadiq, A.K., Wan, S., Coveney, P.V.
Insights into a mutation-assisted lateral drug escape mechanism from the HIV-1 protease active site
BIOCHEMISTRY, 46:14865-14877, DEC 25 2007
abstract,
full text
Curco, D., Nussinov, R., Aleman, C.
Coarse-graining the self-assembly of beta-helical protein building blocks
JOURNAL OF PHYSICAL CHEMISTRY B, 111:14006-14011, DEC 20 2007
abstract,
full text
Hermans, T.M., Broeren, M.A.C., Gomopoulos, N., Smeijers, A.F., Mezari, B., Van Leeuwen, E.N.M., Vos, M.R.J., Magusin, P.C.M.M., Hilbers, P.A.J., Van Genderen, M.H.P., Sommerdijk, N.A.J.M., Fytas, G., Meijer, E.W.
Stepwise noncovalent synthesis leading to dendrimer-based assemblies in water
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:15631-15638, DEC 19 2007
abstract,
full text
Schmid, F.F.F., Meuwly, M.
All-atom simulations of structures and energetics of c-di-GMP-bound and free PleD
JOURNAL OF MOLECULAR BIOLOGY, 374:1270-1285, DEC 14 2007
abstract,
full text
Campen, R.K., Verde, A.V., Kubicki, J.D.
Influence of glycosidic linkage neighbors on disaccharide conformation in vacuum
JOURNAL OF PHYSICAL CHEMISTRY B, 111:13775-13785, DEC 13 2007
abstract,
full text
Hajjar, E., Korkmaz, B., Reuter, N.
Differences in the substrate binding sites of murine and human proteinase 3 and neutrophil elastase
FEBS LETTERS, 581:5685-5690, DEC 11 2007
abstract,
full text
Jayaraman, S., Maginn, E.J.
Computing the melting point and thermodynamic stability of the orthorhombic and monoclinic crystalline polymorphs of the ionic liquid 1-n-butyl-3-methylimidazolium chloride
JOURNAL OF CHEMICAL PHYSICS, 127: Art. No. 214504, DEC 7 2007
abstract,
full text
Yu, J., Ha, T., Schulten, K.
How directional translocation is regulated in a DNA helicase motor
BIOPHYSICAL JOURNAL, 93:3783-3797, DEC 2007
abstract,
full text,
TCBG publications
Spolnik, P., Stopa, B., Piekarska, B., Jagusiak, A., Konieczny, L., Rybarska, J., Krol, M., Roterman, I., Urbanowicz, B., Zieba-Palus, J.
The use of rigid, fibrillar Congo red nanostructures for scaffolding protein assemblies and inducing the formation of amyloid-like arrangement of molecules
CHEMICAL BIOLOGY & DRUG DESIGN, 70:491-501, DEC 2007
abstract,
full text
Ma, B., Levine, A.J.
Probing potential binding modes of the p53 tetramer to DNA based on the symmetries encoded in p53 response elements
NUCLEIC ACIDS RESEARCH, 35:7733-7747, DEC 2007
abstract,
full text
Hamacher, K.
Information theoretical measures to analyze, trajectories in rational molecular design
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2576-2580, DEC 2007
abstract,
full text
Stone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., Schulten, K.
Accelerating molecular modeling applications with graphics processors
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2618-2640, DEC 2007
abstract,
full text,
TCBG publications
Starzec, A., Ladam, P., Vassy, R., Badache, S., Bouchemal, N., Navaza, A., Du Penhoat, C.H., Perret, G.Y.
Structure-function analysis of the antiangiogenic ATWLPPR peptide inhibiting VEGF(165) binding to neuropilin-1 and molecular dynamics simulations of the ATWLPPR/neuropilin-1 complex
PEPTIDES, 28:2397-2402, DEC 2007
abstract,
full text
Christensen, S., Peters, G.H., Hansen, F.Y., Abildskov, J.
Thermodynamic models from fluctuation solution theory analysis of molecular simulations
FLUID PHASE EQUILIBRIA, 261:185-190, DEC 1 2007
abstract,
full text
Xiao, H.G., Tanaka, T., Ogawa, M., Yada, R.Y.
Expression and enzymatic characterization of the soluble recombinant plasmepsin I from Plasmodium falciparum
PROTEIN ENGINEERING DESIGN & SELECTION, 20:625-633, DEC 2007
abstract,
full text
Akitake, B., Anishkin, A., Liu, N., Sukharev, S.
Straightening and sequential buckling of the pore-lining helices define the gating cycle of MscS
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 14:1141-1149, DEC 2007
abstract,
full text
Cui, S.X., Yu, J., Kuhner, F., Schulten, K., Gaub, H.E.
Double-stranded DNA dissociates into single strands when dragged into a poor solvent
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:14710-14716, NOV 28 2007
abstract,
full text,
TCBG publications
Best, R.B., Merchant, K.A., Gopich, I.V., Schuler, B., Bax, A., Eaton, W.A.
Effect of flexibility and cis residues in single-molecule FRET studies of polyproline
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:18964-18969, NOV 27 2007
abstract,
full text
Simona, F., Magistrato, A., Vera, D.M.A., Garau, G., Vila, A.J., Carloni, P.
Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 69:595-605, NOV 15 2007
abstract,
full text
Li, Z.Y., Abramavicius, D., Zhuang, W., Mukamel, S.
Two-dimensional electronic correlation spectroscopy of the n pi* and pi pi* protein backbone transitions: A simulation study
CHEMICAL PHYSICS, 341:29-36, NOV 15 2007
abstract,
full text
Schug, A., Whitford, P.C., Levy, Y., Onuchic, J.N.
Mutations as trapdoors to two competing native conformations of the Rop-dimer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:17674-17679, NOV 6 2007
abstract,
full text
Kim, H.I., Jung, J., Lee, E.S., Kim, Y.C., Lee, W., Lee, S.T.
Molecular dissection of the interaction between the SH3 domain and the SH2-Kinase Linker region in PTK6
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 362:829-834, NOV 3 2007
abstract,
full text
Zheng, J., Jang, H., Ma, B., Tsai, C.J., Nussinov, R.
Modeling the Alzheimer A beta(17-42) fibril architecture: Tight intermolecular sheet-sheet association and intramolecular hydrated cavities
BIOPHYSICAL JOURNAL, 93:3046-3057, NOV 2007
abstract,
full text
Luan, B.Q., Caffrey, M., Aksimentiev, A.
Structure refinement of the OpcA adhesin using molecular dynamics
BIOPHYSICAL JOURNAL, 93:3058-3069, NOV 2007
abstract,
full text
Cohen, J., Schulten, K.
O-2 migration pathways are not conserved across proteins of a similar fold
BIOPHYSICAL JOURNAL, 93:3591-3600, NOV 2007
abstract,
full text,
TCBG publications
Ivanova, A., Jezierski, G., Vladimirov, E., Rosch, N.
Structure of rhodamine 6G-DNA complexes from molecular dynamics Simulations
BIOMACROMOLECULES, 8:3429-3438, NOV 2007
abstract,
full text
Chen, K.M., Spratt, T.E., Stanley, B.A., De Cotiis, D.A., Bewley, M.C., Flanagan, J.M., Desai, D., Das, A., Fiala, E.S., Amin, S., El-Bayoumy, K.
Inhibition of nuclear Factor-kappa B DNA binding by organoselenocyanates through covalent modification of the p50 subunit
CANCER RESEARCH, 67:10475-10483, NOV 1 2007
abstract,
full text
Christensen, S., Peters, G.H., Hansen, F.Y., O'Connell, J.P., Abildskov, J.
State conditions transferability of vapor-liquid equilibria via fluctuation solution theory with correlation function integrals from molecular dynamics simulation
FLUID PHASE EQUILIBRIA, 260:169-176, NOV 1 2007
abstract,
full text
Zanuy, D., Rodriguez-Ropero, F., Nussinov, R., Aleman, C.
Testing beta-helix terminal coils stability by targeted substitutions with non-proteogenic amino acids: A molecular dynamics study
JOURNAL OF STRUCTURAL BIOLOGY, 160:177-189, NOV 2007
abstract,
full text
Legge, E.S., Treutlein, H., Howlett, G.J., Yarovsky, I.
Molecular dynamics simulations of a fibrillogenic peptide derived from apolipoprotein C-II
BIOPHYSICAL CHEMISTRY, 130:102-113, NOV 2007
abstract,
full text
Stanton, C.L., Kuo, I.F.W., Mundy, C.J., Laino, T., Houk, K.N.
QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5 '-monophosphate decarboxylase using two different QM regions: Acceleration too small to explain rate of enzyme catalysis
JOURNAL OF PHYSICAL CHEMISTRY B, 111:12573-12581, NOV 1 2007
abstract,
full text
Amaro, R.E., Swift, R.V., McCammon, J.A.
Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei
PLOS NEGLECTED TROPICAL DISEASES, 1: Art. No. e68, NOV 2007
abstract,
full text
Raman, E.P., Takeda, T., Barsegov, V., Klimov, D.K.
Mechanical unbinding of A beta peptides from amyloid fibrils
JOURNAL OF MOLECULAR BIOLOGY, 373:785-800, OCT 26 2007
abstract,
full text
Fort, J., de la Ballina, L.R., Burghardt, H.E., Ferrer-Costa, C., Turnay, J., Ferrer-Orta, C., Uson, I., Zorzano, A., Fernandez-Recio, J., Orozco, M., Lizarbe, M.A., Fita, I., Palacin, M.
The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:31444-31452, OCT 26 2007
abstract,
full text
Zhao, X.C., Payne, C.M., Cummings, P.T., Lee, J.W.
Single-strand DNA molecule translocation through nanoelectrode gaps
NANOTECHNOLOGY, 18: Art. No. 424018, OCT 24 2007
abstract,
full text
Yakovlev, V.A., Barani, I.J., Rabender, C.S., Black, S.M., Leach, J.K., Graves, P.R., Kellogg, G.E., Mikkelsen, R.B.
Tyrosine nitration of I kappa B alpha: A novel mechanism for NF-kappa B activation
BIOCHEMISTRY, 46:11671-11683, OCT 23 2007
abstract,
full text
Milac, A.L., Buchete, N.V., Fritz, T.A., Hummer, G., Tabak, L.A.
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine: Polypeptide N-acetylgalactosaminyltransferase-2
JOURNAL OF MOLECULAR BIOLOGY, 373:439-451, OCT 19 2007
abstract,
full text
Spiegel, K., Magistrato, A., Carloni, P., Reedijk, J., Klein, M.L.
Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11873-11876, OCT 18 2007
abstract,
full text
Gorfe, A.A., Babakhani, A., McCammon, J.A.
H-ras protein in a bilayer: Interaction and structure perturbation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:12280-12286, OCT 10 2007
abstract,
full text
Widge, A.S., Matsuoka, Y., Kurnikova, M.
Computational modeling of poly(alkylthiophene) conductive polymer insertion into phospholipid bilayers
LANGMUIR, 23:10672-10681, OCT 9 2007
abstract,
full text
Gumbart, J., Schulten, K.
Structural determinants of lateral gate opening in the protein translocon
BIOCHEMISTRY, 46:11147-11157, OCT 2 2007
abstract,
full text,
TCBG publications
Lagerqvist, J., Zwolak, M., Di Ventra, M.
Influence of the environment and probes on rapid DNA sequencing via transverse electronic transport
BIOPHYSICAL JOURNAL, 93:2384-2390, OCT 2007
abstract,
full text
Radhakrishnan, R.
Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage
BIOPHYSICAL JOURNAL, 93:2391-2399, OCT 2007
abstract,
full text
Cheng, X.L., Ivanov, I., Wang, H.L., Sine, S.M., McCammon, J.A.
Nanosecond-timescale conformational dynamics of the human alpha 7 nicotinic acetylcholine receptor
BIOPHYSICAL JOURNAL, 93:2622-2634, OCT 2007
abstract,
full text
Thomas, M., Jayatilaka, D., Corry, B.
The predominant role of coordination number in potassium channel selectivity
BIOPHYSICAL JOURNAL, 93:2635-2643, OCT 2007
abstract,
full text
Damjanovic, A., Schlessman, J.L., Fitch, C.A., Garcia, A.E., Garcia-Moreno, B.
Role of flexibility and polarity as determinants of the hydration of internal cavities and pockets in proteins
BIOPHYSICAL JOURNAL, 93:2791-2804, OCT 2007
abstract,
full text
Zanuy, D., Rodriguez-Ropero, F., Haspel, N., Zheng, J., Nussinov, R., Aleman, C.
Stability of tubular structures based on beta-helical proteins: Self-assembled versus polymerized nanoconstructs and wild-type versus mutated sequences
BIOMACROMOLECULES, 8:3135-3146, OCT 2007
abstract,
full text
Guevara-Salazar, J.A., Espinoza-Fonseca, M., Beltran, H.I., Correa-Basurto, J., Zavala, D.Q., Trujillo-Ferrara, J.G.
The electronic influence on the active site-directed inhibition of acetylcholinesterase by N-aryl-substituted succinimides
JOURNAL OF THE MEXICAN CHEMICAL SOCIETY, 51:222-227, OCT-DEC 2007
abstract,
full text
Mukhopadhyay, B.P., Ghosh, B., Bairagya, H.R., Bera, A.K., Nandi, T.K., Das, S.B.
Modeling study of rusticyanin-cytochrome C-4 complex: An insight to possible H-bond mediated recognition and electron - Transfer process
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 25:157-164, OCT 2007
abstract,
full text
Seeber, M., Cecchini, M., Rao, F., Settanni, G., Caflisch, A.
Wordom: a program for efficient analysis of molecular dynamics simulations
BIOINFORMATICS, 23:2625-2627, OCT 1 2007
abstract,
full text
Gorfe, A.A., Caflisch, A.
Ser170 controls the conformational multiplicity of the loop 166-175 in prion proteins: implication for conversion and species barrier
FASEB JOURNAL, 21:3279-3287, OCT 2007
abstract,
full text
Siggel, L., Bulo, R.E., Molnar, F., Weiss, H., Taeger, T.
Leather relates collagen modeling: The challenges of modeling hierarchical structures
JOURNAL OF THE AMERICAN LEATHER CHEMISTS ASSOCIATION, 102:333-336, OCT 2007
full text
Wells, D.B., Abramkina, V., Aksimentiev, A.
Exploring transmembrane transport through alpha-hemolysin with grid-steered molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 127: Art. No. 125101, SEP 28 2007
abstract,
full text
Moroni, E., Caselle, M., Fogolari, F.
Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes
BMC STRUCTURAL BIOLOGY, 7: Art. No. 61, SEP 27 2007
abstract,
full text
Ivanova, A., Rosch, N.
The structure of LNA : DNA hybrids from molecular dynamics simulations: The effect of locked nucleotides
JOURNAL OF PHYSICAL CHEMISTRY A, 111:9307-9319, SEP 27 2007
abstract,
full text
Shih, A.Y., Arkhipov, A., Freddolino, P.L., Sligar, S.G., Schulten, K.
Assembly of lipids and proteins into lipoprotein particles
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11095-11104, SEP 27 2007
abstract,
full text,
TCBG publications
Mottamal, M., Shen, S., Guembe, C., Krilov, G.
Solvation of transmembrane proteins by isotropic membrane mimetics: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11285-11296, SEP 27 2007
abstract,
full text
Patra, S.M., Bastug, T., Kuyucak, S.
Binding of organic cations to gramicidin a channel studied with AutoDock and molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 111:11303-11311, SEP 27 2007
abstract,
full text
Porter, C.J., Matthews, J.M., Mackay, J.P., Pursglove, S.E., Schmidberger, J.W., Leedman, P.J., Pero, S.C., Krag, D.N., Wilce, M.C.J., Wilce, J.A.
Grb7 SH2 domain structure and interactions with a cyclic peptide inhibitor of cancer cell migration and proliferation
BMC STRUCTURAL BIOLOGY, 7: Art. No. 58, SEP 25 2007
abstract,
full text
Liu, Y., Henry, G.D., Hegde, R.S., Baleja, J.D.
Solution structure of the hDIg/SAP97 PDZ2 domain and its mechanism of interaction with HPV-18 Papillomavirus E6 protein
BIOCHEMISTRY, 46:10864-10874, SEP 25 2007
abstract,
full text
Zhou, H., Wu, T., Dong, X., Wang, Q., Shen, J.W.
Adsorption mechanism of BMP-7 on hydroxyapatite (001) surfaces
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 361:91-96, SEP 14 2007
abstract,
full text
Dehez, F., Tarek, M., Chipot, C.
Energetics of ion transport in a peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 111:10633-10635, SEP 13 2007
abstract,
full text
Henthorn, D.B., Peppas, N.A.
Molecular simulations of recognitive behavior of molecularly imprinted intelligent polymeric networks
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 46:6084-6091, SEP 12 2007
abstract,
full text
Jo, S., Kim, T., Im, W.
Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
PLOS ONE, 2: Art. No. e880, SEP 12 2007
abstract,
full text
Curco, D., Nussinov, R., Aleman, C.
Coarse-grained representation of beta-helical protein building blocks
JOURNAL OF PHYSICAL CHEMISTRY B, 111:10538-10549, SEP 6 2007
abstract,
full text
Roy, A., Taraphder, S.
Identification of proton-transfer pathways in human carbonic anhydrase II
JOURNAL OF PHYSICAL CHEMISTRY B, 111:10563-10576, SEP 6 2007
abstract,
full text
Bender, G.M., Lehmann, A., Zou, H., Cheng, H., Fry, H.C., Engel, D., Therien, M.J., Blasie, J.K., Roder, H., Saven, J.G., DeGrado, W.F.
De novo design of a single-chain diphenylporphyrin metalloprotein
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:10732-10740, SEP 5 2007
abstract,
full text
Jones, P.M., Turner, K.M., Djordjevic, J.T., Sorrell, T.C., Wright, L.C., George, A.M.
Role of conserved active site residues in catalysis by phospholipase B1 from Cryptococcus neoformans
BIOCHEMISTRY, 46:10024-10032, SEP 4 2007
abstract,
full text
Hemp, J., Han, H., Roh, J.H., Kaplan, S., Martinez, T.J., Gennis, R.B.
Comparative genomics and site-directed mutagenesis support the existence of only one input channel for protons in the C-family (cbb(3) oxidase) of heme-copper oxygen reductases
BIOCHEMISTRY, 46:9963-9972, SEP 4 2007
abstract,
full text
Zhuang, W., Abrarnavicius, D., Voronine, D.V., Mukarmel, S.
Simulation of two-dimensional infrared spectroscopy of amyloid fibrils
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:14233-14236, SEP 4 2007
abstract,
full text
Wierzbicki, A., Dalal, P., Cheatham, T.E., Knickelbein, J.E., Haymet, A.D.J., Madura, J.D.
Antifreeze proteins at the Ice/Water interface: Three calculated discriminating properties for orientation of type I proteins
BIOPHYSICAL JOURNAL, 93:1442-1451, SEP 2007
abstract,
full text
Lee, E.H., Hsin, J., Mayans, O., Schulten, K.
Secondary and tertiary structure elasticity of titin Z1Z2 and a titin chain model
BIOPHYSICAL JOURNAL, 93:1719-1735, SEP 2007
abstract,
full text,
TCBG publications
Sliozberg, Y., Abrams, C.F.
Spontaneous conformational changes in the e. coli GroEL subunit from all-atom molecular dynamics Simulations
BIOPHYSICAL JOURNAL, 93:1906-1916, SEP 2007
abstract,
full text
Jang, H., Zheng, J., Nussinov, R.
Models of beta-amyloid ion channels in the membrane suggest that channel formation in the bilayer is a dynamic process
BIOPHYSICAL JOURNAL, 93:1938-1949, SEP 2007
abstract,
full text
Espinoza-Fonseca, L.M., Kast, D., Thomas, D.D.
Molecular dynamics Simulations reveal a disorder-to-order transition on phosphorylation of smooth muscle myosin
BIOPHYSICAL JOURNAL, 93:2083-2090, SEP 2007
abstract,
full text
Rivail, L., Chipot, C., Maigret, B., Bestel, I., Sicsic, S., Tarek, M.
Large-scale molecular dynamics of a G protein-coupled receptor, the human 5-HT4 serotonin receptor, in a lipid bilayer
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 817:19-26, SEP 1 2007
abstract,
full text
Delgado-Buscalioni, R., De Fabritiis, G.
Embedding molecular dynamics within fluctuating hydrodynamics in multiscale simulations of liquids
PHYSICAL REVIEW E, 76: Art. No. 036709, SEP 2007
abstract,
full text
Szarecka, A., Xu, Y., Tang, P.
Dynamics of heteropentameric nicotinic acetylcholine receptor: Implications of the gating mechanism
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:948-960, SEP 2007
abstract,
full text
Nilsson, L.M., Yakovenko, O., Tchesnokova, V., Thomas, W.E., Schembri, M.A., Vogel, V., Klemm, P., Sokurenko, E.V.
The cysteine bond in the Escherichia coli FimH adhesin is critical for adhesion under flow conditions
MOLECULAR MICROBIOLOGY, 65:1158-1169, SEP 2007
abstract,
full text
Merelli, I., Morra, G., Milanesi, L.
Evaluation of a grid based molecular dynamics approach for polypeptide simulations
IEEE TRANSACTIONS ON NANOBIOSCIENCE, 6:229-234, SEP 2007
abstract,
full text
Yesylevskyy, S.O.
ProtSqueeze: Simple and effective automated tool for setting up membrane protein simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 47:1986-1994, SEP-OCT 2007
abstract,
full text
Mazzini, S., Fernandez-Vidal, M., Galbusera, V., Castro-Roman, F., Bellucci, M.C., Ragg, E., Haro, I.
3D-Structure of the interior fusion peptide of HGV/GBV-C by 1H NMR, CD and molecular dynamics studies
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 465:187-196, SEP 1 2007
abstract,
full text
Jojart, B., Martinek, T.A.
Performance of the general amber force field in modeling aqueous POPC membrane bilayers
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2051-2058, SEP 2007
abstract,
full text
Kutzner, C., Van der Spoel, D., Fechner, M., Lindahl, E., Schmitt, U.W., De Groot, B.L., Grubmuller, H.
Software news and update - Speeding up parallel GROMACS on high-latency networks
JOURNAL OF COMPUTATIONAL CHEMISTRY, 28:2075-2084, SEP 2007
abstract,
full text
Tuukkanen, A., Kaila, V.R.I., Laakkonen, L., Hummer, G., Wikstrom, M.
Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1767:1102-1106, SEP 2007
abstract,
full text
Levin, E.J., Kondrashov, D.A., Wesenberg, G.E., Phillips, G.N.
Ensemble refinement of protein crystal structures: Validation and application
STRUCTURE, 15:1040-1052, SEP 2007
abstract,
full text
Boghosian, B., Peter, C., Dong, S., Finn, L., Jha, S., Karniadakis, G., Karonis, N.
NEKTAR, SPICE and Vortonics: using federated grids for large scale scientific applications
CLUSTER COMPUTING-THE JOURNAL OF NETWORKS SOFTWARE TOOLS AND APPLICATIONS, 10:351-364, SEP 2007
abstract,
full text
Herrera, F.E., Zucchelli, S., Jezierska, A., Lavina, Z.S., Gustincich, S., Carloni, P.
On the oligomeric state of DJ-1 protein and its mutants associated with Parkinson disease - A combined computational and in vitro study
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:24905-24914, AUG 24 2007
abstract,
full text
Anavi-Goffer, S., Fleischer, D., Hurst, D.P., Lynch, D.L., Barnett-Norris, J., Shi, S.P., Lewis, D.L., Mukhopadhyay, S., Howlett, A.C., Reggio, P.H., Abood, M.E.
Helix 8 Leu in the CB1 cannabinoid receptor contributes to selective signal transduction mechanisms
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:25100-25113, AUG 24 2007
abstract,
full text
Asthagiri, D., Ashbaugh, H.S., Piryatinski, A., Paulaitis, M.E., Pratt, L.R.
Non-van der waals treatment of the hydrophobic solubilities of CF4
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:10133-10140, AUG 22 2007
abstract,
full text
Zhu, H., May, V., Roder, B., Madjet, M.E.A., Renger, T.
The pheophorbide-a DAB dendrimer P-4 in solution: MD-simulations based studies of exciton states
CHEMICAL PHYSICS LETTERS, 444:118-124, AUG 17 2007
abstract,
full text
Rapedius, M., Fowler, P.W., Shang, L.J., Sansom, M.S.P., Tucker, S.J., Baukrowitz, T.
H bonding at the helix-bundle crossing controls gating in Kir potassium channels
NEURON, 55:602-614, AUG 16 2007
abstract,
full text
Kelkar, M.S., Maginn, E.J.
Calculating the enthalpy of vaporization for ionic liquid clusters
JOURNAL OF PHYSICAL CHEMISTRY B, 111:9424-9427, AUG 16 2007
abstract,
full text
Budiman, M.E., Knaggs, M.H., Fetrow, J.S., Alexander, R.W.
Using molecular dynamics to map interaction networks in an aminoacyl-tRNA synthetase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:670-689, AUG 15 2007
abstract,
full text
Fang, B., Martyna, G., Deng, Y.F.
A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: Application to the 6-D torus QCDOC supercomputer
COMPUTER PHYSICS COMMUNICATIONS, 177:362-377, AUG 15 2007
abstract,
full text
Saam, J., Ivanov, I., Walther, M., Holzhutter, H.G., Kuhn, H.
Molecular dioxygen enters the active site of 12/15-lipoxygenase via dynamic oxygen access channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:13319-13324, AUG 14 2007
abstract,
full text
Aprikian, P., Tchesnokova, V., Kidd, B., Yakovenko, O., Yarov-Yarovoy, V., Trinchina, E., Vogel, V., Thomas, W., Sokurenko, E.
Interdomain interaction in the FimH adhesin of Escherichia coli regulates the affinity to mannose
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:23437-23446, AUG 10 2007
abstract,
full text
Ashbaugh, H.S., Pratt, L.R.
Contrasting nonaqueous against aqueous solvation on the basis of scaled-particle theory
JOURNAL OF PHYSICAL CHEMISTRY B, 111:9330-9336, AUG 9 2007
abstract,
full text
Jones, P.M., George, A.M.
Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette - A computational study of the MJ0796 dimer
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:22793-22803, AUG 3 2007
abstract,
full text
Fuentes-Cabrera, M., Zhao, X., Kent, P.R.C., Sumpter, B.G.
Electronic structure of xDNA
JOURNAL OF PHYSICAL CHEMISTRY B, 111:9057-9061, AUG 2 2007
abstract,
full text
Zheng, X.G., Diraviyam, K., Sept, D.
Nucleotide effects on the structure and dynamics of actin
BIOPHYSICAL JOURNAL, 93:1277-1283, AUG 2007
abstract,
full text
Dong, X.L., Wang, Q., Wu, T., Pan, H.H.
Understanding adsorption-desorption dynamics of BMP-2 on hydroxyapatite (001) surface
BIOPHYSICAL JOURNAL, 93:750-759, AUG 2007
abstract,
full text
Villoutreix, B.O., Renault, N., Lagorce, D., Sperandio, O., Montes, M., Miteva, M.A.
Free resources to assist structure-based virtual ligand screening experiments
CURRENT PROTEIN & PEPTIDE SCIENCE, 8:381-411, AUG 2007
abstract,
full text
Geroult, S., Hooda, M., Virdee, S., Waksman, G.
Prediction of solvation sites at the interface of src SH2 domain complexes using molecular dynamics simulations
CHEMICAL BIOLOGY & DRUG DESIGN, 70:87-99, AUG 2007
abstract,
full text
Vistoli, G., Pedretti, A., Testa, B., Matucci, R.
The conformational and property space of acetylcholine bound to muscarinic receptors: An entropy component accounts for the subtype selectivity of acetylcholine
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 464:112-121, AUG 1 2007
abstract,
full text
Lou, J.H., Yago, T., Mcever, R.P., Zhu, C.
The sliding-rebinding mechanism for catch bonds
JAPANESE JOURNAL OF APPLIED PHYSICS PART 1-REGULAR PAPERS BRIEF COMMUNICATIONS & REVIEW PAPERS, 46:5528-5535, AUG 2007
abstract,
full text
Venkat, A.S., Corni, S., Di Felice, R.
Etectronic coupling between azurin and gold at different protein/substrate orientations
SMALL, 3:1431-1437, AUG 2007
abstract,
full text
Roumen, L., Sanders, M.P.A., Pieterse, K., Hilbers, P.A.J., Plate, R., Custers, E., de Gooyer, M., Smits, J.F.M., Beugels, I., Emmen, J., Ottenheijm, H.C.J., Leysen, D., Hermans, J.J.R.
Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 21:455-471, AUG 2007
abstract,
full text
Gong, H.P., Shen, Y., Rose, G.D.
Building native protein conformation from NMR backbone chemical shifts using Monte Carlo fragment assembly
PROTEIN SCIENCE, 16:1515-1521, AUG 2007
abstract,
full text
Peters, B., Beckham, G.T., Trout, B.L.
Extensions to the likelihood maximization approach for finding reaction coordinates
JOURNAL OF CHEMICAL PHYSICS, 127: Art. No. 034109, JUL 21 2007
abstract,
full text
Krzysko, K.A., Kolinski, M., Filipek, S.
Molecular modelling of the complex of oligomeric rhodopsin and its G protein
JOURNAL OF PHYSICS-CONDENSED MATTER, 19: Art. No. 285204, JUL 18 2007
abstract,
full text
Neelov, A., Ghasemi, S.A., Goedecker, S.
Particle-particle, particle-scaling function algorithm for electrostatic problems in free boundary conditions
JOURNAL OF CHEMICAL PHYSICS, 127: Art. No. 024109, JUL 14 2007
abstract,
full text
Solares, S.D., Crone, J.C.
Real-time simulation of isolated biomolecule characterization with frequency and force modulation atomic force microscopy
JOURNAL OF PHYSICAL CHEMISTRY C, 111:10029-10034, JUL 12 2007
abstract,
full text
Coskuner, O.
Preferred conformation of the glycosidic linkage of methyl-beta-mannose
JOURNAL OF CHEMICAL PHYSICS, 127: Art. No. 015101, JUL 7 2007
abstract,
full text
Ivanov, I., Cheng, X.L., Sine, S.M., McCammon, J.A.
Barriers to ion translocation in cationic and anionic receptors from the Cys-loop family
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:8217-8224, JUL 4 2007
abstract,
full text
Haspel, N., Zanuy, D., Zheng, J., Aleman, C., Wolfson, H., Nussinov, R.
Changing the charge distribution of beta-helical-based nanostructures can provide the conditions for charge transfer
BIOPHYSICAL JOURNAL, 93:245-253, JUL 2007
abstract,
full text
Gumbart, J., Wiener, M.C., Tajkhorshid, E.
Mechanics of force propagation in TonB-dependent outer membrane transport
BIOPHYSICAL JOURNAL, 93:496-504, JUL 2007
abstract,
full text
Krol, M., Tournier, A.L., Bates, P.A.
Flexible relaxation of rigid-body docking solutions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:159-169, JUL 2007
abstract,
full text
Ni, F.Y., Cai, B., Ding, Z.C., Zheng, F., Zhang, M.J., Wu, H.M., Sun, H.Z., Huang, Z.X.
Structural prediction of the beta-domain of metallothionein-3 by molecular dynamics simulation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:255-266, JUL 2007
abstract,
full text
Kuang, Z.F., Mahankali, U., Beck, T.L.
Proton pathways and H(+)/Cl(-) stoichiometry in bacterial chloride transporters
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 68:26-33, JUL 2007
abstract,
full text
Zhang, D.J., Chippada, U., Jordan, K.
Effect of the structural water on the mechanical properties of collagen-like microfibrils: A molecular dynamics study
ANNALS OF BIOMEDICAL ENGINEERING, 35:1216-1230, JUL 2007
abstract,
full text
Cilurzo, F., Selmin, F., Vistoli, G., Minghetti, P., Montanari, L.
Binary polymeric blends to microencapsulate nitroflurbiprofen: Physicochemical and in silico studies
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES, 31:202-210, JUL 2007
abstract,
full text
Dawelbait, G., Winter, C., Zhang, Y., Pilarsky, C., Grutzmann, R., Heinrich, J.C., Schroeder, M.
Structural templates predict novel protein interactions and targets from pancreas tumour gene expression data
BIOINFORMATICS, 23:I115-I124, JUL 1 2007
abstract,
full text
Skeel, R.D., Hardy, D.J., Phillips, J.C.
Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations
JOURNAL OF COMPUTATIONAL PHYSICS, 225:1-5, JUL 1 2007
full text
Cyr, E.C., Bond, S.D.
Using the method of weighted residuals to compute potentials of mean force
JOURNAL OF COMPUTATIONAL PHYSICS, 225:714-729, JUL 1 2007
abstract,
full text
Mamonov, A.B., Coalson, R.D., Zeidel, M.L., Mathai, J.C.
Water and deuterium oxide permeability through aquaporin 1: MD predictions and experimental verification
JOURNAL OF GENERAL PHYSIOLOGY, 130:111-116, JUL 2007
abstract,
full text
Boiteux, C., Kraszewski, S., Ramseyer, C., Girardet, C.
Ion conductance vs. pore gating and selectivity in KcsA channel: Modeling achievements and perspectives
JOURNAL OF MOLECULAR MODELING, 13:699-713, JUL 2007
abstract,
full text
Orlowski, S., Nowak, W.
Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin
JOURNAL OF MOLECULAR MODELING, 13:715-723, JUL 2007
abstract,
full text
Peplowski, L., Kubiak, K., Nowak, W.
Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides
JOURNAL OF MOLECULAR MODELING, 13:725-730, JUL 2007
abstract,
full text
Wang, B.Y., Kral, P.
Chemically tunable nanoscale propellers of liquids
PHYSICAL REVIEW LETTERS, 98: Art. No. 266102, JUN 29 2007
abstract,
full text
Bellesia, G., Shea, J.E.
Self-assembly of beta-sheet forming peptides into chiral fibrillar aggregates
JOURNAL OF CHEMICAL PHYSICS, 126: Art. No. 245104, JUN 28 2007
abstract,
full text
Floquet, N., Mouilleron, S., Daher, R., Maigret, B., Badet, B., Badet-Denisot, M.A.
Ammonia channeling in bacterial glucosamine-6-phosphate synthase (Glms): Molecular dynamics simulations and kinetic studies of protein mutants
FEBS LETTERS, 581:2981-2987, JUN 26 2007
abstract,
full text
Johnson, B.J., Cohen, J., Welford, R.W., Pearson, A.R., Schulten, K., Klinman, J.P., Wilmot, C.M.
Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:17767-17776, JUN 15 2007
abstract,
full text,
TCBG publications
Tucinska-Daneluti, A.M., Gorecki, A., Czubaty, A., Kowalska-Loth, B., Girstun, A., Murawska, M., Lesyng, B., Staron, K.
RRM proteins-interacting with the cap region of topoisomerase I
JOURNAL OF MOLECULAR BIOLOGY, 369:1098-1112, JUN 15 2007
abstract,
full text
O'Brien, E.P., Dima, R.I., Brooks, B., Thirumalai, D.
Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:7346-7353, JUN 13 2007
abstract,
full text
Sonne, J., Jensen, M.O., Hansen, F.Y., Hemmingsen, L., Peters, G.H.
Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension
BIOPHYSICAL JOURNAL, 92:4157-4167, JUN 2007
abstract,
full text
Oberhofer, H., Dellago, C., Boresch, S.
Single molecule pulling with large time steps
PHYSICAL REVIEW E, 75: Art. No. 061106, JUN 2007
abstract,
full text
Zhao, Q., Sigalov, G., Dimitrov, V., Dorvel, B., Mirsaidov, U., Sligar, S., Aksimentiev, A., Timp, G.
Detecting SNPs using a synthetic nanopore
NANO LETTERS, 7:1680-1685, JUN 2007
abstract,
full text
Shih, A.Y., Freddolino, P.L., Sligar, S.G., Schulten, K.
Disassembly of nanodiscs with cholate
NANO LETTERS, 7:1692-1696, JUN 2007
abstract,
full text,
TCBG publications
Raman, E.P., Barsegov, V., Klimov, D.K.
Folding of tandem-linked domains
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 67:795-810, JUN 2007
abstract,
full text
Glykos, N.M.
On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 63:705-713, JUN 2007
abstract,
full text
Burden, C.J., Oakley, A.J.
Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations
PHYSICAL BIOLOGY, 4:79-90, JUN 2007
abstract,
full text
Xaplanteri, M.A., Papadopoulos, G., Leontiadou, F., Choli-Papadopoulou, T., Kalpaxis, D.L.
The contribution of the zinc-finger motif to the function of Thermus thermophilus ribosomal protein S14
JOURNAL OF MOLECULAR BIOLOGY, 369:489-497, JUN 1 2007
abstract,
full text
Hill, C.L., Hung, L.C., Smith, D.J., Verma, C.S., Grogan, G.
On the resolution of chiral substrates by a retro-claisenase enzyme: Biotransformations of heteroannular bicyclic beta-diketones by 6-oxocamphor hydrolase
ADVANCED SYNTHESIS & CATALYSIS, 349:1353-1360, JUN 2007
abstract,
full text
Jorgensen, A.M., Tagmose, L., Jorgensen, A.M.M., Bogeso, K.P., Peters, G.H.
Molecular dynamics simulations of Na+/Cl--dependent neurotransmitter transporters in a membrane-aqueous system
CHEMMEDCHEM, 2:827-840, JUN 2007
abstract,
full text
Buehler, M.J.
Hierarchical chemo-nanomechanics of proteins: Entropic elasticity, protein unfolding and molecular fracture
JOURNAL OF MECHANICS OF MATERIALS AND STRUCTURES, 2:1019-1057, JUN 2007
abstract,
full text
De Fabritiis, G.
Performance of the Cell processor for biomolecular simulations
COMPUTER PHYSICS COMMUNICATIONS, 176:660-664, JUN 2007
abstract,
full text
Waibel, B., Scheiber, J., Meier, C., Hammitzsch, M., Baumann, K., Scriba, G.K.E., Holzgrabe, U.
Comparison of cyclodextrin-dipeptide inclusion complexes in the absence and presence of urea by means of capillary electrophoresis, nuclear magnetic resonance and molecular modeling
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 18, 2921-2930, JUN 2007
abstract,
full text
Sotomayor, M., Schulten, K.
Single-molecule experiments in vitro and in silico
SCIENCE, 316:1144-1148, MAY 25 2007
abstract,
full text,
TCBG publications
Budi, A., Legge, F.S., Treutlein, H., Yarovsky, I.
Effect of frequency on insulin response to electric field stress
JOURNAL OF PHYSICAL CHEMISTRY B, 111:5748-5756, MAY 24 2007
abstract,
full text
Guo, J.T., Jaromczyk, J.W., Xu, Y.
Analysis of chameleon sequences and their implications in biological processes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 67:548-558, MAY 15 2007
abstract,
full text
Takeda, T., Klimov, D.K.
Dissociation of A beta(16-22) amyloid fibrils probed by molecular dynamics
JOURNAL OF MOLECULAR BIOLOGY, 368:1202-1213, MAY 11 2007
abstract,
full text
Kelkar, M.S., Maginn, E.J.
Effect of temperature and water content on the shear viscosity of the ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide as studied by atomistic simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 111:4867-4876, MAY 10 2007
abstract,
full text
Sass, H.J., Schmid, F.F.F., Grzesiek, S.
Correlation of protein structure and dynamics to scalar couplings across hydrogen bonds
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:5898-5903, MAY 9 2007
abstract,
full text
Ramos, L.S., Chen, M.H., Knox, B.E., Birge, R.R.
Regulation of photoactivation in vertebrate short wavelength visual pigments: Protonation of the retinylidene Schiff base and a counterion switch
BIOCHEMISTRY, 46:5330-5340, MAY 8 2007
abstract,
full text
Munson, K., Law, R.J., Sachs, G.
Analysis of the gastric H,K ATPase for ion pathways and inhibitor binding sites
BIOCHEMISTRY, 46:5398-5417, MAY 8 2007
abstract,
full text
Buchete, N.V., Hummer, G.
Structure and dynamics of parallel beta-sheets, hydrophobic core, and loops in Alzheimer's A beta fibrils
BIOPHYSICAL JOURNAL, 92:3032-3039, MAY 1 2007
abstract,
full text
Weronski, P., Jiang, Y., Rasmussen, S.
Molecular dynamics study of small PNA molecules in lipid-water system
BIOPHYSICAL JOURNAL, 92:3081-3091, MAY 1 2007
abstract,
full text
Lamoureux, G., Klein, M.L., Berneche, S.
A stable water chain in the hydrophobic pore of the AmtB ammonium transporter
BIOPHYSICAL JOURNAL, 92:L82-L84, MAY 1 2007
abstract,
full text
Sorensen, J., Hamelberg, D., Schiott, B., McCammon, J.A.
Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism
BIOPOLYMERS, 86:73-82, MAY 2007
abstract,
full text
Bulo, R.E., Donadio, D., Laio, A., Molnar, F., Rieger, J., Parrinello, M.
"Site binding" of Ca(2+) ions to polyacrylates in water: A molecular dynamics study of coiling and aggregation
MACROMOLECULES, 40:3437-3442, MAY 1 2007
abstract,
full text
Fowler, P.W., Geroult, S., Jha, S., Waksman, G., Coveney, P.V.
Rapid, accurate, and precise calculation of relative binding affinities for the SH2 domain using a computational grid
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 3:1193-1202, MAY-JUN 2007
abstract,
full text
Rueda, M., Chacon, P., Orozco, M.
Thorough validation of protein normal mode analysis: A comparative study with essential dynamics
STRUCTURE, 15:565-575, MAY 2007
abstract,
full text
Chen, X., Deng, Y.F.
Long-time molecular dynamics simulations of botulinum biotoxin type-A at different pH values and temperatures
JOURNAL OF MOLECULAR MODELING, 13:559-572, MAY 2007
abstract,
full text
Tayefeh, S., Kloss, T., Thiel, G., Hertel, B., Moroni, A., Kast, S.M.
Molecular dynamics simulation of the cytosolic mouth in Kcv-type potassium channels
BIOCHEMISTRY, 46:4826-4839, APR 24 2007
abstract,
full text
Wang, Z.H., Lin, Y.W., Rosell, F.I., Ni, F.Y., Lu, H.J., Yang, P.Y., Tan, X.S., Li, X.Y., Huang, Z.X., Mauk, A.G.
Converting cytochrome c into a peroxidase-like metalloenzyme by molecular design
CHEMBIOCHEM, 8:607-609, APR 16 2007
full text
Christensen, S., Peters, G.H., Hansen, F.Y., O'Connell, J.P., Abildskov, J.
Generation of thermodynamic data for organic liquid mixtures from molecular simulations
MOLECULAR SIMULATION, 33:449-457, APR 15 2007
abstract,
full text
Pedretti, A., Vistoli, G.
Modeling of human ghrelin receptor (hGHS-R1a) in its close state and validation by molecular docking
BIOORGANIC & MEDICINAL CHEMISTRY, 15:3054-3064, APR 15 2007
abstract,
full text
Johnson, C.P., Gaetani, M., Ortiz, V., Bhasin, N., Harper, S., Gallagher, P.G., Speicher, D.W., Discher, D.E.
Pathogenic proline mutation in the linker between spectrin repeats: disease caused by spectrin unfolding
BLOOD, 109:3538-3543, APR 15 2007
abstract,
full text
Klauda, J.B., Brooks, B.R.
Sugar binding in lactose permease: Anomeric state of a disaccharide influences binding structure
JOURNAL OF MOLECULAR BIOLOGY, 367:1523-1534, APR 13 2007
abstract,
full text
Migliore, A., Corni, S., Di Felice, R., Molinari, E.
Water-mediated electron transfer between protein redox centers
JOURNAL OF PHYSICAL CHEMISTRY B, 111:3774-3781, APR 12 2007
abstract,
full text
Zollner, A., Pasquinelli, M.A., Bernhardt, R., Beratan, D.N.
Protein phosphorylation and intermolecular electron transfer: A joint experimental and computational study of a hormone biosynthesis pathway
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:4206-4216, APR 11 2007
abstract,
full text
Ou, T.M., Lu, Y.J., Zhang, C., Huang, Z.S., Wang, X.D., Tan, J.H., Chen, Y., Ma, D.L., Wong, K.Y., Tang, J.C.O., Chan, A.S.C., Gu, L.Q.
Stabilization of G-quadruplex DNA and down-regulation of oncogene c-myc by quindoline derivatives
JOURNAL OF MEDICINAL CHEMISTRY, 50:1465-1474, APR 5 2007
abstract,
full text
Sinkovits, A.F., Bryksa, B.C., Tanaka, T., Yada, R.Y.
Understanding the structure-function role of specific catalytic residues in a model food related enzyme: Pepsin
ENZYME AND MICROBIAL TECHNOLOGY, 40:1175-1180, APR 3 2007
abstract,
full text
Zhou, R.H., Eleftheriou, M., Royyuru, A.K., Berne, B.J.
Destruction of long-range interactions by a single mutation in lysozyme
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:5824-5829, APR 3 2007
abstract,
full text
Jang, H., Ma, B.Y., Nussinov, R.
Conformational study of the protegrin-I (PG-I) dimer interaction with lipid bilayers and its effect
BMC STRUCTURAL BIOLOGY, 7: Art. No. 21, APR 2 2007
abstract,
full text
Katti, D.R., Schmidt, S.R., Ghosh, P., Katti, K.S.
Molecular modeling of the mechanical behavior and interactions in dry and slightly hydrated sodium montmorillonite interlayer
CANADIAN GEOTECHNICAL JOURNAL, 44:425-435, APR 2007
abstract,
full text
Wang, B., Kral, P.
Optimal atomistic modifications of material surfaces: Design of selective nesting sites for biomolecules
SMALL, 3:580-584, APR 2007
full text
Tsigelny, I.F., Bar-On, P., Sharikov, Y., Crews, L., Hashimoto, M., Miller, M.A., Keller, S.H., Platoshyn, O., Yuan, J.X.J., Masliah, E.
Dynamics of alpha-synuclein aggregation and inhibition of pore-like oligomer development by beta-synuclein
FEBS JOURNAL, 274:1862-1877, APR 2007
abstract,
full text
Floquet, N., Richez, C., Durand, P., Maigret, B., Badet, B., Badet-Denisot, M.A.
Discovering new inhibitors of bacterial glucosamine-6P synthase (GlmS) by docking simulations
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 17:1966-1970, APR 1 2007
abstract,
full text
Leroux, V., Gresh, N., Liu, W.Q., Garbay, C., Maigret, B.
Role of water molecules for binding inhibitors in the SH2 domain of Grb2: A molecular dynamics study
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 806:51-66, MAR 31 2007
abstract,
full text
Zanuy, D., Jimenez, A.I., Cativiela, C., Nussinov, R., Aleman, C.
Use of constrained synthetic amino acids in beta-helix proteins for conformational control
JOURNAL OF PHYSICAL CHEMISTRY B, 111:3236-3242, MAR 29 2007
abstract,
full text
Fowler, P.W., Balali-Mood, K., Deol, S., Coveney, P.V., Sansom, M.S.P.
Monotopic enzymes and lipid bilayers: A comparative study
BIOCHEMISTRY, 46:3108-3115, MAR 20 2007
abstract,
full text
Casanovas, J., Zanuy, D., Nussinov, R., Aleman, C.
Intrinsic conformational characteristics of alpha,alpha-diphenylglycine
JOURNAL OF ORGANIC CHEMISTRY, 72:2174-2181, MAR 16 2007
abstract,
full text
Knaggs, M.H., Salsbury, F.R., Edgell, M.H., Fetrow, J.S.
Insights into correlated motions and long-range interactions in CheY derived from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 92:2062-2079, MAR 15 2007
abstract,
full text
Karain, W.I., Ajarmah, B., Qaraeen, N.I.
The dynamics of inter-residue distances in bovine pancreatic trypsin inhibitor
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 376:394-400, MAR 15 2007
abstract,
full text
Coveney, P.V., Saksena, R.S., Zasada, S.J., McKeown, M., Pickles, S.
The application hosting environment: Lightweight middleware for grid-based computational science
COMPUTER PHYSICS COMMUNICATIONS, 176:406-418, MAR 15 2007
abstract,
full text
Bastug, T., Kuyucak, S.
Free energy simulations of single and double ion occupancy in gramicidin A
JOURNAL OF CHEMICAL PHYSICS, 126: Art. No. 105103, MAR 14 2007
abstract,
full text
Solares, S.D.
Single biomolecule imaging with frequency and force modulation in tapping-mode atomic force microscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 111:2125-2129, MAR 8 2007
abstract,
full text
Lou, J.Z., Zhu, C.
A structure-based sliding-rebinding mechanism for catch bonds
BIOPHYSICAL JOURNAL, 92:1471-1485, MAR 1 2007
abstract,
full text
Fogolari, F., Corazza, A., Viglino, P., Zuccato, P., Pieri, L., Faccioli, P., Bellotti, V., Esposito, G.
Molecular dynamics simulation suggests possible interaction patterns at early steps of beta(2)-microglobulin aggregation
BIOPHYSICAL JOURNAL, 92:1673-1681, MAR 1 2007
abstract,
full text
Balog, E., Laberge, M., Fidy, J.
The influence of interdomain interactions on the intradomain motions in yeast phosphoglycerate kinase: A molecular dynamics study
BIOPHYSICAL JOURNAL, 92:1709-1716, MAR 1 2007
abstract,
full text
Ghosh, P., Katti, D.R., Katti, K.S.
Mineral proximity influences mechanical response of proteins in biological mineral-protein hybrid systems
BIOMACROMOLECULES, 8:851-856, MAR 2007
abstract,
full text
Dalle-Donne, I., Carini, M., Vistoli, G., Gamberoni, L., Giustarini, D., Colombo, R., Facino, R.M., Rossi, R., Milzani, A., Aldini, G.
Actin Cys374 as a nucleophilic target of alpha,beta-unsaturated aldehydes
FREE RADICAL BIOLOGY AND MEDICINE, 42:583-598, MAR 1 2007
abstract,
full text
Orlowski, J., Boniecki, M., Bujnicki, J.M.
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
BIOINFORMATICS, 23:527-530, MAR 2007
abstract,
full text
Dal Peraro, M., Spiegel, K., Lamoureux, G., De Vivo, M., DeGrado, W.F., Klein, M.L.
Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
JOURNAL OF STRUCTURAL BIOLOGY, 157:444-453, MAR 2007
abstract,
full text
Sanbonmatsu, K.Y., Tung, C.S.
High performance computing in biology: Multimillion atom simulations of nanoscale systems
JOURNAL OF STRUCTURAL BIOLOGY, 157:470-480, MAR 2007
abstract,
full text
Wang, Y., Cohen, J., Boron, W.F., Schulten, K., Tajkhorshid, E.
Exploring gas permeability of cellular membranes and membrane channels with molecular dynamics
JOURNAL OF STRUCTURAL BIOLOGY, 157:534-544, MAR 2007
abstract,
full text,
TCBG publications
Shih, A.Y., Freddolino, P.L., Arkhipov, A., Schulten, K.
Assembly of lipoprotein particles revealed by coarse-grained molecular dynamics simulations
JOURNAL OF STRUCTURAL BIOLOGY, 157:579-592, MAR 2007
abstract,
full text,
TCBG publications
Linderoth, L., Peters, G.H., Jorgensen, K., Madsen, R., Andresen, T.L.
Synthesis of sn-1 functionalized phospholipids as substrates for secretory phospholipase A(2)
CHEMISTRY AND PHYSICS OF LIPIDS, 146:54-66, MAR 2007
full text
Palmer, B., Kathmann, S., Krishnan, M., Tipparaju, V., Nieplocha, J.
The use of processor groups in molecular dynamics simulations to sample free-energy states
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 3:583-592, MAR-APR 2007
abstract,
full text
Tagami, K., Tsukada, M.
Simulated non-contact AFM images of an alcohol molecule in an alkanethiol self-assembled monolayer
NANOTECHNOLOGY, 18: Art. No. 084005, FEB 28 2007
abstract,
full text
Calderon, C.P.
On the use of local diffusion models for path ensemble averaging in potential of mean force computations
JOURNAL OF CHEMICAL PHYSICS, 126: Art. No. 084106, FEB 28 2007
abstract,
full text
Amaro, R.E., Sethi, A., Myers, R.S., Davisson, V.J., Luthey-Schulten, Z.A.
A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
BIOCHEMISTRY, 46:2156-2173, FEB 27 2007
abstract,
full text
Kim, K., McCully, M.E., Bhattacharya, N., Butler, B., Sept, D., Cooper, J.A.
Structure/function analysis of the interaction of phosphatidylinositol 4,5-bisphosphate with actin-capping protein - Implications for how capping protein binds the actin filament
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:5871-5879, FEB 23 2007
abstract,
full text
Gorfe, A.A., Hanzal-Bayer, M., Abankwa, D., Hancock, J.F., McCammon, J.A.
Structure and dynamics of the full-length lipid-modified H-ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer
JOURNAL OF MEDICINAL CHEMISTRY, 50:674-684, FEB 22 2007
abstract,
full text
Wei, K., Liu, L., Cheng, Y.H., Fu, Y., Guo, Q.X.
Theoretical examination of two opposite mechanisms proposed for hepatitis delta virus ribozyme
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1514-1516, FEB 22 2007
abstract,
full text
Zou, H.L., Strzalka, J., Xu, T., Tronin, A., Blasie, J.K.
Three-dimensional structure and dynamics of a de novo designed, amphiphilic, metallo-porphyrin-binding protein maquette at soft interfaces by molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1823-1833, FEB 22 2007
abstract,
full text
Celik, L., Lund, J.D.D., Schiott, B.
Conformational dynamics of the estrogen receptor alpha: Molecular dynamics simulations of the influence of binding site structure on protein dynamics
BIOCHEMISTRY, 46:1743-1758, FEB 20 2007
abstract,
full text
Golosov, A.A., Karplus, M.
Probing polar solvation dynamics in proteins: A molecular dynamics simulation analysis
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1482-1490, FEB 15 2007
abstract,
full text
Fishelovitch, D., Hazan, C., Shaik, S., Wolfson, H.J., Nussinov, R.
Structural dynamics of the cooperative binding of organic molecules in the human cytochrome P450 3A4
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:1602-1611, FEB 14 2007
abstract,
full text
Bulo, R.E., Siggel, L., Molnar, F., Weiss, H.
Modeling of bovine Type-I collagen fibrils: Interaction with pickling and retanning agents
MACROMOLECULAR BIOSCIENCE, 7:234-240, FEB 12 2007
abstract,
full text
Isgro, T.A., Schulten, K.
Association of nuclear pore FG-repeat domains to NTF2 import and export complexes
JOURNAL OF MOLECULAR BIOLOGY, 366:330-345, FEB 9 2007
abstract,
full text,
TCBG publications
Kutteh, R., Vandenberg, J.I., Kuyucak, S.
Molecular dynamics and continuum electrostatics studies of inactivation in the HERG potassium channel
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1090-1098, FEB 8 2007
abstract,
full text
Yamazaki, T., Imai, T., Hirata, F., Kovalenko, A.
Theoretical study of the cosolvent effect on the partial molar volume change of staphylococcal nuclease associated with pressure denaturation
JOURNAL OF PHYSICAL CHEMISTRY B, 111:1206-1212, FEB 8 2007
abstract,
full text
Zheng, J., Zanuy, D., Haspel, N., Tsai, C.J., Aleman, C., Nussinov, R.
Nanostructure design using protein building blocks enhanced by conformationally constrained synthetic residues
BIOCHEMISTRY, 46:1205-1218, FEB 6 2007
abstract,
full text
Sotomayor, M., Vasquez, V., Perozo, E., Schulten, K.
Ion conduction through MscS as determined by electrophysiology and simulation
BIOPHYSICAL JOURNAL, 92:886-902, FEB 2007
abstract,
full text,
TCBG publications
Zhao, X.L., Sun, M., Zhao, J., Leyva, J.A., Zhu, H.W., Yang, W., Zeng, X., Ao, Y., Liu, Q., Liu, G.Y., Lo, W.H.Y., Jabs, E.W., Amzel, L.M., Shan, X.N., Zhang, X.
Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome
AMERICAN JOURNAL OF HUMAN GENETICS, 80:361-371, FEB 2007
abstract,
full text
Zanuy, D., Aleman, C.
Molecular dynamics study of complexes of poly(glutamate) and dodecyltrimethylammonium
BIOMACROMOLECULES, 8:663-671, FEB 2007
abstract,
full text
De Fabritiis, G., Serrano, M., Delgado-Buscalioni, R., Coveney, P.V.
Fluctuating hydrodynamic modeling of fluids at the nanoscale
PHYSICAL REVIEW E, 75: Art. No. 026307, FEB 2007
abstract,
full text
Grabe, M., Lai, H.C., Jain, M., Jan, Y.N., Jan, L.Y.
Structure prediction for the down state of a potassium channel voltage sensor
NATURE, 445:550-553, FEB 1 2007
abstract,
full text
Nakano, A., Kalia, R.K., Nomura, K., Sharma, A., Vashishta, P., Shimojo, F., van Duin, A.C.T., Goddard, W.A., Biswas, R., Srivastava, D.
A divide-and-conquer/cellular-decomposition framework for million-to-billion atom simulations of chemical reactions
COMPUTATIONAL MATERIALS SCIENCE, 38:642-652, FEB 2007
abstract,
full text
Taboureau, O., Olsen, O.H.
Computational study of coagulation factor VIIa's affinity for phospholipid membranes
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 36:133-144, FEB 2007
abstract,
full text
Pickholz, M., Oliveira, O.N., Skaf, M.S.
Interactions of chlorpromazine with phospholipid monolayers: Effects of the ionization state of the drug
BIOPHYSICAL CHEMISTRY, 125:425-434, FEB 2007
abstract,
full text
Orlowski, S., Nowak, W.
Oxygen diffusion in minihemoglobin from Cerebratulus lacteus: a locally enhanced sampling study
THEORETICAL CHEMISTRY ACCOUNTS, 117:253-258, FEB 2007
abstract,
full text
Ivanov, I., Tainer, J.A., McCammon, J.A.
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:1465-1470, JAN 30 2007
abstract,
full text
Lippert, R.A., Bowers, K.J., Dror, R.O., Eastwood, M.P., Gregersen, B.A., Klepeis, J.L., Kolossvary, I., Shaw, D.E.
A common, avoidable source of error in molecular dynamics integrators
JOURNAL OF CHEMICAL PHYSICS, 126: Art. No. 046101, JAN 28 2007
full text
Pogorelov, T.V., Autenrieth, F., Roberts, E., Luthey-Schulten, Z.A.
Cytochrome c(2) exit strategy: Dissociation studies and evolutionary implications
JOURNAL OF PHYSICAL CHEMISTRY B, 111:618-634, JAN 25 2007
abstract,
full text
Chen, X., Wang, Q., Shen, J.W., Pan, H.H., Wu, T.
Adsorption of leucine-rich amelogenin protein on hydroxyapatite (001) surface through -COO- claws
JOURNAL OF PHYSICAL CHEMISTRY C, 111:1284-1290, JAN 25 2007
abstract,
full text
Reyes-Vivas, H., Diaz, A., Peon, J., Mendoza-Hernandez, G., Hernandez-Alcantara, G., De la Mora-De la Mora, I., Enriquez-Flores, S., Dominguez-Ramirez, L., Lopez-Velazquez, G.
Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity
JOURNAL OF MOLECULAR BIOLOGY, 365:752-763, JAN 19 2007
abstract,
full text
Subramanian, S., Boder, E.T., Discher, D.E.
Phylogenetic divergence of CD47 interactions with human signal regulatory protein alpha reveals locus of species specificity - Implications for the binding site
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:1805-1818, JAN 19 2007
abstract,
full text
Korkmaz, B., Hajjar, E., Kalupov, T., Reuter, N., Brillard-Bourdet, M., Moreau, T., Juliano, L., Gauthier, F.
Influence of charge distribution at the active site surface on the substrate specificity of human neutrophil protease 3 and elastase - A kinetic and molecular modeling analysis
JOURNAL OF BIOLOGICAL CHEMISTRY, 282:1989-1997, JAN 19 2007
abstract,
full text
De Vivo, M., Ensing, B., Dal Peraro, M., Gomez, G.A., Christianson, D.W., Klein, M.L.
Proton shuttles and phosphatase activity in soluble epoxide hydrolase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129:387-394, JAN 17 2007
abstract,
full text
Rueda, M., Ferrer-Costa, C., Meyer, T., Perez, A., Camps, J., Hospital, A., Gelpi, J.L., Orozco, M.
A consensus view of protein dynamics
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 104:796-801, JAN 16 2007
abstract,
full text
Aird, A., Wrachtrup, J., Schulten, K., Tietz, C.
Possible pathway for ubiquinone shuttling in Rhodospirillum rubrum revealed by molecular dynamics simulation
BIOPHYSICAL JOURNAL, 92:23-33, JAN 2007
abstract,
full text,
TCBG publications
Jaud, S., Tobias, D.J., Falke, J.J., White, S.H.
Self-induced docking site of a deeply embedded peripheral membrane protein
BIOPHYSICAL JOURNAL, 92:517-524, JAN 2007
abstract,
full text
Stitham, J., Arehart, E.J., Gleim, S.R., Douville, K.L., Hwa, J.
Human prostacyclin receptor structure and function from naturally-occurring and synthetic mutations
PROSTAGLANDINS & OTHER LIPID MEDIATORS, 82:95-108, JAN 2007
abstract,
full text
Cachau, R.E., Gonzalez-Nilo, F.D., Ventura, O.N., Fritts, M.J.
In-silico nanobio-design. A new frontier in computational biology
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 7:1537-1540, 2007
abstract,
full text
Carrieri, A., Fano, A.
The in silico insights of alpha-adrenergic receptors over the last decade: Methodological approaches and structural features of the 3D models
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 7:195-205, 2007
abstract,
full text
Nagata, T.
Automated design of protecting molecules for metal nanoparticles by combinatorial molecular simulations
JOURNAL OF ORGANOMETALLIC CHEMISTRY, 692:225-233, JAN 1 2007
abstract,
full text
Veloso, C.J.M., Silveira, C.H., Melo, R.C., Ribeiro, C., Lopes, J.C.D., Santoro, M.M., Meira, W.
On the characterization of energy networks of proteins
GENETICS AND MOLECULAR RESEARCH, 6:799-820, 2007
abstract,
full text
Sun, L., Le, C., Saied, F., Murthy, J.Y.
Performance of a parallel molecular dynamics program for computation of thermal properties
NUMERICAL HEAT TRANSFER PART B-FUNDAMENTALS, 51:315-331, 2007
abstract,
full text
Gorfe, A.A., Babakhani, A., McCammon, J.A.
Free energy profile of h-ras membrane anchor upon membrane insertion
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 46:8234-8237, 2007
full text
Bellesia, G., Fedorov, M.V., Timoshenko, E.G.
Molecular dynamics study of structural properties of beta-sheet assemblies formed by synthetic de novo oligopeptides
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 373:455-476, JAN 1 2007
abstract,
full text
Poghosyan, A.H., Yeghiazaryan, G.A., Gharabekyan, H.H., Koetz, J., Shahinyan, A.A.
A molecular dynamics study of Na-dodecylsulfate/water liquid crystalline phase
MOLECULAR SIMULATION, 33:1155-1163, 2007
abstract,
full text
Pappalardo, M., Milardi, D., Grasso, D., La Rosa, C.
Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species
NEW JOURNAL OF CHEMISTRY, 31:901-905, 2007
abstract,
full text
Dittrich, M., Yu, J., Schulten, K.
PcrA helicase, a molecular motor studied from the electronic to the functional level
ATOMISTIC APPROACHES IN MODERN BIOLOGY: FROM QUANTUM CHEMISTRY TO MOLECULAR SIMULATIONS, 268:319-347, 2007
abstract,
full text,
TCBG publications
Kowadlo, G., Hall, N.E., Burgess, A.W.
De novo design of beta-helical polypeptides
GROWTH FACTORS, 25:168-190, 2007
abstract,
full text
Rosales-Leon, L., Ortega-Lule, G., Ruiz-Ordaz, B.
Analysis of the domain interactions between the protease and helicase of NS3 in dengue and hepatitis C virus
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 25:585-594, JAN 2007
abstract,
full text
Patra, M., Hyvonen, M.T., Falck, E., Sabouri-Ghomi, M., Vattulainen, I., Karttunen, M.
Long-range interactions and parallel scalability in molecular simulations
COMPUTER PHYSICS COMMUNICATIONS, 176:14-22, JAN 1 2007
abstract,
full text
Ngo, J.C.K., Gullingsrud, J., Giang, K., Yeh, M.J., Fu, X.D., Adams, J.A., McCammon, J.A., Ghosh, G.
SR protein kinase 1 is resilient to inactivation
STRUCTURE, 15:123-133, JAN 2007
abstract,
full text
Zanuy, D., Aleman, C.
Contraction process of an electroactive actuator based on a one microsecond atomistic molecular dynamics simulation
CHEMISTRY-A EUROPEAN JOURNAL, 13:2695-2700, 2007
abstract,
full text
Chang, T., Pieterse, K., Broeren, M.A.C., Kooijman, H., Spek, A.L., Hilbers, P.A.I., Meijer, E.W.
Structural elucidation of dendritic host-guest complexes by X-ray crystallography and molecular dynamics Simulations
CHEMISTRY-A EUROPEAN JOURNAL, 13:7883-7889, 2007
abstract,
full text
Reymond, C., Ouellet, J., Bisaillon, M., Perreault, J.P.
Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop
RNA-A PUBLICATION OF THE RNA SOCIETY, 13:44-54, JAN 2007
abstract,
full text
Pedersen, U.R., Peters, G.H., Westh, P.
Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation
BIOPHYSICAL CHEMISTRY, 125:104-111, JAN 2007
abstract,
full text
Lakhiaev, A.V., Nalian, A., Koenig, K., Idell, S.
Thrombin-thrombomodulin inhibits prourokinase-mediated pleural mesothelial cell-dependent fibrinolysis
THROMBOSIS RESEARCH, 120:715-725, 2007
abstract,
full text
Allen, M.P.
Educational aspects of molecular simulation
MOLECULAR PHYSICS, 105:157-166, JAN-FEB 2007
abstract,
full text
Chatterjee, S., Gersten, B., Thakur, S., Burin, A.
Molecular dynamics simulations of a single stranded (ss) DNA
MOLECULAR SIMULATION, 33:573-576, 2007
abstract,
full text
Poghosyan, A.H., Gharabekyan, H.H., Shahinyan, A.A.
Molecular dynamics simulations of DMPC/DPPC mixed bilayers
INTERNATIONAL JOURNAL OF MODERN PHYSICS C, 18:73-89, JAN 2007
abstract,
full text
Cavallari, M., Calzolari, A., Garbesi, A., Di Felice, R.
Stability and migration of metal ions in G4-wires by molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:26337-26348, DEC 28 2006
abstract,
full text
Hwang, H., Schatz, G.C., Ratner, M.A.
Steered molecular dynamics studies of the potential of mean force of a Na+ or K+ ion in a cyclic peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 110:26448-26460, DEC 28 2006
abstract,
full text
Zhang, Z.Y., Boyle, P.C., Lu, B.Y., Chang, J.Y., Wriggers, W.
Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations
BIOCHEMISTRY, 45:15269-15278, DEC 26 2006
abstract,
full text
Wang, B.Y., Kral, P.
Coulombic dragging of molecules on surfaces induced by separately flowing liquids
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:15984-15985, DEC 20 2006
full text
Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Toward a rational design of selective multi-trypanosomatid inhibitors: A computational docking study
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:6288-6292, DEC 15 2006
abstract,
full text
Yin, Y., Jensen, M.O., Tajkhorshid, E., Schulten, K.
Sugar binding and protein conformational changes in lactose permease
BIOPHYSICAL JOURNAL, 91:3972-3985, DEC 2006
abstract,
full text,
TCBG publications
Nygaard, T.P., Rovira, C., Peters, G.H., Jensen, M.O.
Ammonium recruitment and ammonia transport by E-coli ammonia channel AmtB
BIOPHYSICAL JOURNAL, 91:4401-4412, DEC 2006
abstract,
full text
Arkhipov, A., Freddolino, P.L., Imada, K., Namba, K., Schulten, K.
Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum
BIOPHYSICAL JOURNAL, 91:4589-4597, DEC 2006
abstract,
full text,
TCBG publications
Noda, K., Nakamura, M., Nishida, R., Yoneda, Y., Yamaguchi, Y., Tamura, Y., Nakamura, H., Yasunaga, T.
Atomic model construction of protein complexes from electron micrographs and visualization of their 3D structure using a virtual reality system
JOURNAL OF PLASMA PHYSICS, 72:1037-1040, DEC 2006
abstract,
full text
Seminario, J.M., Ma, Y.F., Tarigopula, V.
The nanocell: A chemically assembled molecular electronic circuit
IEEE SENSORS JOURNAL, 6:1614-1626, DEC 2006
abstract,
full text
Stitham, J., Gleim, S.R., Douville, K., Arehart, E., Hwa, J.
Versatility and differential roles of cysteine residues in human prostacyclin receptor structure and function
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:37227-37236, DEC 1 2006
abstract,
full text
Humeres, E., Mascayano, C., Riadi, G., Gonzalez-Nilo, F.
Molecular dynamics simulation of the aqueous solvation shell of cellulose and xanthate ester derivatives
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 19:896-901, DEC 2006
abstract,
full text
Yao, S.G., Liu, M.S., Masters, S.L., Zhang, J.G., Babon, J.J., Nicola, N.A., Nicholson, S.E., Norton, R.S.
Dynamics of the SPRY domain-containing SOCS box protein 2: Flexibility of key functional loops
PROTEIN SCIENCE, 15:2761-2772, DEC 2006
abstract,
full text
Arkhipov, A., Freddolino, P.L., Schulten, K.
Stability and dynamics of virus capsids described by coarse-grained modeling
STRUCTURE, 14:1767-1777, DEC 2006
abstract,
full text,
TCBG publications
Thevenard, J., Floquet, N., Ramont, L., Prost, E., Nuzillard, J.M., Dauchez, M., Yezid, H., Alix, A.J.P., Maquart, F.X., Brassart-Plasco, S.
Structural and antitumor properties of the YSNSG cyclopeptide derived from tumstatin
CHEMISTRY & BIOLOGY, 13:1307-1315, DEC 2006
abstract,
full text
Castro-Roman, F., Benz, R.W., White, S.H., Tobias, D.J.
Investigation of finite system size effects in molecular dynamics simulations of lipid bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 110:24157-24164, NOV 30 2006
abstract,
full text
Bazeley, P.S., Prithivi, S., Struble, C.A., Povinelli, R.J., Sem, D.S.
Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:2698-2708, NOV 27 2006
abstract,
full text
Khurana, E., Nielsen, S.O., Klein, M.L.
Gemini surfactants at the air/water interface: A fully atomistic molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:22136-22142, NOV 9 2006
abstract,
full text
Cruz-Chu, E.R., Aksimentiev, A., Schulten, K.
Water-silica force field for simulating nanodevices
JOURNAL OF PHYSICAL CHEMISTRY B, 110:21497-21508, NOV 2 2006
abstract,
full text,
TCBG publications
Foley, M.C., Arora, K., Schlick, T.
Sequential side-chain residue motions transform the binary into the ternary state of DNA polymerase lambda
BIOPHYSICAL JOURNAL, 91:3182-3195, NOV 2006
abstract,
full text
Streiff, J.H., Allen, T.W., Atanasova, E., Juranic, N., Macura, S., Penheiter, A.R., Jones, K.A.
Prediction of volatile anesthetic binding sites in proteins
BIOPHYSICAL JOURNAL, 91:3405-3414, NOV 2006
abstract,
full text
Paramore, S., Voth, G.A.
Examining the influence of linkers and tertiary structure in the forced unfolding of multiple-repeat spectrin molecules
BIOPHYSICAL JOURNAL, 91:3436-3445, NOV 2006
abstract,
full text
Benz, R.W., Nanda, H., Castro-Roman, F., White, S.H., Tobias, D.J.
Diffraction-based density restraints for membrane and membrane-peptide molecular dynamics simulations
BIOPHYSICAL JOURNAL, 91:3617-3629, NOV 2006
abstract,
full text
Freddolino, P.L., Dittrich, M., Schulten, K.
Dynamic switching mechanisms in LOV1 and LOV2 domains of plant phototropins
BIOPHYSICAL JOURNAL, 91:3630-3639, NOV 2006
abstract,
full text,
TCBG publications
Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Conformational changes of the p53-binding cleft of MDM2 revealed by molecular dynamics simulations
BIOPOLYMERS, 83:365-373, NOV 2006
abstract,
full text
Grandi, F., Sandal, M., Guarguaglini, G., Capriotti, E., Casadio, R., Samori, B.
Hierarchical mechanochemical switches in angiostatin
CHEMBIOCHEM, 7:1774-1782, NOV 2006
abstract,
full text
Wang, K., Chang, A., Kale, L.V., Dantzig, J.A.
Parallelization of a level set method for simulating dendritic growth
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 66:1379-1386, NOV 2006
abstract,
full text
Muller, M., Katsov, K., Schick, M.
Biological and synthetic membranes: What can be learned from a coarse-grained description?
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 434:113-176, NOV 2006
abstract,
full text
Jensen, J.K., Malmendal, A., Schiott, B., Skeldal, S., Pedersen, K.E., Celik, L., Nielsen, N.C., Andreasen, P.A., Wind, T.
Inhibition of plasminogen activator inhibitor-1 binding to endocytosis receptors of the low-density-lipoprotein receptor family by a peptide isolated from a phage display library
BIOCHEMICAL JOURNAL, 399:387-396, NOV 1 2006
abstract,
full text
Ivanov, I., Chapados, B.R., McCammon, J.A., Tainer, J.A.
Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implications
NUCLEIC ACIDS RESEARCH, 34:6023-6033, NOV 2006
abstract,
full text
Aleman, C., Zanuy, D., Casanovas, J., Cativiela, C., Nussinov, R.
Backbone conformational preferences and pseudorotational ring puckering of 1-aminocyclopentane-1-carboxylic acid
JOURNAL OF PHYSICAL CHEMISTRY B, 110:21264-21271, OCT 26 2006
abstract,
full text
Blumberger, J., Klein, M.L.
Reorganization free energies for long-range electron transfer in a porphyrin-binding four-helix bundle protein
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:13854-13867, OCT 25 2006
abstract,
full text
Puklin-Faucher, E., Gao, M., Schulten, K., Vogel, V.
How the headpiece hinge angle is opened: new insights into the dynamics of integrin activation
JOURNAL OF CELL BIOLOGY, 175:349-360, OCT 23 2006
abstract,
full text,
TCBG publications
Yraola, F., Garcia-Vicente, S., Fernandez-Recio, J., Albericio, F., Zorzano, A., Marti, L., Royo, M.
New efficient substrates for semicarbazide-sensitive amine oxidase/VAP-1 enzyme: Analysis by SARs and computational docking
JOURNAL OF MEDICINAL CHEMISTRY, 49:6197-6208, OCT 19 2006
abstract,
full text
Trzaskowski, B., Jalbout, A.F., Adamowicz, L.
Molecular dynamics studies of protein-fragment models encapsulated into carbon nanotubes
CHEMICAL PHYSICS LETTERS, 430:97-100, OCT 19 2006
abstract,
full text
Klauda, J.B., Brooks, B.R., Pastor, R.W.
Dynamical motions of lipids and a finite size effect in simulations of bilayers
JOURNAL OF CHEMICAL PHYSICS, 125: Art. No. 144710, OCT 14 2006
abstract,
full text
Yeong, S.S., Zhu, Y., Smith, D., Verma, C., Lim, W.G., Tan, B.J., Li, Q.T., Cheung, N.S., Cai, M., Zhu, Y.Z., Zhou, S.F., Tan, S.L., Duan, W.
The last 10 amino acid residues beyond the hydrophobic motif are critical for the catalytic competence and function of protein kinase C alpha
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:30768-30781, OCT 13 2006
abstract,
full text
Bhattacharya, N., Ghosh, S., Sept, D., Cooper, J.A.
Binding of myotrophin/V-1 to actin-capping protein - Implications for how capping protein binds to the filament barbed end
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:31021-31030, OCT 13 2006
abstract,
full text
Adhangale, P.S., Gaver, D.P.
Equation of state for a coarse-grained DPPC monolayer at the air/water interface
MOLECULAR PHYSICS, 104:3011-3019, OCT 10 2006
abstract,
full text
Blood, P.D., Voth, G.A.
Direct observation of Bin/amphiphysin/Rvs (BAR) domain-induced membrane curvature by means of molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:15068-15072, OCT 10 2006
abstract,
full text
Casanovas, J., Zanuy, D., Nussinov, R., Aleman, C.
Identification of the intrinsic conformational properties of 1-aminocyclobutane-1-carboxylic acid
CHEMICAL PHYSICS LETTERS, 429:558-562, OCT 5 2006
abstract,
full text
Roh, J.H., Curtis, J.E., Azzam, S., Novikov, V.N., Peral, I., Chowdhuri, Z., Gregory, R.B., Sokolov, A.P.
Influence of hydration on the dynamics of lysozyme
BIOPHYSICAL JOURNAL, 91:2573-2588, OCT 2006
abstract,
full text
Fiorin, G., Pastore, A., Carloni, P., Parrinello, M.
Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail
BIOPHYSICAL JOURNAL, 91:2768-2777, OCT 2006
abstract,
full text
Vemparala, S., Saiz, L., Eckenhoff, R.G., Klein, M.L.
Partitioning of anesthetics into a lipid bilayer and their interaction with membrane-bound peptide bundles
BIOPHYSICAL JOURNAL, 91:2815-2825, OCT 2006
abstract,
full text
Jang, H., Ma, B., Woolf, T.B., Nussinov, R.
Interaction of protegrin-1 with lipid bilayers: Membrane thinning effect
BIOPHYSICAL JOURNAL, 91:2848-2859, OCT 2006
abstract,
full text
Papadopoulos, G., Grudinin, S., Kalpaxis, D.L., Choli-Papadopoulou, T.
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 35:675-683, OCT 2006
abstract,
full text
Buehler, M.J.
Large-scale hierarchical molecular modeling of nanostructured biological materials
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:603-623, OCT 2006
abstract,
full text
Liu, M.S., Todd, B.D., Sadus, R.J.
Dynamic and coordinating domain motions in the active subunits of the F-1-ATPase molecular motor
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1764:1553-1560, OCT 2006
abstract,
full text
Kikuzawa, Y., Nagata, T., Tahara, T., Ishii, K.
Photo- and redox-active dendritic molecules with soft, layered nanostructures
CHEMISTRY-AN ASIAN JOURNAL, 1:516-528, OCT 2006
abstract,
full text
De Fabritiis, G., Delgado-Buscalioni, R., Coveney, P.V.
Multiscale modeling of liquids with molecular specificity
PHYSICAL REVIEW LETTERS, 97: Art. No. 134501, SEP 29 2006
abstract,
full text
Khurana, E., Nielsen, S.O., Ensing, B., Klein, M.L.
Self-assembling cyclic peptides: Molecular dynamics studies of dimers in polar and nonpolar solvents
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18965-18972, SEP 28 2006
abstract,
full text
Jun, S., Becker, J.S., Yonkunas, M., Coalson, R., Saxena, S.
Unfolding of alanine-based peptides using electron spin resonance distance measurements
BIOCHEMISTRY, 45:11666-11673, SEP 26 2006
abstract,
full text
Bichet, D., Grabe, M., Jan, Y.N., Jan, L.Y.
Electrostatic interactions in the channel cavity as an important determinant of potassium channel selectivity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:14355-14360, SEP 26 2006
abstract,
full text
Grabe, M., Bichet, D., Qian, X., Jan, Y.N., Jan, L.Y.
K+ channel selectivity depends on kinetic as well as thermodynamic factors
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:14361-14366, SEP 26 2006
abstract,
full text
Lou, J.Z., Yago, T., Klopocki, A.G., Mehta, P., Chen, W., Zarnitsyna, V.I., Bovin, N.V., Zhu, C., McEver, R.P.
Flow-enhanced adhesion regulated by a selectin interdomain hinge
JOURNAL OF CELL BIOLOGY, 174:1107-1117, SEP 25 2006
abstract,
full text
Ma, K., Forbes, J.G., Gutierrez-Cruz, G., Wang, K.
Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways - The clustering of novel overlap ligand motifs in the elastic PEVK segment
JOURNAL OF BIOLOGICAL CHEMISTRY, 281:27539-27556, SEP 15 2006
abstract,
full text
Cadena, C., Maginn, E.J.
Molecular simulation study of some thermophysical and transport properties of triazolium-based ionic liquids
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18026-18039, SEP 14 2006
abstract,
full text
Sanchez, V.M., Crespo, A., Gutkind, J.S., Turjanski, A.G.
Investigation of the catalytic mechanism of farnesyl pyrophosphate synthase by computer simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 110:18052-18057, SEP 14 2006
abstract,
full text
Glykos, N.M., Papanikolau, Y., Vlassi, M., Kotsifaki, D., Cesareni, G., Kokkinidis, M.
Loopless rop: Structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein
BIOCHEMISTRY, 45:10905-10919, SEP 12 2006
abstract,
full text
Meyer, G.R., Gullingsrud, J., Schulten, K., Martinac, B.
Molecular dynamics study of MscL interactions with a curved lipid bilayer
BIOPHYSICAL JOURNAL, 91:1630-1637, SEP 2006
abstract,
full text,
TCBG publications
Cohen, J., Arkhipov, A., Braun, R., Schulten, K.
Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin
BIOPHYSICAL JOURNAL, 91:1844-1857, SEP 2006
abstract,
full text,
TCBG publications
Yu, J., Ha, T., Schulten, K.
Structure-based model of the stepping motor of PcrA helicase
BIOPHYSICAL JOURNAL, 91:2097-2114, SEP 2006
abstract,
full text,
TCBG publications
Khalili-Araghi, F., Tajkhorshid, E., Schulten, K.
Dynamics of K+ ion conduction through Kv1.2
BIOPHYSICAL JOURNAL, 91:L2-L4, SEP 2006
abstract,
full text,
TCBG publications
Lu, Z.Y., Hu, H., Yang, W.T., Marszaleky, P.E.
Simulating force-induced conformational transitions in polysaccharides with the SMD replica exchange method
BIOPHYSICAL JOURNAL, 91:L57-L59, SEP 2006
abstract,
full text
Seminario, J.A., Yan, L.M., Ma, Y.F.
Encoding and transport of information in molecular and biomolecular systems
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 5:436-440, SEP 2006
abstract,
full text
Gao, Q., Tagami, K., Fujihira, M., Tsukada, M.
Quenching mechanism of mechanically compressed green fluorescent protein studied by CASSCF/AM1
JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS & EXPRESS LETTERS, 45:L929-L931, SEP 2006
abstract,
full text
Salapura, V., Walkup, R., Gara, A.
Exploiting workload parallelism for performance and power optimization in Blue Gene
IEEE MICRO, 26:67-81, SEP-OCT 2006
abstract,
full text
Alonso, H., Bliznyuk, A.A., Gready, J.E.
Combining docking and molecular dynamic simulations in drug design
MEDICINAL RESEARCH REVIEWS, 26:531-568, SEP 2006
abstract,
full text
Ghosh, P., Katti, D.R., Katti, K.S.
Impact of beta-sheet conformations on the mechanical response of protein in biocomposites
MATERIALS AND MANUFACTURING PROCESSES, 21:676-682, SEP-OCT 2006
abstract,
full text
George, A.M., Jones, P.M.
Molecular Dynamics Simulations and Analysis of ABC Transporters
CURRENT COMPUTER-AIDED DRUG DESIGN, 2:203-214, SEP 2006
abstract,
full text
Cheng, X.L., Wang, H.L., Grant, B., Sine, S.M., McCammon, J.A.
Targeted molecular dynamics study of C-loop closure and channel gating in nicotinic receptors
PLOS COMPUTATIONAL BIOLOGY, 2:1173-1184, SEP 2006
abstract,
full text
Tuukkanen, A., Verkhovsky, M.I., Laakkonen, L., Wikstrom, M.
The K-pathway revisited: A computational study on cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:1117-1121, SEP-OCT 2006
abstract,
full text
Yu, J., Yool, A.J., Schulten, K., Tajkhorshid, E.
Mechanism of gating and ion conductivity of a possible tetrameric pore in aquaporin-1
STRUCTURE, 14:1411-1423, SEP 2006
abstract,
full text,
TCBG publications
Sikdar, D., Katti, D.R., Katti, K.S.
A molecular model for epsilon-caprolactam-based intercalated polymer clay nanocomposite: Integrating modeling and experiments
LANGMUIR, 22:7738-7747, AUG 29 2006
abstract,
full text
Mitra, A., Sept, D.
Binding and interaction of dinitroanilines with apicomplexan and kinetoplastid alpha-tubulin
JOURNAL OF MEDICINAL CHEMISTRY, 49:5226-5231, AUG 24 2006
abstract,
full text
Henin, J., Schulten, K., Chipot, C.
Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 110:16718-16723, AUG 24 2006
abstract,
full text,
TCBG publications
Moskovsky, A.A., Vanovschi, V.V., Konyukhov, S.S., Nemukhin, A.V.
Implementation of the replica-exchange molecular dynamics method for rigid bodies
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106:2208-2213, AUG 15 2006
abstract,
full text
Treptow, W., Tarek, M.
Molecular restraints in the permeation pathway of ion channels
BIOPHYSICAL JOURNAL, 91:L26-L28, AUG 2006
abstract,
full text
Gorecki, A., Trylska, J., Lesyng, B.
Causal relations in molecular dynamics from the multi-variate autoregressive model
EUROPHYSICS LETTERS, 75:503-509, AUG 2006
abstract,
full text
Rebelo, S.L., Bainbridge, S.E., Amel-Kashipaz, M.R., Radford, P.M., Powell, R.J., Todd, I., Tighe, P.J.
Modeling of tumor necrosis factor receptor superfamily 1A mutants associated with tumor necrosis factor receptor-associated periodic syndrome indicates misfolding consistent with abnormal function
ARTHRITIS AND RHEUMATISM, 54:2674-2687, AUG 2006
abstract,
full text
Gullingsrud, J., Babakhani, A., McCammon, J.A.
Computational investigation of pressure profiles in lipid bilayers with embedded proteins
MOLECULAR SIMULATION, 32:831-838, AUG-SEP 2006
abstract,
full text
Weetman, P., Wartak, M.S.
Advanced approach to modelling quantum well semiconductor lasers based on the quantum Boltzmann equation: Green's function approach
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:463-478, AUG 2006
abstract,
full text
Buehler, M.J.
Atomistic and continuum modeling of mechanical properties of collagen: Elasticity, fracture, and self-assembly
JOURNAL OF MATERIALS RESEARCH, 21:1947-1961, AUG 2006
abstract,
full text
Krystek, S.R., Kimura, S.R., Tebben, A.J.
Modeling and active site refinement for G protein-coupled receptors: application to the beta-2 adrenergic receptor
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:463-470, AUG 2006
abstract,
full text
Lynch, D.L., Reggio, P.H.
Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:495-509, AUG 2006
abstract,
full text
Poghosyan, A.H., Yeghiazaryan, G.A., Charabekyan, H.H., Shahinyan, A.A.
The GROMACS and NAMD software packages comparison
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 1:736-743, AUG 2006
abstract,
full text
Zhang, Q.M., Lu, Z.Y., Hu, H., Yang, W.T., Marszalek, P.E.
Direct detection of the formation of V-amylose helix by single molecule force spectroscopy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:9387-9393, JUL 26 2006
abstract,
full text
Fowler, P.W., Coveney, P.V.
A computational protocol for the integration of the monotopic protein prostaglandin H2 synthase into a phospholipid bilayer
BIOPHYSICAL JOURNAL, 91:401-410, JUL 15 2006
abstract,
full text
Gracheva, M.E., Aksimentiev, A., Leburton, J.P.
Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor
NANOTECHNOLOGY, 17:3160-3165, JUL 14 2006
abstract,
full text
Asthagiri, D., Pratt, L.R., Paulaitis, M.E.
Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity
JOURNAL OF CHEMICAL PHYSICS, 125: Art. No. 024701, JUL 14 2006
abstract,
full text
Bravaya, K., Bochenkova, A., Grigorenko, B., Topol, I., Burt, S., Nemukhin, A.
Molecular modeling the reaction mechanism of serine-carboxyl peptidases
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:1168-1175, JUL 11 2006
abstract,
full text
Zuckerman, D.M., Lyman, E.
A second look at canonical sampling of biomolecules using replica exchange simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:1200-1202, JUL 11 2006
abstract,
full text
Henin, J., Chipot, C.
Hydrogen-bonding patterns of cholesterol in lipid membranes
CHEMICAL PHYSICS LETTERS, 425:329-335, JUL 10 2006
abstract,
full text
Bastug, T., Patra, S.M., Kuyucak, S.
Finite system and periodicity effects in free energy simulations of membrane proteins
CHEMICAL PHYSICS LETTERS, 425:320-323, JUL 10 2006
abstract,
full text
Starovoitova, V., Budarz, T.E., Wyllie, G.R.A., Scheidt, W.R., Sturhahn, W., Alp, E.E., Prohofsky, E.W., Durbin, S.M.
Vibrational spectroscopy and normal-mode analysis of Fe(II) octaethylporphyrin
JOURNAL OF PHYSICAL CHEMISTRY B, 110:13277-13282, JUL 6 2006
abstract,
full text
Lyman, E., Zuckerman, D.M.
Ensemble-based convergence analysis of biomolecular trajectories
BIOPHYSICAL JOURNAL, 91:164-172, JUL 2006
abstract,
full text
Zikic, R., Krstic, P.S., Zhang, X.G., Fuentes-Cabrera, M., Wells, J., Zhao, X.C.
Characterization of the tunneling conductance across DNA bases
PHYSICAL REVIEW E, 74: Art. No. 011919, JUL 2006
abstract,
full text
Interlandi, G., Settanni, G., Caflisch, A.
Unfolding transition state and intermediates of the tumor suppressor p16(INK4a) investigated by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 64:178-192, JUL 1 2006
abstract,
full text
Belessi, C.J., Davi, F.B., Stamatopoulos, K.E., Degano, M., Andreou, T.M., Moreno, C., Merle-Beral, H., Crespo, M., Laoutaris, N.P., Montserrat, E., Caligaris-Cappio, F., Anagnostopoulos, A.Z., Ghia, P.
IGHV gene insertions and deletions in chronic lymphocytic leukemia: "CLL-biased" deletions in a subset of cases with stereotyped receptors
EUROPEAN JOURNAL OF IMMUNOLOGY, 36:1963-1974, JUL 2006
abstract,
full text
Moretti, S., Macchiarulo, A., De Falco, V., Avenia, N., Barbi, F., Carta, C., Cavaliere, A., Melillo, R.M., Passeri, L., Santeusanio, F., Tartaglia, M., Santoro, M., Puxeddu, E.
Biochemical and molecular characterization of the novel BRAF(V599Ins) mutation detected in a classic papillary thyroid carcinoma
ONCOGENE, 25:4235-4240, JUL 2006
abstract,
full text
Haspel, N., Zanuy, D., Aleman, C., Wolfson, H., Nussinov, R.
De novo tubular nanostructure design based on self-assembly of beta-helical protein motifs
STRUCTURE, 14:1137-1148, JUL 2006
abstract,
full text
Janosi, L., Kosztin, I., Damjanovic, A.
Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes
JOURNAL OF CHEMICAL PHYSICS, 125: Art. No. 014903, JUL 1 2006
abstract,
full text
Liu, Z.W., Xu, Y., Tang, P.
Steered molecular dynamics simulations of Na+ permeation across the gramicidin a channel
JOURNAL OF PHYSICAL CHEMISTRY B, 110:12789-12795, JUN 29 2006
abstract,
full text
Samel, S.A., Wagner, B., Marahiel, M.A., Essen, L.O.
The thioesterase domain of the fengycin biosynthesis cluster: A structural base for the macrocyclization of a non-ribosomal lipopeptide
JOURNAL OF MOLECULAR BIOLOGY, 359:876-889, JUN 16 2006
abstract,
full text
Paliwal, A., Asthagiri, D., Pratt, L.R., Ashbaugh, H.S., Paulaitis, M.E.
An analysis of molecular packing and chemical association in liquid water using quasichemical theory
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 224502, JUN 14 2006
abstract,
full text
Bastug, T., Kuyucak, S.
Molecular dynamics simulations of calcium binding in gramicidin A
CHEMICAL PHYSICS LETTERS, 424:82-85, JUN 12 2006
abstract,
full text
Karain, W.I., Qaraeen, N.I., Ajarmah, B.
A stochastic model for correlated protein motions
PHYSICS LETTERS A, 354:497-500, JUN 12 2006
abstract,
full text
Bastug, T., Kuyucak, S.
Energetics of ion permeation, rejection, binding, and block in gramicidin A from free energy simulations
BIOPHYSICAL JOURNAL, 90:3941-3950, JUN 2006
abstract,
full text
Catte, A., Patterson, J.C., Jones, M.K., Jerome, W.G., Bashtovyy, D., Su, Z.C., Gu, F.F., Chen, J.G., Aliste, M.P., Harvey, S.C., Li, L., Weinstein, G., Segrest, J.P.
Novel changes in discoidal high density lipoprotein morphology: A molecular dynamics study
BIOPHYSICAL JOURNAL, 90:4345-4360, JUN 2006
abstract,
full text
Pedretti, A., Villa, M., Pallavicini, M., Valoti, E., Vistoli, G.
Construction of human ghrelin receptor (hGHS-R1a) model using a fragmental prediction approach and validation through docking analysis
JOURNAL OF MEDICINAL CHEMISTRY, 49:3077-3085, JUN 1 2006
abstract,
full text
Vistoli, G., Pedretti, A., Cattaneo, M., Aldini, G., Testa, B.
Homology modeling of human serum carnosinase, a potential medicinal target, and MD simulations of its allosteric activation by citrate
JOURNAL OF MEDICINAL CHEMISTRY, 49:3269-3277, JUN 1 2006
abstract,
full text
Vasenkov, A.V., Fedoseyev, A.I., Kolobov, V.I., Choi, H.S., Hong, K.H., Kim, K., Kim, J., Lee, H.S., Shin, J.K.
Computational framework for modeling of multi-scale processes
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 3:453-458, JUN 2006
abstract,
full text
Zhu, Y.M., Smith, D., Verma, C., Lim, W.G., Tan, B.J., Armstrong, J.S., Zhou, S.F., Chan, E., Tan, S.L., Zhu, Y.Z., Cheung, N.S., Duan, W.
The very C-terminus of protein kinase C epsilon is critical for the full catalytic competence but its hydrophobic motif is dispensable for the interaction with 3-phosphoinositide-dependent kinase-1
CELLULAR SIGNALLING, 18:807-818, JUN 2006
abstract,
full text
Jacobsen, R.B., Sale, K.L., Ayson, M.J., Novak, P., Hong, J.H., Lane, P., Wood, N.L., Kruppa, G.H., Young, M.M., Schoeniger, J.S.
Structure and dynamics of dark-state bovine rhodopsin revealed by chemical cross-linking and high-resolution mass spectrometry
PROTEIN SCIENCE, 15:1303-1317, JUN 2006
abstract,
full text
Bastug, T., Patra, S.M., Kuyucak, S.
Molecular dynamics simulations of gramicidin A in a lipid bilayer: From structure-function relations to force fields
CHEMISTRY AND PHYSICS OF LIPIDS, 141:197-204, JUN 2006
abstract,
full text
Xu, L.N., Zhang, L.L., Gu, Z., Zhou, L.X.
Full electronic structure calculation of the biological activity in P173L enzyme
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106:1544-1550, JUN 2006
abstract,
full text
Zanuy, D., Casanovas, J., Aleman, C.
Conformational features of an actuator containing calix[4] arene and thiophene: A molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:9876-9881, MAY 25 2006
abstract,
full text
James, S., Maresca, K.P., Allis, D.G., Valliant, J.F., Eckelman, W., Babich, J.W., Zubieta, J.
Extension of the single amino acid chelate concept (SAAC) to bifunctional biotin analogues for complexation of the M(CO)(3)(+1) core (M = Tc and Re): Syntheses, characterization, biotinidase stability, and avidin binding
BIOCONJUGATE CHEMISTRY, 17:579-589, MAY 17 2006
abstract,
full text
Sharma, V., Puustinen, A., Wikstrom, M., Laakkonen, L.
Sequence analysis of the cbb(3) oxidases and an atomic model for the Rhodobacter sphaeroides enzyme
BIOCHEMISTRY, 45:5754-5765, MAY 9 2006
abstract,
full text
Pickholz, M., Oliveira, O.N., Skaf, M.S.
Molecular dynamics simulations of neutral chlorpromazine in zwitterionic phospholipid monolayers
JOURNAL OF PHYSICAL CHEMISTRY B, 110:8804-8814, MAY 4 2006
abstract,
full text
Vasil'ev, S., Bruce, D.
A protein dynamics study of photosystem II: The effects of protein conformation on reaction center function
BIOPHYSICAL JOURNAL, 90:3062-3073, MAY 2006
abstract,
full text
Gao, M., Schulten, K.
Onset of anthrax toxin pore formation
BIOPHYSICAL JOURNAL, 90:3267-3279, MAY 2006
abstract,
full text,
TCBG publications
Sotomayor, M., van der Straaten, T.A., Ravaioli, U., Schulten, K.
Electrostatic properties of the mechanosensitive channel of small conductance MscS
BIOPHYSICAL JOURNAL, 90:3496-3510, MAY 2006
abstract,
full text,
TCBG publications
Manetti, F., Tintori, C., Armand-Ugon, M., Clotet-Codina, I., Massa, S., Ragno, R., Este, J.A., Botta, M.
A combination of molecular dynamics and docking calculations to explore the binding mode of ADS-J1, a polyanionic compound endowed with anti-HIV-1 activity
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:1344-1351, MAY 2006
abstract,
full text
Sild, S., Maran, U., Lomaka, A., Karelson, M.
Open computing grid for molecular science and engineering
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 46:953-959, MAY 2006
abstract,
full text
Lopez, C.F., Nielsen, S.O., Srinivas, G., DeGrado, W.F., Klein, M.L.
Probing membrane insertion activity of antimicrobial polymers via coarse-grain molecular dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:649-655, MAY 2006
abstract,
full text
Rodinger, T., Howell, P.L., Pomes, R.
Distributed replica sampling
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:725-731, MAY 2006
abstract,
full text
Pedersen, U.R., Leidy, C., Westh, P., Peters, G.H.
The effect of calcium on the properties of charged phospholipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1758:573-582, MAY 2006
abstract,
full text
Limbach, H.J., Arnold, A., Mann, B.A., Holm, C.
ESPResSo - an extensible simulation package for research on soft matter systems
COMPUTER PHYSICS COMMUNICATIONS, 174:704-727, MAY 1 2006
abstract,
full text
Gu, Y., VanCourt, T., Herbordt, M.C.
Accelerating molecular dynamics simulations with configurable circuits
IEE PROCEEDINGS-COMPUTERS AND DIGITAL TECHNIQUES, 153:189-195, MAY 2006
abstract,
full text
Yio, X., Diamond, M., Zhang, J.Y., Weinstein, H., Wang, L.H., Werther, L., Itzkowitz, S.
Trefoil factor family-1 mutations enhance gastric cancer cell invasion through distinct signaling pathways
GASTROENTEROLOGY, 130:1696-1706, MAY 2006
abstract,
full text
Adcock, S.A., McCammon, J.A.
Molecular dynamics: Survey of methods for simulating the activity of proteins
CHEMICAL REVIEWS, 106:1589-1615, MAY 2006
full text
Siggel, L., Molnar, F.
Computer modelling of a type-1 collagen fibril in water. 1. Model development and validation
JOURNAL OF THE AMERICAN LEATHER CHEMISTS ASSOCIATION, 101:179-+, MAY 2006
abstract,
full text
Kezuka, Y., Ohishi, M., Itoh, Y., Watanabe, J., Mitsutomi, M., Watarabe, T., Nonaka, T.
Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037
JOURNAL OF MOLECULAR BIOLOGY, 358:472-484, APR 28 2006
abstract,
full text
Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Transient stability of the helical pattern of region F19-L22 of the N-terminal domain of p53: A molecular dynamics simulation study
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 343:110-116, APR 28 2006
abstract,
full text
Eike, D.M., Maginn, E.J.
Atomistic simulation of solid-liquid coexistence for molecular systems: Application to triazole and benzene
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 164503, APR 28 2006
abstract,
full text
Hamacher, K., Hubsch, A., McCammon, J.A.
A minimal model for stabilization of biomolecules by hydrocarbon cross-linking
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 164907, APR 28 2006
abstract,
full text
Mathews, D.H., Case, D.A.
Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair
JOURNAL OF MOLECULAR BIOLOGY, 357:1683-1693, APR 14 2006
abstract,
full text
Cecchini, M., Curcio, R., Pappalardo, M., Melki, R., Caflisch, A.
A molecular dynamics approach to the structural characterization of amyloid aggregation
JOURNAL OF MOLECULAR BIOLOGY, 357:1306-1321, APR 7 2006
abstract,
full text
Zhao, X.G., Cummings, P.T.
Molecular dynamics study of carbon nanotube oscillators revisited
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 134705, APR 7 2006
abstract,
full text
Hwang, H., Schatz, G.C., Ratner, M.A.
Ion current calculations based on three dimensional Poisson-Nernst-Planck theory for a cyclic peptide nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 110:6999-7008, APR 6 2006
abstract,
full text
Jensen, M.O., Mouritsen, O.G.
Single-channel water permeabilities of Escherichia coli aquaporins AqpZ and GlpF
BIOPHYSICAL JOURNAL, 90:2270-2284, APR 2006
abstract,
full text
Bastug, T., Gray-Weale, A., Patra, S.M., Kuyucak, S.
Role of protein flexibility in ion permeation: A case study in gramicidin A
BIOPHYSICAL JOURNAL, 90:2285-2296, APR 2006
abstract,
full text
Gumbart, J., Schulten, K.
Molecular dynamics studies of the archaeal translocon
BIOPHYSICAL JOURNAL, 90:2356-2367, APR 2006
abstract,
full text,
TCBG publications
Anishkin, A., Sukharev, S., Colombini, M.
Searching for the molecular arrangement of transmembrane ceramide channels
BIOPHYSICAL JOURNAL, 90:2414-2426, APR 2006
abstract,
full text
Ramirez, E., Santana, A., Cruz, A., Plasencia, I., Lopez, G.E.
Molecular dynamics of surfactant protein C: From single molecule to heptameric aggregates
BIOPHYSICAL JOURNAL, 90:2698-2705, APR 2006
abstract,
full text
Fitch, C.A., Whitten, S.T., Hilser, V.J., Garcia-Moreno, B.
Molecular mechanisms of pH-driven conformational transitions of proteins: Insights from continuum electrostatics calculations of acid unfolding
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63:113-126, APR 1 2006
abstract,
full text
Lagerqvist, J., Zwolak, M., Di Ventra, M.
Fast DNA sequencing via transverse electronic transport
NANO LETTERS, 6:779-782, APR 2006
abstract,
full text
Clark, M.G., Teply, J., Haarer, B.K., Viggiano, S.C., Sept, D., Amberg, D.C.
A genetic dissection of Aip1p's interactions leads to a model for Aip1p-cofilin cooperative activities
MOLECULAR BIOLOGY OF THE CELL, 17:1971-1984, APR 2006
abstract,
full text
Janosi, L., Keer, H., Kosztin, I., Ritz, T.
Influence of subunit structure on the oligomerization state of light-harvesting complexes: A free energy calculation study
CHEMICAL PHYSICS, 323:117-128, MAR 31 2006
abstract,
full text
Yu, Y.M., Chipot, C., Cai, W.S., Shao, X.G.
Molecular dynamics study of the inclusion of cholesterol into cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 110:6372-6378, MAR 30 2006
abstract,
full text
Spijker, P., Vaidehi, N., Freddolino, P.L., Hilbers, P.A.J., Goddard, W.A.
Dynamic behavior of fully solvated beta 2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 103:4882-4887, MAR 28 2006
abstract,
full text
Kawatsu, T., Beratan, D.N., Kakitani, T.
Conformationally averaged score functions for electronic propagation in proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 110:5747-5757, MAR 23 2006
abstract,
full text
Romanov, S., Wiesner, R., Myagkova, G., Kuhn, H., Ivanov, I.
Affinity Labeling of the rabbit 12/15-lipoxygenase using azido derivatives of arachidonic acid
BIOCHEMISTRY, 45:3554-3562, MAR 21 2006
abstract,
full text
Pophristic, V., Vemparala, S., Ivanov, I., Liu, Z.W., Klein, M.L., DeGrado, W.F.
Controlling the shape and flexibility of arylamides: A combined ab initio, ab initio molecular dynamics, and classical molecular dynamics study
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3517-3526, MAR 2 2006
abstract,
full text
Baer, M., Schreiner, E., Kohlmeyer, A., Rousseau, R., Marx, D.
Inverse temperature transition of a biomimetic elastin model: Reactive flux analysis of folding/unfolding and its coupling to solvent dielectric relaxation
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3576-3587, MAR 2 2006
abstract,
full text
Shih, A.Y., Arkhipov, A., Freddolino, P.L., Schulten, K.
Coarse grained protein-lipid model with application to lipoprotein particles
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3674-3684, MAR 2 2006
abstract,
full text,
TCBG publications
Balaeff, A., Mahadevan, L., Schulten, K.
Modeling DNA loops using the theory of elasticity
PHYSICAL REVIEW E, 73: Art. No. 031919, MAR 2006
abstract,
full text,
TCBG publications
Yan, L.M., Ma, Y.F., Seminario, J.M.
Encoding information using molecular vibronics
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 6:675-684, MAR 2006
abstract,
full text
Chipot, C., Tarek, M.
Interaction of a peptide nanotube with a water-membrane interface
PHYSICAL BIOLOGY, 3:S20-S25, MAR 2006
abstract,
full text
Lu, D.Y., Aksimentiev, A., Shih, A.Y., Cruz-Chu, E., Freddolino, P.L., Arkhipov, A., Schulten, K.
The role of molecular modeling in bionanotechnology
PHYSICAL BIOLOGY, 3:S40-S53, MAR 2006
abstract,
full text,
TCBG publications
Meyer, T., Ferrer-Costa, C., Perez, A., Rueda, M., Bidon-Chanal, A., Luque, F.J., Laughton, C.A., Orozco, M.
Essential dynamics: A tool for efficient trajectory compression and management
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2:251-258, MAR-APR 2006
abstract,
full text
Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
The existence of a second allosteric site on the M-1 muscarinic acetylcholine receptor and its implications for drug design
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 16:1217-1220, MAR 1 2006
abstract,
full text
Freddolino, P.L., Arkhipov, A.S., Larson, S.B., McPherson, A., Schulten, K.
Molecular dynamics simulations of the complete satellite tobacco mosaic virus
STRUCTURE, 14:437-449, MAR 2006
abstract,
full text,
TCBG publications
Lee, E.H., Gao, M., Pinotsis, N., Wilmanns, M., Schulten, K.
Mechanical strength of the titin Z1Z2-telethonin complex
STRUCTURE, 14:497-509, MAR 2006
abstract,
full text,
TCBG publications
Hajjar, E., Korkmaz, B., Gauthier, F., Brandsdal, B.O., Witko-Sarsat, V., Reuter, N.
Inspection of the binding sites of proteinase3 for the design of a highly specific substrate
JOURNAL OF MEDICINAL CHEMISTRY, 49:1248-1260, FEB 23 2006
abstract,
full text
Zhuang, W., Abramavicius, D., Hayashi, T., Mukamel, S.
Simulation protocols for coherent femtosecond vibrational spectra of peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 110:3362-3374, FEB 23 2006
abstract,
full text
Sapay, N., Montserret, R., Chipot, C., Brass, V., Moradpour, D., Deleage, G., Penin, F.
NMR structure and molecular dynamics of the in-plane membrane anchor of nonstructural. protein 5A from bovine viral diarrhea virus
BIOCHEMISTRY, 45:2221-2233, FEB 21 2006
abstract,
full text
Cadena, C., Zhao, Q., Snurr, R.Q., Maginn, E.J.
Molecular modeling and experimental studies of the thermodynamic and transport properties of pyridinium-based ionic liquids
JOURNAL OF PHYSICAL CHEMISTRY B, 110:2821-2832, FEB 16 2006
abstract,
full text
Ivanov, I., Vemparala, S., Pophristic, V., Kuroda, K., DeGrado, W.F., McCammon, J.A., Klein, M.L.
Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 128:1778-1779, FEB 15 2006
full text
Gracheva, M.E., Xiong, A.L., Aksimentiev, A., Schulten, K., Timp, G., Leburton, J.P.
Simulation of the electric response of DNA translocation through a semiconductor nanopore-capacitor
NANOTECHNOLOGY, 17:622-633, FEB 14 2006
abstract,
full text,
TCBG publications
Kosztin I., Barz, B., Janosi, L.
Calculating potentials of mean force and diffusion coefficients from nonequilibrium processes without Jarzynski's equality
JOURNAL OF CHEMICAL PHYSICS, 124: Art. No. 064106, FEB 14 2006
abstract,
full text
Tornroth-Horsefield, S., Wang, Y., Hedfalk, K., Johanson, U., Karlsson, M., Tajkhorshid, E., Neutze, R., Kjellbom, P.
Structural mechanism of plant aquaporin gating
NATURE, 439:688-694, FEB 9 2006
abstract,
full text
Heng, J.B., Aksimentiev, A., Ho, C., Marks, P., Grinkova, Y.V., Sligar, S., Schulten, K., Timp, G.
The electromechanics of DNA in a synthetic nanopore
BIOPHYSICAL JOURNAL, 90:1098-1106, FEB 2006
abstract,
full text,
TCBG publications
Bronson, J., Lee, O.S., Saven, J.G.
Molecular dynamics simulation of WSK-3, a computationally designed, water-soluble variant of the integral membrane protein KcsA
BIOPHYSICAL JOURNAL, 90:1156-1163, FEB 2006
abstract,
full text
Henin, J., Maigret, B., Tarek, M., Escrieut, C., Fourmy, D., Chipot, C.
Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor
BIOPHYSICAL JOURNAL, 90:1232-1240, FEB 2006
abstract,
full text
Corry, B.
An energy-efficient gating mechanism in the acetylcholine receptor channel suggested by molecular and Brownian dynamics
BIOPHYSICAL JOURNAL, 90:799-810, FEB 2006
abstract,
full text
Seroka, P., Plosinski, M., Czub, J., Sowinski, P., Pawlak, J.
Monosaccharides as internal probes for the determination of the absolute configuration of 2-butanol
MAGNETIC RESONANCE IN CHEMISTRY, 44:132-138, FEB 2006
abstract,
full text
Kale, L.V., Zheng, G.B., Lee, C.W., Kumar, S.
Scaling applications to massively parallel machines using Projections performance analysis tool
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING THEORY METHODS AND APPLICATIONS, 22:347-358, FEB 2006
abstract,
full text
Mezei, M., Filizola, M.
TRAJELIX: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 20:97-107, FEB 2006
abstract,
full text
Legge, F.S., Budi, A., Treutlein, H., Yarovsky, I.
Protein flexibility: Multiple molecular dynamics simulations of insulin chain B
BIOPHYSICAL CHEMISTRY, 119:146-157, JAN 20 2006
abstract,
full text
Martinez, L., Webb, P., Polikarpov, I., Skaf, M.S.
Molecular dynamics simulations of ligand dissociation from thyroid hormone receptors: Evidence of the likeliest escape pathway and its implications for the design of novel ligands
JOURNAL OF MEDICINAL CHEMISTRY, 49:23-26, JAN 12 2006
abstract,
full text
Benitez, B.A.S., Arora, K., Schlick, T.
In silico studies of the African swine fever virus DNA polymerase X support an induced-fit mechanism
BIOPHYSICAL JOURNAL, 90:42-56, JAN 2006
abstract,
full text
Gao, M., Sotomayor, M., Villa, E., Lee, E.H., Schulten, K.
Molecular mechanisms of cellular mechanics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 8:3692-3706, 2006
abstract,
full text,
TCBG publications
Modzelewska, A., Filipek, S., Palczewski, K., Park, P.S.H.
Arrestin interaction with rhodopsin - Conceptual models
CELL BIOCHEMISTRY AND BIOPHYSICS, 46:1-15, 2006
abstract,
full text
Casanovas, J., Zanuy, D., Aleman, C.
Conducting polymer actuator mechanism based on the conformational flexibility of calix[4]arene
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 45:1103-1105, 2006
full text
Sadiq, S.K., Zasada, S.J., Coveney, P.V.
Grid assisted ensemble molecular dynamics simulations of HIV-1 proteases reveal novel conformations of the inhibitor saquinavir
COMPUTATIONAL LIFE SCIENCES II, PROCEEDINGS, 4216:150-161, 2006
abstract,
full text
Mulholland, A.J.
Modelling Biological Systems
CHEMICAL MODELLING: APPLICATIONS AND THEORY, VOL 4, 4:23-68, 2006
full text
Fitch, B.G., Rayshubskiy, A., Eleftheriou, M., Ward, T.J.C., Giampapa, M., Zhestkov, Y., Pitman, M.C., Suits, F., Grossfield, A., Pitera, J., Swope, W., Zhou, R.H., Feller, S., Germain, R.S.
Blue matter: Strong scaling of molecular dynamics on blue Gene/L
COMPUTATIONAL SCIENCE - ICCS 2006, PT 2, PROCEEDINGS, 3992:846-854, 2006
abstract,
full text
Strahs, D., Zhu, C.X., Cheng, B.K., Chen, J., Tse-Dinh, Y.C.
Experimental and computational investigations of Ser10 and Lys13 in the binding and cleavage of DNA substrates by Escherichia coli DNA topoisomerase I
NUCLEIC ACIDS RESEARCH, 34:1785-1797, 2006
abstract,
full text
Salsbury, F.R., Clodfelter, J.E., Gentry, M.B., Hollis, T., Scarpinato, K.D.
The molecular mechanism of DNA damage recognition by MutS homologs and its consequences for cell death response
NUCLEIC ACIDS RESEARCH, 34:2173-2185, 2006
abstract,
full text
Pedretti, A., Vistoli, G., Marconi, C., Testa, B.
Muscarinic receptors: A comparative analysis of structural features and binding modes through homology modelling and molecular docking
CHEMISTRY & BIODIVERSITY, 3:481-501, 2006
abstract,
full text
Miguet, L., Zhang, Z.D., Grigorov, M.G.
Computational studies of ligand-receptor interactions in bitter taste receptors
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 26:611-630, 2006
abstract,
full text
Li, A.Q., Dowell, E.H.
Modal reduction of mathematical models of biological molecules
JOURNAL OF COMPUTATIONAL PHYSICS, 211:262-288, JAN 1 2006
abstract,
full text
Plummer, M., Hein, J., Guest, M.F., D'Mellow, K.J., Bush, I.J., Refson, K., Pringle, G.J., Smith, L., Trew, A.
Terascale materials modelling on high performance system HPCx
JOURNAL OF MATERIALS CHEMISTRY, 16:1885-1893, 2006
abstract,
full text
Wang, Y.L., Arora, K., Schlick, T.
Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass
PROTEIN SCIENCE, 15:135-151, JAN 2006
abstract,
full text
Park, S., Saven, J.G.
Simulation of pH-dependent edge strand rearrangement in human beta-2 microglobulin
PROTEIN SCIENCE, 15:200-207, JAN 2006
abstract,
full text
Correia, B.E., Loureiro-Ferreira, N., Rodrigues, J.R., Brito, R.M.M.
A structural model of an amyloid protofilament of transthyretin
PROTEIN SCIENCE, 15:28-32, JAN 2006
abstract,
full text
Gullingsrud, J., Kim, C., Taylor, S.S., McCammon, J.A.
Dynamic binding of PKA regulatory subunit RI alpha
STRUCTURE, 14:141-149, JAN 2006
abstract,
full text
Patny, A., Desai, P.V., Avery, M.A.
Homology modeling of G-protein-coupled receptors and implications in drug design
CURRENT MEDICINAL CHEMISTRY, 13:1667-1691, 2006
abstract,
full text
Curini, M., Epifano, F., Genovese, S., Menghini, L., Ricci, D., Fraternale, D., Giamperi, L., Bucchini, A., Bellacchio, E.
Lipoxygenase inhibitory activity of boropinic acid, active principle of Boronia pinnata
NATURAL PRODUCT COMMUNICATIONS, 1:1141-1145, 2006
abstract,
full text
Barreca, M.L., De Luca, L., Ferro, S., Rao, A., Monforte, A.M., Chimirri, A.
Computational and synthetic approaches for the discovery of HIV-1 integrase inhibitors
ARKIVOC, Part 7, 224-244, 2006
abstract,
full text
Dixon, M.F.
A runtime adaptive load balancing algorithm for particle simulations
APPLIED PARALLEL COMPUTING: STATE OF THE ART IN SCIENTIFIC COMPUTING, 3732:709-718, 2006
abstract,
full text
Senapati, S., Bui, J.M., McCammon, J.A.
Induced fit in mouse acetylcholinesterase upon binding a femtomolar inhibitor: A molecular dynamics study
JOURNAL OF MEDICINAL CHEMISTRY, 48:8155-8162, DEC 29 2005
abstract,
full text
Wang, P., Yan, B., Guo, J.T., Hicks, C., Xu, Y.
Structural genomics analysis of alternative splicing and application to isoform structure modeling
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:18920-18925, DEC 27 2005
abstract,
full text
O'Donoghue, P., Sethi, A., Woese, C.R., Luthey-Schulten, Z.A.
The evolutionary history of Cys-tRNA(Cys) formation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:19003-19008, DEC 27 2005
abstract,
full text
Chipot, C., Henin, J.
Exploring the free-energy landscape of a short peptide using an average force
JOURNAL OF CHEMICAL PHYSICS, 123: Art. No. 244906, DEC 22 2005
abstract,
full text
Sohn, R., Parks, J.M., Buhrman, G., Brown, P., Kristjansdottir, K., Safi, A., Edelsbrunner, H., Yang, W.T., Rudolph, J.
Experimental validation of the docking orientation of Cdc25 with its Cdk2-CycA protein substrate
BIOCHEMISTRY, 44:16563-16573, DEC 20 2005
abstract,
full text
Cruz, L., Urbanc, B., Borreguero, J.M., Lazo, N.D., Teplow, D.B., Stanley, H.E.
Solvent and mutation effects on the nucleation of amyloid beta-protein folding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:18258-18263, DEC 20 2005
abstract,
full text
Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Identification of multiple allosteric sites on the M-1 muscarinic acetylcholine receptor
FEBS LETTERS, 579:6726-6732, DEC 19 2005
abstract,
full text
Chung, S.H., Corry, B.
Three computational methods for studying permeation, selectivity and dynamics in biological ion channels
SOFT MATTER, 1:417-427, DEC 14 2005
abstract,
full text
Thomas, S., Tanase, G., Dale, L.K., Moreira, J.M., Rauchwerger, L., Amato, N.M.
Parallel protein folding with STAPL
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17:1643-1656, DEC 10 2005
abstract,
full text
Petersen, F.N.R., Jensen, M.O., Nielsen, C.H.
Interfacial tryptophan residues: A role for the cation-pi effect?
BIOPHYSICAL JOURNAL, 89:3985-3996, DEC 2005
abstract,
full text
Case, D.A., Cheatham, T.E., Darden, T., Gohlke, H., Luo, R., Merz, K.M., Onufriev, A., Simmerling, C., Wang, B., Woods, R.J.
The Amber biomolecular simulation programs
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1668-1688, DEC 2005
abstract,
full text
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., Schulten, K.
Scalable molecular dynamics with NAMD
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1781-1802, DEC 2005
abstract,
full text,
TCBG publications
Forbes, J.G., Jin, A.J., Ma, K., Gutierrez-Cruz, G., Tsai, W.L., Wang, K.A.
Titin PEVK segment: charge-driven elasticity of the open and flexible polyampholyte
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY, 26:291-301, DEC 2005
abstract,
full text
Wells, S.A., Menor, S., Hespenheide, B., Thorpe, M.F.
Constrained geometric simulation of diffusive motion in proteins
PHYSICAL BIOLOGY, 2:S127-S136, DEC 2005
abstract,
full text
Lim, R.Y.H., Aebi, U.
In silico access to the nuclear pore complex
STRUCTURE, 13:1741-1743, DEC 2005
full text
Isgro, T.A., Schulten, K.
Binding dynamics of isolated nucleoporin repeat regions to importin-beta
STRUCTURE, 13:1869-1879, DEC 2005
abstract,
full text,
TCBG publications
Budi, A., Legge, F.S., Treutlein, H., Yarovsky, I.
Electric field effects on insulin chain-B conformation
JOURNAL OF PHYSICAL CHEMISTRY B, 109:22641-22648, DEC 1 2005
abstract,
full text
Jha, S., Coveney, P.V., Laughton, C.A.
Force field validation for nucleic acid simulations: Comparing energies and dynamics of a DNA dodecamer
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1617-1627, NOV 30 2005
abstract,
full text
Buchete, N.V., Tycko, R., Hummer, G.
Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments
JOURNAL OF MOLECULAR BIOLOGY, 353:804-821, NOV 4 2005
abstract,
full text
De Luca, L., Vistoli, G., Pedretti, A., Barreca, M.L., Chimirri, A.
Molecular dynamics studies of the full-length integrase-DNA complex
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 336:1010-1016, NOV 4 2005
abstract,
full text
Vistoli, G., Pedretti, A., Villa, L., Testa, B.
Solvent constraints on the property space of acetylcholine. 2. Ordered media
JOURNAL OF MEDICINAL CHEMISTRY, 48:6926-6935, NOV 3 2005
abstract,
full text
Seminario, J.M., Yan, L.M., Ma, Y.F.
Transmission of vibronic signals in molecular circuits
JOURNAL OF PHYSICAL CHEMISTRY A, 109:9712-9715, NOV 3 2005
abstract,
full text
Baudry, J., Smith, J.C.
Can proteins and crystals self-catalyze methyl rotations?
JOURNAL OF PHYSICAL CHEMISTRY B, 109:20572-20578, NOV 3 2005
abstract,
full text
Liu, T.Y., Jenwitheesuk, E., Teller, D.C., Samudrala, R.
Structural insights into the cellular retinaldehyde-binding protein (CRALBP)
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 61:412-422, NOV 1 2005
abstract,
full text
Katti, D.R., Ghosh, P., Schmidt, S., Katti, K.S.
Mechanical properties of the sodium montmorillonite interlayer intercalated with amino acids
BIOMACROMOLECULES, 6:3276-3282, NOV-DEC 2005
abstract,
full text
Chipot, C., Rozanska, X., Dixit, S.B.
Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 19:765-770, NOV 2005
abstract,
full text
Sanbonmatsu, K.Y., Joseph, S., Tung, C.S.
Simulating movement of tRNA into the ribosome during decoding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:15854-15859, NOV 1 2005
abstract,
full text
Zhang, D.Q., McCammon, J.A.
The association of tetrameric acetylcholinesterase with CoIQ tail: A block normal mode analysis
PLOS COMPUTATIONAL BIOLOGY, 1:484-491, NOV 2005
abstract,
full text
Wang, W., Skeel, R.D.
Fast evaluation of polarizable forces
JOURNAL OF CHEMICAL PHYSICS, 123: Art. No. 164107, OCT 22 2005
abstract,
full text
Freites, J.A., Tobias, D.J., von Heijne, G., White, S.H.
Interface connections of a transmembrane voltage sensor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:15059-15064, OCT 18 2005
abstract,
full text
Hosokawa, Y., Maki, S., Nagata, T.
Gold nanoparticles stabilized by tripod thioether oligomers: Synthesis and molecular dynamics studies
BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, 78:1773-1782, OCT 15 2005
abstract,
full text
Rai, B.K., Prohofsky, E.W., Durbin, S.M.
Single-atom test of all-atom empirical potentials: Fe in myoglobin
JOURNAL OF PHYSICAL CHEMISTRY B, 109:18983-18987, OCT 13 2005
abstract,
full text
Weinbach, Y., Elber, R.
Revisiting and parallelizing SHAKE
JOURNAL OF COMPUTATIONAL PHYSICS, 209:193-206, OCT 10 2005
abstract,
full text
Seminario, J.M., Yan, L.M., Ma, Y.F.
Scenarios for molecular-level signal processing
PROCEEDINGS OF THE IEEE, 93:1753-1764, OCT 2005
abstract,
full text
Yonkunas, M.J., Xu, Y., Tang, P.
Anesthetic interaction with ketosteroid isomerase: Insights from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 89:2350-2356, OCT 2005
abstract,
full text
Pedersen, T.B., Kaasgaard, T., Jensen, M.O., Frokjaer, S., Mouritsen, O.G., Jorgensen, K.
Phase behavior and nanoscale structure of phospholipid membranes incorporated with acylated C(14)-peptides
BIOPHYSICAL JOURNAL, 89:2494-2503, OCT 2005
abstract,
full text
Stagg, S.M., Harvey, S.C.
Exploring the flexibility of ribosome recycling factor using molecular dynamics
BIOPHYSICAL JOURNAL, 89:2659-2666, OCT 2005
abstract,
full text
Gorfe, A.A., Caflisch, A.
Functional plasticity in the substrate binding site of beta-secretase
STRUCTURE, 13:1487-1498, OCT 2005
abstract,
full text
Jolley, C., Ben-Shem, A., Nelson, N., Fromme, P.
Structure of plant photosystem I revealed by theoretical modeling
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:33627-33636, SEP 30 2005
abstract,
full text
Coveney, P.V., Fowler, P.W.
Modelling biological complexity: a physical scientist's perspective
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 2:267-280, SEP 22 2005
abstract,
full text
Franklin, J., Doniach, S.
Adaptive time stepping in biomolecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 123: Art. No. 124909, SEP 22 2005
abstract,
full text
Myers, R.S., Amaro, R.E., Luthey-Schulten, Z.A., Davisson, V.J.
Reaction coupling through interdomain contacts in imidazole glycerol phosphate synthase
BIOCHEMISTRY, 44:11974-11985, SEP 13 2005
abstract,
full text
Bae, E., Phillips, G.N.
Identifying and engineering ion pairs in adenylate kinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:30943-30948, SEP 2 2005
abstract,
full text
Paliwal, A., Asthagiri, D., Abras, D., Lenhoff, A.M., Paulaitis, M.E.
Light-scattering studies of protein solutions: Role of hydration in weak protein-protein interactions
BIOPHYSICAL JOURNAL, 89:1564-1573, SEP 2005
abstract,
full text
Cohen, J., Kim, K., King, P., Seibert, M., Schulten, K.
Finding gas diffusion pathways in proteins: Application to O-2 and H-2 transport in Cpl [FeFe]-hydrogenase and the role of packing defects
STRUCTURE, 13:1321-1329, SEP 2005
abstract,
full text,
TCBG publications
Filipek, S.
Organization of rhodopsin molecules in native membranes of rod cells - an old theoretical model compared to new experimental data
JOURNAL OF MOLECULAR MODELING, 11:385-391, SEP 2005
abstract,
full text
Mathe, J., Aksimentiev, A., Nelson, D.R., Schulten, K., Meller, A.
Orientation discrimination of single-stranded DNA inside the alpha-hemolysin membrane channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:12377-12382, AUG 30 2005
abstract,
full text,
TCBG publications
Dublet, B., Ruello, A., Pederzoli, M., Hajjar, E., Courbebaisse, M., Canteloup, S., Reuter, N., Witko-Sarsat, V.
Cleavage of p21/WAF1/CIP1 by proteinase 3 modulates differentiation of a monocytic cell line
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:30242-30253, AUG 26 2005
abstract,
full text
Ashworth, M., Bush, I.J., Guest, M.F., Sunderland, A.G., Booth, S., Hein, J., Smith, L., Stratford, K., Curioni, A.
HPCx: towards capability computing
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 17:1329-1361, AUG 25 2005
abstract,
full text
Hemp, J., Christian, C., Barquera, B., Gennis, R.B., Martinez, T.J.
Helix switching of a key active-site residue in the cytochrome cbb(3) oxidases
BIOCHEMISTRY, 44:10766-10775, AUG 16 2005
abstract,
full text
Schmidt, S.R., Katti, D.R., Ghosh, P., Katti, K.S.
Evolution of mechanical response of sodium montmorillonite interlayer with increasing hydration by molecular dynamics
LANGMUIR, 21:8069-8076, AUG 16 2005
abstract,
full text
Damjanovic, A., Garcia-Moreno, B., Lattman, E.E., Garcia, A.E.
Molecular dynamics study of water penetration in staphylococcal nuclease
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 60:433-449, AUG 15 2005
abstract,
full text
Park, S., Saven, J.G.
Statistical and molecular dynamics studies of buried waters in globular proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 60:450-463, AUG 15 2005
abstract,
full text
Pickles, S.M., Haines, R., Pinning, R.L., Porter, A.R.
A practical toolkit for computational steering
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1843-1853, AUG 15 2005
abstract,
full text
Kalawsky, R.S., Nee, S.P., Holmes, I., Coveney, P.V.
A grid-enabled lightweight computational steering client: a .NET PDA implementation
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1885-1894, AUG 15 2005
abstract,
full text
Hein, J.I., Reid, F., Smith, L., Bush, I., Guest, M., Sherwood, P.
On the performance of molecular dynamics applications on current high-end systems
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1987-1998, AUG 15 2005
abstract,
full text
Fowler, P.W., Jha, S., Coveney, P.V.
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:1999-2015, AUG 15 2005
abstract,
full text
Woods, C.J., Ng, M.H., Johnston, S., Murdock, S.E., Wu, B., Tai, K., Fangohr, H., Jeffreys, P., Cox, S., Frey, J.G., Sansom, M.S.P., Essex, J.W.
Grid computing and biomolecular simulation
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2017-2035, AUG 15 2005
abstract,
full text
Wan, S.Z., Coveney, P.V., Flower, D.R.
Peptide recognition by the T cell receptor: comparison of binding free energies from thermodynamic integration, Poisson-Boltzmann and linear interaction energy approximations
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2037-2053, AUG 15 2005
abstract,
full text
Giordanetto, F., Fowler, P.W., Saqi, M., Coveney, P.V.
Large scale molecular dynamics simulation of native and mutant dihydropteroate synthase-sulphanilamide complexes suggests the molecular basis for dihydropteroate synthase drug resistance
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2055-2073, AUG 15 2005
abstract,
full text
Rousay, E.R., Fu, H.C., Robinson, J.M., Essex, J.W., Frey, J.G.
Grid-based dynamic electronic publication: a case study using combined experiment and simulation studies of crown ethers at the air/water interface
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 363:2075-2095, AUG 15 2005
abstract,
full text
Ota, N., Agard, D.A.
Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion
JOURNAL OF MOLECULAR BIOLOGY, 351:345-354, AUG 12 2005
abstract,
full text
de Brevern, A.G., Wong, H., Tournamille, C., Colin, Y., Van Kim, C.L., Etchebest, C.
A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC)
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1724:288-306, AUG 5 2005
abstract,
full text
Carrillo-Tripp, M., Feller, S.E.
Evidence for a mechanism by which omega-3 polyunsaturated lipids may affect membrane protein function
BIOCHEMISTRY, 44:10164-10169, AUG 2 2005
abstract,
full text
Izaguirre, J.A., Hampton, S.S., Matthey, T.
Parallel multigrid summation for the N-body problem
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 65:949-962, AUG 2005
abstract,
full text
McGillivray, G., Savarirayan, R., Cox, T.C., Stojkoski, C., McNeil, R., Bankier, A., Bateman, J.F., Roscioli, T., Gardner, R.J.M., Lamande, S.R.
Familial scaphocephaly syndrome caused by a novel mutation in the FGFR2 tyrosine kinase domain
JOURNAL OF MEDICAL GENETICS, 42:656-662, AUG 2005
full text
Mulkidjanian, A.Y., Kozlova, M.A., Cherepanov, D.A.
Ubiquinone reduction in the photosynthetic reaction centre of Rhodobacter sphaeroides: interplay between electron transfer, proton binding and flips of the quinone ring
BIOCHEMICAL SOCIETY TRANSACTIONS, 33:845-850, AUG 2005
abstract,
full text
Veluraja, K., Margulis, C.J.
Conformational dynamics of sialyl Lewis(x) in aqueous solution and its interaction with selectinE. A study by molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 23:101-111, AUG 2005
abstract,
full text
Wan, S.Z., Coveney, P.V., Flower, D.R.
Molecular basis of peptide recognition by the TCR: Affinity differences calculated using large scale computing
JOURNAL OF IMMUNOLOGY, 175:1715-1723, AUG 1 2005
abstract,
full text
Wang, Y., Schulten, K., Tajkhorshid, E.
What makes an aquaporin a glycerol channel? A comparative study of AqpZ and GlpF
STRUCTURE, 13:1107-1118, AUG 2005
abstract,
full text,
TCBG publications
Makrodimitris, K., Fernandez, E.J., Woolf, T.B., O'Connell, J.P.
ALLD: An object-oriented mesoscopic simulation program for polar biomolecules in hydrophobic chromatography or biomembranes
MOLECULAR SIMULATION, 31:623-636, AUG 2005
abstract,
full text
Crocker, M.S., Hampton, S.S., Matthey, T., Izaguirre, J.A.
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:1021-1031, JUL 30 2005
abstract,
full text
Lynch, D.L., Reggio, P.H.
Molecular dynamics simulations of the endocannabinoid N-arachidonoylethanolamine (Anandamide) in a phospholipid bilayer: Probing structure and dynamics
JOURNAL OF MEDICINAL CHEMISTRY, 48:4824-4833, JUL 28 2005
abstract,
full text
Borza, D.B., Bondar, O., Colon, S., Todd, P., Sado, Y., Neilson, E.G., Hudson, B.G.
Goodpasture autoantibodies unmask cryptic epitopes by selectively dissociating autoantigen complexes lacking structural reinforcement - Novel mechanisms for immune privilege and autoimmune pathogenesis
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:27147-27154, JUL 22 2005
abstract,
full text
Roh, J.H., Novikov, V.N., Gregory, R.B., Curtis, J.E., Chowdhuri, Z., Sokolov, A.P.
Onsets of anharmonicity in protein dynamics
PHYSICAL REVIEW LETTERS, 95: Art. No. 038101, JUL 15 2005
abstract,
full text
Dittrich, M., Freddolino, P.L., Schulten, K.
When light falls in LOV: A quantum mechanical/molecular mechanical study of photoexcitation in Phot-LOV1 of Chlamydomonas reinhardtii
JOURNAL OF PHYSICAL CHEMISTRY B, 109:13006-13013, JUL 7 2005
abstract,
full text,
TCBG publications
Mezzenga, R., Grigorov, M., Zhang, Z.D., Servais, C., Sagalowicz, L., Romoscanu, A.I., Khanna, V., Meyer, C.
Polysaccharide-induced order-to-order transitions in lyotropic liquid crystals
LANGMUIR, 21:6165-6169, JUL 5 2005
abstract,
full text
Fernandez, L.E., Perez, C., Segovia, L., Rodriguez, M.H., Gill, S.S., Bravo, A., Soberon, M.
Cry11Aa toxin from Bacillus thuringiensis binds its receptor in Aedes aegypti mosquito larvae through loop alpha-8 of domain II
FEBS LETTERS, 579:3508-3514, JUL 4 2005
abstract,
full text
Amaro, R.E., Myers, R.S., Davisson, V.J., Luthey-Schulten, Z.A.
Structural elements in IGP synthase exclude water to optimize ammonia transfer
BIOPHYSICAL JOURNAL, 89:475-487, JUL 2005
abstract,
full text
Aldini, G., Dalle-Donne, I., Vistoli, G., Facino, R.M., Carini, M.
Covalent modification of actin by 4-hydroxy-trans-2-nonenal (HNE): LC-ESI-MS/MS evidence for Cys374 Michael adduction
JOURNAL OF MASS SPECTROMETRY, 40:946-954, JUL 2005
abstract,
full text
Engle, R.D., Skeel, R.D., Drees, M.
Monitoring energy drift with shadow Hamiltonians
JOURNAL OF COMPUTATIONAL PHYSICS, 206:432-452, JUL 1 2005
abstract,
full text
Damjanovic, A., Garcia-Moreno, B., Lattman, E.E., Garcia, A.E.
Molecular dynamics study of hydration of the protein interior
COMPUTER PHYSICS COMMUNICATIONS, 169:126-129, JUL 1 2005
abstract,
full text
Fleming, P.J., Rose, G.D.
Do all backbone polar groups in proteins form hydrogen bonds?
PROTEIN SCIENCE, 14:1911-1917, JUL 2005
abstract,
full text
Henin, J., Pohorille, A., Chipot, C.
Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127:8478-8484, JUN 15 2005
abstract,
full text
Chao, S.D., Kress, J.D., Redondo, A.
Coarse-grained rigid blob model for soft matter simulations
JOURNAL OF CHEMICAL PHYSICS, 122: Art. No. 234912, JUN 15 2005
abstract,
full text
Ortiz, V., Nielsen, S.O., Klein, M.L., Discher, D.E.
Unfolding a linker between helical repeats
JOURNAL OF MOLECULAR BIOLOGY, 349:638-647, JUN 10 2005
abstract,
full text
Aksimentiev, A., Schulten, K.
Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
BIOPHYSICAL JOURNAL, 88:3745-3761, JUN 2005
abstract,
full text,
TCBG publications
Liu, Z.W., Xu, Y., Tang, P.
Molecular dynamics Simulations of C2F6 effects on gramicidin A: Implications of the mechanisms of general anesthesia
BIOPHYSICAL JOURNAL, 88:3784-3791, JUN 2005
abstract,
full text
Tarek, M.
Membrane electroporation: A molecular dynamics simulation
BIOPHYSICAL JOURNAL, 88:4045-4053, JUN 2005
abstract,
full text
Brigo, A., Lee, K.W., Fogolari, F., Mustata, G.L., Briggs, J.M.
Comparative molecular dynamics simulations of HIV-1 integrase and the T66I/M154I mutant: Binding modes and drug resistance to a diketo acid inhibitor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 59:723-741, JUN 1 2005
abstract,
full text
Zheng, G.B., Wilmarth, T., Jagadishprasad, P., Kale, L.V.
Simulation-based performance prediction for large parallel machines
INTERNATIONAL JOURNAL OF PARALLEL PROGRAMMING, 33:183-207, JUN 2005
abstract,
full text
Bishop, T.C.
Molecular dynamics simulations of a nucleosome and free DNA
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 22:673-685, JUN 2005
abstract,
full text
Zhang, Q.M., Lee, G.R., Marszalek, P.E.
Atomic cranks and levers control sugar ring conformations
JOURNAL OF PHYSICS-CONDENSED MATTER, 17:S1427-S1442, MAY 11 2005
abstract,
full text
Villa, E., Balaeff, A., Schulten, K.
Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6783-6788, MAY 10 2005
abstract,
full text,
TCBG publications
Law, R.J., Henchman, R.H., McCammon, J.A.
A gating mechanism proposed from a simulation of a human alpha 7 nicotinic acetylcholine receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 102:6813-6818, MAY 10 2005
abstract,
full text
Costantino, G., Entrena-Guadix, A., Macchiarulo, A., Gioiello, A., Pellicciari, R.
Molecular dynamics simulation of the ligand binding domain of farnesoid X receptor. Insights into helix-12 stability and coactivator peptide stabilization in response to agonist binding
JOURNAL OF MEDICINAL CHEMISTRY, 48:3251-3259, MAY 5 2005
abstract,
full text
Chinta, S.J., Kommaddi, R.P., Turman, C.M., Strobel, H.W., Ravindranath, V.
Constitutive expression and localization of cytochrome P-450 1A1 in rat and human brain: presence of a splice variant form in human brain
JOURNAL OF NEUROCHEMISTRY, 93:724-736, MAY 2005
abstract,
full text
Brigo, A., Lee, K.W., Mustata, G.I., Briggs, J.M.
Comparison of multiple molecular dynamics trajectories calculated for the drug-resistant HIV-1 integrase T66I/M154I catalytic domain
BIOPHYSICAL JOURNAL, 88:3072-3082, MAY 2005
abstract,
full text
Asthagiri, D., Paliwal, A., Abras, D., Lenhoff, A.M., Paulaitis, M.E.
A consistent experimental and modeling approach to light-scattering studies of protein-protein interactions in solution
BIOPHYSICAL JOURNAL, 88:3300-3309, MAY 2005
abstract,
full text
Kamath, S.A., Buolamwini, J.K.
Asp746 to glycine change may have a greater influence than cys751 to serine change in accounting for ligand selectivity between EGFR and HER-2 at the ATP site
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 19:287-291, MAY 2005
abstract,
full text
Bourgault, R., Oakley, A.J., Bewley, J.D., Wilce, M.C.J.
Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit
PROTEIN SCIENCE, 14:1233-1241, MAY 2005
abstract,
full text
Park, S., Boder, E.T., Saven, J.G.
Modulating the DNA affinity of Elk-1 with computationally selected mutations
JOURNAL OF MOLECULAR BIOLOGY, 348:75-83, APR 22 2005
abstract,
full text
Adisa, B., Bruce, D.A.
Molecular dynamics Simulations of helix-forming, amine-functionalized m-poly(phenyleneethynylene)s
JOURNAL OF PHYSICAL CHEMISTRY B, 109:7548-7556, APR 21 2005
abstract,
full text
Kahle, C., Deubner, R., Schollmayer, C., Scheiber, J., Baumann, K., Holzgrabe, U.
NMR spectroscopic and molecular modelling studies on cyclodextrin-dipeptide inclusion complexes
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8, 1578-1589, APR 15 2005
abstract,
full text
Henchman, R.H., Wang, H.L., Sine, S.M., Taylor, P., McCammon, J.A.
Ligand-induced conformational change in the alpha 7 nicotinic receptor ligand binding domain
BIOPHYSICAL JOURNAL, 88:2564-2576, APR 2005
abstract,
full text
Alexopoulos, E., Jares-Erijman, E.A., Jovin, T.M., Klement, R., Machinek, R., Sheldrick, G.M., Uson, I.
Crystal and solution structures of 7-amino-actinomycin D complexes with d(TTAGBrUT), d(TTAGTT) and d(TTTAGTTT)
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 61:407-415, APR 2005
abstract,
full text
Swain, M.D., Benson, D.E.
Geometric preferences of crosslinked protein-derived cofactors reveal a high propensity for near-sequence pairs
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 59:64-71, APR 1 2005
abstract,
full text
Katti, D.R., Schmidt, S.R., Ghosh, P., Katti, K.S.
Modeling the response of pyrophyllite interlayer to applied stress using steered molecular dynamics
CLAYS AND CLAY MINERALS, 53:171-178, APR 2005
abstract,
full text
Sokal, I., Dupps, W.J., Grassi, M.A., Brown, J., Affatigato, L.M., Roychowdhury, N., Yang, L.L., Filipek, S., Palczewski, K., Stone, E.M., Baehr, W.
A novel GCAP1 missense mutation (L151F) in a large family with autosomal dominant cone-rod dystrophy (adCORD)
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, 46:1124-1132, APR 2005
abstract,
full text
Sotomayor, M., Corey, D.P., Schulten, K.
In search of the hair-cell gating spring: Elastic properties of ankyrin and cadherin repeats
STRUCTURE, 13:669-682, APR 2005
abstract,
full text,
TCBG publications
Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Structural considerations for the rational design of selective anti-trypanosomal agents: The role of the aromatic clusters at the interface of triosephosphate isomerase dimer
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 328:922-928, MAR 25 2005
abstract,
full text
Jenwitheesuk, E., Samudrala, R.
Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics
AIDS, 19:529-531, MAR 25 2005
abstract,
full text
Vistoli, G., Pedretti, A., Villa, L., Testa, B.
Solvent constraints on the property space of acetylcholine. I. Isotropic solvents
JOURNAL OF MEDICINAL CHEMISTRY, 48:1759-1767, MAR 24 2005
abstract,
full text
Sonne, J., Hansen, F.Y., Peters, G.H.
Methodological problems in pressure profile calculations for lipid bilayers
JOURNAL OF CHEMICAL PHYSICS, 122: Art. No. 124903, MAR 22 2005
abstract,
full text
Hollup, S.M., Salensminde, G., Reuter, N.
WEBnm@: a web application for normal mode analyses of proteins
BMC BIOINFORMATICS, 6: Art. No. 52, MAR 11 2005
abstract,
full text
Miller, F., Kentsis, A., Osman, R., Pan, Z.Q.
Inactivation of VHL by tumorigenic mutations that disrupt dynamic coupling of the pVHL(.)hypoxia-inducible transcription factor-1 alpha complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 280:7985-7996, MAR 4 2005
abstract,
full text
Germain, R.S., Zhestkov, Y., Eleftheriou, M., Rayshubskiy, A., Suits, F., Ward, T.J.C., Fitch, B.G.
Early performance data on the Blue Matter molecular simulation framework
IBM JOURNAL OF RESEARCH AND DEVELOPMENT, 49:447-455, MAR-MAY 2005
abstract,
full text
Delaforge, M., Pruvost, A., Perrin, L., Andre, F.
Cytochrome P450-mediated oxidation of glucuronide derivatives: Example of estradiol-17 beta-glucuronide oxidation to 2-hydroxyestradiol-17 beta-glucuronide by CYP2C8
DRUG METABOLISM AND DISPOSITION, 33:466-473, MAR 2005
abstract,
full text
Cozmuta, I., O'Keeffe, J.T., Bose, D., Stolc, V.
Hybrid MD-Nernst Planck model of alpha-hemolysin conductance properties
MOLECULAR SIMULATION, 31:79-93, FEB 15 2005
abstract,
full text
Roman, C., Ciontu, F., Courtois, B.
Nanoscopic modeling of a carbon nanotube force-measuring biosensor
MOLECULAR SIMULATION, 31:123-133, FEB 15 2005
abstract,
full text
Saladino, A.C., Xu, Y., Tang, P.
Homology Modeling and molecular dynamics simulations of transmembrane domain structure of human neuronal nicotinic acetylcholine receptor
BIOPHYSICAL JOURNAL, 88:1009-1017, FEB 2005
abstract,
full text
Benz, R.W., Castro-Roman, F., Tobias, D.J., White, S.H.
Experimental validation of molecular dynamics simulations of lipid bilayers: A new approach
BIOPHYSICAL JOURNAL, 88:805-817, FEB 2005
abstract,
full text
Moran, O., Galietta, L.J.V., Zegarra-Moran, O.
Binding site of activators of the cystic fibrosis transmembrane conductance regulator in the nucleotide binding domains
CELLULAR AND MOLECULAR LIFE SCIENCES, 62:446-460, FEB 2005
abstract,
full text
Cohen, J., Kim, K., Posewitz, M., Ghirardi, M.L., Schulten, K., Seibert, M., King, P.
Molecular dynamics and experimental investigation of H-2 and O-2 diffusion in [Fe]-hydrogenase
BIOCHEMICAL SOCIETY TRANSACTIONS, 33:80-82, FEB 2005
abstract,
full text,
TCBG publications
Meineke, M.A., Vardeman, C.F., Lin, T., Fennell, C.J., Gezelter, J.D.
OOPSE: An object-oriented parallel simulation engine for molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 26:252-271, FEB 2005
abstract,
full text
Cojocaru, V., Nottrott, S., Klement, R., Jovin, T.M.
The snRNP 15.5K protein folds its cognate K-turn RNA: A combined theoretical and biochemical study
RNA-A PUBLICATION OF THE RNA SOCIETY, 11:197-209, FEB 2005
abstract,
full text
Molnar, F., Rieger, J.
"Like-charge attraction" between anionic polyelectrolytes: Molecular dynamics simulations
LANGMUIR, 21:786-789, JAN 18 2005
abstract,
full text
Williams, E.T., Turman, C.M., Strobel, H.W.
NAMD-LP: Filtering and translating NAMD-generated files
MOLECULAR SIMULATION, 31:67-68, JAN 15 2005
full text
Goodyear, D.J., Sharpe, S., Grant, C.W.M., Morrow, M.R.
Molecular dynamics simulation of transmembrane polypeptide orientational fluctuations
BIOPHYSICAL JOURNAL, 88:105-117, JAN 2005
abstract,
full text
Bolhuis, P.G.
Kinetic pathways of beta-hairpin (Un)folding in explicit solvent
BIOPHYSICAL JOURNAL, 88:50-61, JAN 2005
abstract,
full text
Shih, A.Y., Denisov, I.G., Phillips, J.C., Sligar, S.G., Schulten, K.
Molecular dynamics simulations of discoidal bilayers assembled from truncated human lipoproteins
BIOPHYSICAL JOURNAL, 88:548-556, JAN 2005
abstract,
full text,
TCBG publications
Zhang, Q.M., Jaroniec, J., Lee, G., Marszalek, P.E.
Direct detection of inter-residue hydrogen bonds in polysaccharides by single-molecule force spectroscopy
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 44:2723-2727, 2005
full text
Choi, S., Clements, D.J., Pophristic, V., Ivanov, I., Vemparala, S., Bennett, J.S., Klein, M.L., Winkler, J.D., DeGrado, W.E.
The design and evaluation of heparin-binding foldamers
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 44:6685-6689, 2005
full text
Azevedo, P.J., Silva, C.G., Rodrigues, J.R., Loureiro-Ferreira, N., Brito, R.M.M.
Detection of hydrophobic clusters in molecular dynamics protein unfolding simulations using association rules
BIOLOGICAL AND MEDICAL DATA ANALYSIS, PROCEEDINGS, 3745:329-337, 2005
abstract,
full text
Jenkins, J., Sengupta, D., Sundaram, S.
Characterization of a solid state DNA nanopore sequencer using multi-scale (nano-to-device) modeling
COMPUTATIONAL SCIENCE - ICCS 2005, PT 3, 3516:309-316, 2005
abstract,
full text
Scott, L.R., Clark, T., Bagheri, B.
Education and research challenges in parallel computing
COMPUTATIONAL SCIENCE - ICCS 2005, PT 2, 3515:44-51, 2005
abstract,
full text
Sidiqi, M., Wilce, J.A., Vivian, J.P., Porter, C.J., Barker, A., Leedman, P.J., Wilce, M.C.J.
Structure and RNA binding of the third KH domain of poly(C)-binding protein 1
NUCLEIC ACIDS RESEARCH, 33:1213-1221, 2005
abstract,
full text
Lemke, K., Wojciechowski, M., Laine, W., Bailly, C., Colson, P., Baginski, M., Larsen, A.K., Skladanowski, A.
Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities
NUCLEIC ACIDS RESEARCH, 33:6034-6047, 2005
abstract,
full text
Espinoza-Fonseca, L.M.
Targeting MDM2 by the small molecule RITA: towards the development of new multi-target drugs against cancer
THEORETICAL BIOLOGY AND MEDICAL MODELLING, 2: Art. No. 38, 2005
abstract,
full text
Lu, B.Z., Wong, C.F., Mccammon, J.A.
Release of ADP from the catalytic subunit of protein kinase A: A molecular dynamics simulation study
PROTEIN SCIENCE, 14:159-168, JAN 2005
abstract,
full text
Debnath, A.K.
Application of 3D-QSAR techniques in anti-HIV-1 drug design - An overview
CURRENT PHARMACEUTICAL DESIGN, 11:3091-3110, 2005
abstract,
full text
Wiley, A.P., Swain, M.T., Phillips, S.C., Essex, J.W., Edge, C.M.
Parametrization of reversible digitally filtered molecular dynamics simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1:24-35, JAN-FEB 2005
abstract,
full text
Witheesuk, E.J., Samudrala, R.
Prediction of HIV-1 protease inhibitor resistance using a protein-inhibitor flexible docking approach
ANTIVIRAL THERAPY, 10:157-166, 2005
abstract,
full text
Autenrieth, F., Tajkhorshid, E., Schulten, K., Luthey-Schulten, Z.
Role of water in transient cytochrome c(2) docking
JOURNAL OF PHYSICAL CHEMISTRY B, 108:20376-20387, DEC 30 2004
abstract,
full text,
TCBG publications
Amaro, R., Luthey-Schulten, Z.
Molecular dynamics simulations of substrate channeling through an alpha-beta barrel protein
CHEMICAL PHYSICS, 307:147-155, DEC 27 2004
abstract,
full text
De Fabritiis, G., Delgado-Buscalioni, R., Coveney, P.V.
Energy controlled insertion of polar molecules in dense fluids
JOURNAL OF CHEMICAL PHYSICS, 121:12139-12142, DEC 22 2004
abstract,
full text
Pedesseau, L., Jouanna, P.
Phases, periphases, and interphases equilibrium by molecular modeling. I. Mass equilibrium by the semianalytical stochastic perturbations method and application to a solution between (120) gypsum faces
JOURNAL OF CHEMICAL PHYSICS, 121:12511-12522, DEC 22 2004
abstract,
full text
Grabe, M., Lecar, H., Jan, Y.N., Jan, L.Y.
A quantitative assessment of models for voltage-dependent gating of ion channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101:17640-17645, DEC 21 2004
abstract,
full text
Tang, D.M., Li, A.Q., Attar, P., Dowell, E.H.
Reduced order dynamic model for polysaccharides molecule attached to an atomic force microscope
JOURNAL OF COMPUTATIONAL PHYSICS, 201:723-752, DEC 10 2004
abstract,
full text
Scott, L.R.
Bioinformatics
PERSPECTIVES IN BIOLOGY AND MEDICINE, 47:135-139, WIN 2004
full text
Zhu, F.Q., Tajkhorshid, E., Schulten, K.
Collective diffusion model for water permeation through microscopic channels
PHYSICAL REVIEW LETTERS, 93: Art. No. 224501, NOV 26 2004
abstract,
full text,
TCBG publications
Saladino, A.C., Tang, P.
Optimization of structures and LJ parameters of 1-chloro-1,2,2-trifluorocyclobutane and 1,2-dichlorohexafluorocyclobutane
JOURNAL OF PHYSICAL CHEMISTRY A, 108:10560-10564, NOV 25 2004
abstract,
full text
Mitra, A., Sept, D.
Localization of the antimitotic peptide and depsipeptide binding site on beta-tubulin
BIOCHEMISTRY, 43:13955-13962, NOV 9 2004
abstract,
full text
Jensen, M.O., Mouritsen, O.G.
Lipids do influence protein function - the hydrophobic matching hypothesis revisited
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1666:205-226, NOV 3 2004
abstract,
full text
Sotomayor, M., Schulten, K.
Molecular dynamics study of Gating in the mechanosensitive channel of small conductance MscS
BIOPHYSICAL JOURNAL, 87:3050-3065, NOV 2004
abstract,
full text,
TCBG publications
Paliwal, A., Asthagiri, D., Bossev, D.P., Paulaitis, M.E.
Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation
BIOPHYSICAL JOURNAL, 87:3479-3492, NOV 2004
abstract,
full text
Zhang, D.Q., Konecny, R., Baker, N.A., McCammon, J.A.
Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach
BIOPOLYMERS, 75:325-337, NOV 2004
abstract,
full text
Bertola, D.R., Pereira, A.C., de Oliveira, P.S.L., Kim, C.A., Krieger, J.E.
Clinical variability in a Noonan syndrome family with a new PTPN11 gene mutation
AMERICAN JOURNAL OF MEDICAL GENETICS PART A, 130A:378-383, NOV 1 2004
abstract,
full text
Turjanski, A.G., Estrin, D.A., Rosenstein, R.E., McCormick, J.E., Martin, S.R., Pastore, A., Biekofsky, R.R., Martorana, V.
NMR and molecular dynamics studies of the interaction of melatonin with calmodulin
PROTEIN SCIENCE, 13:2925-2938, NOV 2004
abstract,
full text
Craig, D., Gao, M., Schulten, K., Vogel, V.
Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force
STRUCTURE, 12:2049-2058, NOV 2004
abstract,
full text,
TCBG publications
Espinoza-Fonseca, L.M.
Molecular docking of four beta-amyloid(1-42) fragments on the alpha 7 nicotinic receptor: delineating the binding site of the A beta peptides
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 323:1191-1196, OCT 29 2004
abstract,
full text
Dima, R.I., Thirumalai, D.
Probing the instabilities in the dynamics of helical fragments from mouse PrPc
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101:15335-15340, OCT 26 2004
abstract,
full text
Tanaka, T., Yada, R.Y.
Redesign of catalytic center of an enzyme: aspartic to serine proteinase
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 323:947-953, OCT 22 2004
abstract,
full text
Saccani, J., Castano, S., Beaurain, F., Laguerre, M., Desbat, B.
Stabilization of phospholipid multilayers at the air-water interface by compression beyond the collapse: A BAM, PM-IRRAS, and molecular dynamics study
LANGMUIR, 20:9190-9197, OCT 12 2004
abstract,
full text
Treptow, W., Maigret, B., Chipot, C., Tarek, M.
Coupled motions between pore and voltage-sensor domains: A model for Shaker B, a voltage-gated potassium channel
BIOPHYSICAL JOURNAL, 87:2365-2379, OCT 2004
abstract,
full text
Tung, C.S., Sanbonmatsu, K.Y.
Atomic model of the Thermus thermophilus 70S ribosome developed in silico
BIOPHYSICAL JOURNAL, 87:2714-2722, OCT 2004
abstract,
full text
Muller, M., Gumbiowski, K., Cherepanov, D.A., Winkler, S., Junge, W., Engelbrecht, S., Panke, O.
Rotary F-1-ATPase - Is the C-terminus of subunit gamma fixed or mobile?
EUROPEAN JOURNAL OF BIOCHEMISTRY, 271:3914-3922, OCT 2004
abstract,
full text
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.
UCSF chimera - A visualization system for exploratory research and analysis
JOURNAL OF COMPUTATIONAL CHEMISTRY, 25:1605-1612, OCT 2004
abstract,
full text
Autenrieth, F., Tajkhorshid, E., Baudry, J., Luthey-Schulten, Z.
Classical force field parameters for the heme prosthetic group of cytochrome c
JOURNAL OF COMPUTATIONAL CHEMISTRY, 25:1613-1622, OCT 2004
abstract,
full text
Kalsotra, A., Turman, C.M., Kikuta, Y., Strobel, H.W.
Expression and characterization of human cytochrome P450 4F11: Putative role in the metabolism of therapeutic drugs and eicosanoids
TOXICOLOGY AND APPLIED PHARMACOLOGY, 199:295-304, SEP 15 2004
abstract,
full text
Chiarini, R., Moran, O., Revoltella, R.P.
Identification of an antigenic domain near the C terminus of human granulocyte-macrophage colony-stimulating factor and its spatial localization
JOURNAL OF BIOLOGICAL CHEMISTRY, 279:37908-37917, SEP 3 2004
abstract,
full text
Lee, G., Nowak, W., Jaroniec, J., Zhang, Q.M., Marszalek, P.E.
Molecular dynamics simulations of forced conformational transitions in 1,6-linked polysaccharides
BIOPHYSICAL JOURNAL, 87:1456-1465, SEP 2004
abstract,
full text
Aksimentiev, A., Heng, J.B., Timp, G., Schulten, K.
Microscopic kinetics of DNA translocation through synthetic nanopores
BIOPHYSICAL JOURNAL, 87:2086-2097, SEP 2004
abstract,
full text,
TCBG publications
Pedersen, A.K., Peters, G.H., Moller, K.B., Iversen, L.F., Kastrup, J.S.
Water-molecule network and active-site flexibility of apo protein tyrosine phosphatase 1B
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 60:1527-1534, SEP 2004
abstract,
full text
Matthey, T., Cickovski, T., Hampton, S., Ko, A., Ma, Q., Nyerges, M., Raeder, T., Slabach, T., Izaguirre, J.A.
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics
ACM TRANSACTIONS ON MATHEMATICAL SOFTWARE, 30:237-265, SEP 2004
abstract,
full text
Yeh, I.C., Hummer, G.
Nucleic acid transport through carbon nanotube membranes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101:12177-12182, AUG 17 2004
abstract,
full text
Glykos, N.M., Kokkindis, M.
Structural polymorphism of a marginally stable 4-alpha-helical bundle. Images of a trapped molten globule?
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 56:420-425, AUG 15 2004
full text
Henin, J., Chipot, C.
Overcoming free energy barriers using unconstrained molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 121:2904-2914, AUG 15 2004
abstract,
full text
Lee, O.S., Saven, J.G.
Simulation studies of a helical m-phenylene ethynylene foldamer
JOURNAL OF PHYSICAL CHEMISTRY B, 108:11988-11994, AUG 12 2004
abstract,
full text
Braun, R., Engelman, D.M., Schulten, K.
Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices
BIOPHYSICAL JOURNAL, 87:754-763, AUG 2004
abstract,
full text,
TCBG publications
Roux, B., Schulten, K.
Computational studies of membrane channels
STRUCTURE, 12:1343-1351, AUG 2004
abstract,
full text,
TCBG publications
Sutherland, J.J., O'Brien, L.A., Lillicrap, D., Weaver, D.F.
Molecular modeling of the von Willebrand factor A2 domain and the effects of associated type 2A von Willebrand disease mutations
JOURNAL OF MOLECULAR MODELING, 10:259-270, AUG 2004
abstract,
full text
Espinoza-Fonseca, L.M.
Base docking model of the homomeric alpha 7 nicotinic receptor-beta-amyloid(1-42) complex
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 320:587-591, JUL 23 2004
abstract,
full text
Pogorelov, T.V., Luthey-Schulten, Z.
Variations in the fast folding rates of the lambda-repressor: A hybrid molecular dynamics study
BIOPHYSICAL JOURNAL, 87:207-214, JUL 2004
abstract,
full text
O'Brien, L.A., Sutherland, J.J., Hegadorn, C., Benford, K., Racz, H., Rapson, D., Hough, C., Lillicrap, D.
A novel type 2A (Group II) von Willebrand disease mutation (L1503Q) associated with loss of the highest molecular weight von Willebrand factor multimers
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 2:1135-1142, JUL 2004
abstract,
full text
Ouellet, J., Perreault, J.P.
Cross-linking experiments reveal the presence of novel structural features between a hepatitis delta virus ribozyme and its substrate
RNA-A PUBLICATION OF THE RNA SOCIETY, 10:1059-1072, JUL 2004
abstract,
full text
Larios, E., Li, J.S., Schulten, K., Kihara, H., Gruebele, M.
Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitin
JOURNAL OF MOLECULAR BIOLOGY, 340:115-125, JUN 25 2004
abstract,
full text,
TCBG publications
Pedretti, A., Silva, M.E., Villa, L., Vistoli, G.
Binding site analysis of full-length alpha(1a) adrenergic receptor using homology modeling and molecular docking
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 319:493-500, JUN 25 2004
abstract,
full text
Espinoza-Fonseca, L.M., Trujillo-Ferrara, J.G.
Exploring the possible binding sites at the interface of triosephosphate isomerase dimer as a potential target for anti-tripanosomal drug design
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 14:3151-3154, JUN 21 2004
abstract,
full text
Gullingsrud, J., Schulten, K.
Lipid bilayer pressure profiles and mechanosensitive channel gating
BIOPHYSICAL JOURNAL, 86:3496-3509, JUN 2004
abstract,
full text,
TCBG publications
Jensen, M.O., Mouritsen, O.G., Peters, G.H.
Simulations of a membrane-anchored peptide: Structure, dynamics, and influence on bilayer properties
BIOPHYSICAL JOURNAL, 86:3556-3575, JUN 2004
abstract,
full text
Ala-Laurila, P., Donner, K., Koskelainen, A.
Thermal activation and photoactivation of visual pigments
BIOPHYSICAL JOURNAL, 86:3653-3662, JUN 2004
abstract,
full text
Kasson, P.M., Pande, V.S.
Molecular dynamics simulation of lipid reorientation at bilayer edges
BIOPHYSICAL JOURNAL, 86:3744-3749, JUN 2004
abstract,
full text
Brito, R.M.M., Dubitzky, W., Rodrigues, J.R.
Protein folding and unfolding simulations: A new challenge for data mining
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, 8:153-166, SUM 2004
abstract,
full text
Garofoli, S., Falconi, M., Desideri, A.
Thermophilicity of wild type and mutant cold shock proteins by molecular dynamics simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 21:771-779, JUN 2004
abstract,
full text
Zhu, H.B., Chun, T.K.Y., Wang, L.Z., Cai, W.T., See, S.
A prototype of distributed molecular visualization on computational grids
FUTURE GENERATION COMPUTER SYSTEMS, 20:727-737, JUN 2004
abstract,
full text
Deng, Y., Glimm, J., Davenport, J.W., Cai, X., Santos, E.
Performance models on QCDOC for molecular dynamics with Coulomb potentials
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 18:183-195, SUM 2004
abstract,
full text
Sternal, K., Czub, J., Baginski, M.
Molecular aspects of the interaction between amphotericin B and a phospholipid bilayer: molecular dynamics studies
JOURNAL OF MOLECULAR MODELING, 10:223-232, JUN 2004
abstract,
full text
Jensen, M.O., Mouritsen, O.G., Peters, G.H.
The hydrophobic effect: Molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces
JOURNAL OF CHEMICAL PHYSICS, 120:9729-9744, MAY 22 2004
abstract,
full text
Boulet, P., Covency, P.V., Stackhouse, S.
Simulation of hydrated Li(+)-, Na(+)- and K(+)-montmorillonite/polymer nanocomposites using large-scale molecular dynamics
CHEMICAL PHYSICS LETTERS, 389:261-267, MAY 11 2004
abstract,
full text
Anishkin, A., Sukharev, S.
Water dynamics and dewetting transitions in the small mechanosensitive channel MscS
BIOPHYSICAL JOURNAL, 86:2883-2895, MAY 2004
abstract,
full text
Cadena, C., Anthony, J.L., Shah, J.K., Morrow, T.I., Brennecke, J.F., Maginn, E.J.
Why is CO2 so soluble in imidazolium-based ionic liquids?
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 126:5300-5308, APR 28 2004
abstract,
full text
Rousseau, R., Kleinschmidt, V., Schmitt, U.W., Marx, D.
Modeling protonated water networks in bacteriorhodopsin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 6:1848-1859, APR 21 2004
abstract,
full text
Nielsen, S.O., Lopez, C.F., Srinivas, G., Klein, M.L.
Coarse grain models and the computer simulation of soft materials
JOURNAL OF PHYSICS-CONDENSED MATTER, 16:R481-R512, APR 21 2004
abstract,
full text
Gronwald, W., Kalbitzer, H.R.
Automated structure determination of proteins by NMR spectroscopy
PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY, 44:33-96, APR 16 2004
full text
Hoyrup, P., Callisen, T.H., Jensen, M.O., Halperin, A., Mouritsen, O.G.
Lipid protrusions, membrane softness, and enzymatic activity
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 6:1608-1615, APR 7 2004
abstract,
full text
Linke, S., Stojkoski, C., Kewley, R.J., Booker, G.W., Whitelaw, M.L., Peet, D.J.
Substrate requirements of the oxygen-sensing asparaginyl hydroxylase factor-inhibiting hypoxia-inducible factor
JOURNAL OF BIOLOGICAL CHEMISTRY, 279:14391-14397, APR 2 2004
abstract,
full text
Huber, T., Botelho, A.V., Beyer, K., Brown, M.F.
Membrane model for the G-protein-coupled receptor rhodopsin: Hydrophobic interface and dynamical structure
BIOPHYSICAL JOURNAL, 86:2078-2100, APR 2004
abstract,
full text
Gursoy, A., Kale, L.V.
Performance and modularity benefits of message-driven execution
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 64:461-480, APR 2004
abstract,
full text
Budi, A., Legge, S., Treutlein, H., Yarovsky, I.
Effect of external stresses on protein conformation: a computer modelling study
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 33:121-129, APR 2004
abstract,
full text
Dromey, J.A., Weenink, S.M., Peters, G.H., Endl, J., Tighe, P.J., Todd, I., Christie, M.R.
Mapping of epitopes for autoantibodies to the type 1 diabetes autoantigen IA-2 by peptide phage display and molecular modeling: Overlap of antibody and T cell determinants
JOURNAL OF IMMUNOLOGY, 172:4084-4090, APR 1 2004
abstract,
full text
Morrissette, N.S., Mitra, A., Sept, D., Sibley, L.D.
Dinitroanilines bind alpha-tubulin to disrupt microtubules
MOLECULAR BIOLOGY OF THE CELL, 15:1960-1968, APR 2004
abstract,
full text
Park, S., Schulten, K.
Calculating potentials of mean force from steered molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 120:5946-5961, APR 1 2004
abstract,
full text,
TCBG publications
Morrow, T.I., Maginn, E.J.
Density, local composition and diffusivity of aqueous choline chloride solutions: a molecular dynamics study
FLUID PHASE EQUILIBRIA, 217:97-104, MAR 10 2004
abstract,
full text
Aksimentiev, A., Balabin, I.A., Fillingame, R.H., Schulten, K.
Insights into the molecular mechanism of rotation in the F-o sector of ATP synthase
BIOPHYSICAL JOURNAL, 86:1332-1344, MAR 2004
abstract,
full text,
TCBG publications
Tan, M.L., Balabin, I., Onuchic, J.N.
Dynamics of electron transfer pathways in cytochrome c oxidase
BIOPHYSICAL JOURNAL, 86:1813-1819, MAR 2004
abstract,
full text
Ikeguchi, M.
Partial rigid-body dynamics in NPT, NPAT and NP gamma T ensembles for proteins and membranes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 25:529-541, MAR 2004
abstract,
full text
Pedretti, A., Villa, L., Vistoli, G.
VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 18:167-173, MAR 2004
abstract,
full text
Mustata, G., Briggs, J.M.
Cluster analysis of water molecules in alanine racemase and their putative structural role
PROTEIN ENGINEERING DESIGN & SELECTION, 17:223-234, MAR 2004
abstract,
full text
Zhang, L.L., Ruan, Q., Zhou, L.X.
Nonlinear indices analyzing method for molecular dynamics of protein dynamical transition
INTERNATIONAL JOURNAL OF MODERN PHYSICS C, 15:351-361, MAR 2004
abstract,
full text
Liu, Z.W., Xu, Y., Saladino, A.C., Wymore, T., Tang, P.
Parametrization of 2-bromo-2-chloro-1,1,1-trifluoroethane (halothane) and hexafluoroethane for nonbonded interactions
JOURNAL OF PHYSICAL CHEMISTRY A, 108:781-786, FEB 5 2004
abstract,
full text
Yeh, I.C., Hummer, G.
Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations
BIOPHYSICAL JOURNAL, 86:681-689, FEB 2004
abstract,
full text
Cohen, J., Schulten, K.
Mechanism of anionic conduction across ClC
BIOPHYSICAL JOURNAL, 86:836-845, FEB 2004
abstract,
full text,
TCBG publications
Tindbaek, N., Svendsen, A., Oestergaard, P.R., Draborg, H.
Engineering a substrate-specific cold-adapted subtilisin
PROTEIN ENGINEERING DESIGN & SELECTION, 17:149-156, FEB 2004
abstract,
full text
Bishop, T.C., Cortez, R., Zhmudsky, O.O.
Investigation of bend and shear waves in a geometrically exact elastic rod model
JOURNAL OF COMPUTATIONAL PHYSICS, 193:642-665, JAN 20 2004
abstract,
full text
Buchete, N.V., Straub, J.E., Thirumalai, D.
Orientation-dependent coarse-grained potentials derived by statistical analysis of molecular structural databases
POLYMER, 45:597-608, JAN 15 2004
abstract,
full text
Mursinna, R.S., Lee, K.W., Briggs, J.M., Martinis, S.A.
Molecular dissection of a critical specificity determinant within the amino acid editing domain of leucyl-tRNA synthetase
BIOCHEMISTRY, 43:155-165, JAN 13 2004
abstract,
full text
Collins, L.A., Mazevet, S., Kress, J.D., Schneider, B.I., Feder, D.L.
Time-dependent simulations of large-scale quantum dynamics
PHYSICA SCRIPTA, T110:408-412, 2004
abstract,
full text
Zhu, F.Q., Tajkhorshid, E., Schulten, K.
Theory and simulation of water permeation in aquaporin-1
BIOPHYSICAL JOURNAL, 86:50-57, JAN 2004
abstract,
full text,
TCBG publications
Lu, S.Q., Long, M.
Forced extension of P-selectin construct using steered molecular dynamics
CHINESE SCIENCE BULLETIN, 49:10-17, JAN 2004
abstract,
full text
Schleif, R.
Modeling and studying proteins with molecular dynamics
NUMERICAL COMPUTER METHODS, PT D, 383:28-47, 2004
full text
Gao, H.J., Kong, Y.
Simulation of DNA-nanotube interactions
ANNUAL REVIEW OF MATERIALS RESEARCH, 34:123-150, 2004
abstract,
full text
Cao, X.L., Mo, Z.Y.
A new scalable parallel method for molecular dynamics based on cell-block data structure
PARALLEL AND DISTRIBUTED PROCESSING AND APPLICATIONS, PROCEEDINGS, 3358:757-764, 2004
abstract,
full text
Yu, J., Ha, T.J., Schulten, K.
Conformational model of the Holliday junction transition deduced from molecular dynamics simulations
NUCLEIC ACIDS RESEARCH, 32:6683-6695, 2004
abstract,
full text,
TCBG publications
Wypychowski, J., Pytlinski, J., Skorwider, L., Nazaruk, M., Benedyczak, K., Wronski, M., Bala, P.
Life sciences grid in EUROGRID and GRIP projects
NEW GENERATION COMPUTING, 22:147-156, 2004
abstract,
full text
Villa, E., Balaeff, A., Mahadevan, L., Schulten, K.
Multiscale method for simulating protein-DNA complexes
MULTISCALE MODELING & SIMULATION, 2:527-553, 2004
abstract,
full text,
TCBG publications
Tai, K.S., Murdock, S., Wu, B., Ng, M.H., Johnston, S., Fangohr, H., Cox, S.J., Jeffreys, P., Essex, J.W., Sansom, M.S.P.
BioSimGrid: towards a worldwide repository for biomolecular simulations
ORGANIC & BIOMOLECULAR CHEMISTRY, 2:3219-3221, 2004
abstract,
full text
Yang, W.Y., Larios, E., Gruebele, M.
On the extended beta-conformation propensity of polypeptides at high temperature
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 125:16220-16227, DEC 31 2003
abstract,
full text
Hoseki, J., Okamoto, A., Takada, N., Suenaga, A., Futatsugi, N., Konagaya, A., Taiji, M., Yano, T., Kuramitsu, S., Kagamiyama, H.
Increased rigidity of domain structures enhances the stability of a mutant enzyme created by directed evolution
BIOCHEMISTRY, 42:14469-14475, DEC 16 2003
abstract,
full text
Gao, M., Craig, D., Lequin, O., Campbell, I.D., Vogel, V., Schulten, K.
Structure and functional significance of mechanically unfolded fibronectin type III1 intermediates
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100:14784-14789, DEC 9 2003
abstract,
full text,
TCBG publications
Jenwitheesuk, E., Samudrala, R.
Identifying inhibitors of the SARS coronavirus proteinase
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 13:3989-3992, NOV 17 2003
abstract,
full text
Jensen, M.O., Tajkhorshid, E., Schulten, K.
Electrostatic tuning of permeation and selectivity in aquaporin water channels
BIOPHYSICAL JOURNAL, 85:2884-2899, NOV 1 2003
abstract,
full text,
TCBG publications
Lu, D.Y., Grayson, P., Schulten, K.
Glycerol conductance and physical asymmetry of the Escherichia coli glycerol facilitator GlpF
BIOPHYSICAL JOURNAL, 85:2977-2987, NOV 1 2003
abstract,
full text,
TCBG publications
Bolhuis, P.G.
Transition-path sampling of beta-hairpin folding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100:12129-12134, OCT 14 2003
abstract,
full text
Frank, M., Gutbrod, P., Hassayoun, C., von der Lieth, C.W.
Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts
JOURNAL OF MOLECULAR MODELING, 9:308-315, OCT 2003
abstract,
full text
Gullingsrud, J., Schulten, K.
Gating of MscL studied by steered molecular dynamics
BIOPHYSICAL JOURNAL, 85:2087-2099, OCT 2003
abstract,
full text,
TCBG publications
Dittrich, M., Hayashi, S., Schulten, K.
On the mechanism of ATP hydrolysis in F(1)-ATPase
BIOPHYSICAL JOURNAL, 85:2253-2266, OCT 2003
abstract,
full text,
TCBG publications
Tarek, M., Maigret, B., Chipot, C.
Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers
BIOPHYSICAL JOURNAL, 85:2287-2298, OCT 2003
abstract,
full text
Mustata, G.I., Soares, T.A., Briggs, J.M.
Molecular dynamics studies of alanine racemase: A structural model for drug design
BIOPOLYMERS, 70:186-200, OCT 2003
abstract,
full text
Likic, V.A., Strehler, E.E., Gooley, P.R.
Dynamics of Ca(2+)-saturated calmodulin D129N mutant studied by multiple molecular dynamics simulations
PROTEIN SCIENCE, 12:2215-2229, OCT 2003
abstract,
full text
Niccolai, N., Spiga, O., Bernini, A., Scarselli, M., Ciutti, A., Fiaschi, I., Chiellini, S., Molinari, H., Temussi, P.A.
NMR studies of protein hydration and TEMPOL accessibility
JOURNAL OF MOLECULAR BIOLOGY, 332:437-447, SEP 12 2003
abstract,
full text
Lamb, H.K., Leslie, K., Dodds, A.L., Nutley, M., Cooper, A., Johnson, C., Thompson, P., Stammers, D.K., Hawkins, A.R.
The negative transcriptional regulator NmrA discriminates between oxidized and reduced dinucleotides
JOURNAL OF BIOLOGICAL CHEMISTRY, 278:32107-32114, AUG 22 2003
abstract,
full text
Park, S., Khalili-Araghi, F., Tajkhorshid, E., Schulten, K.
Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality
JOURNAL OF CHEMICAL PHYSICS, 119:3559-3566, AUG 8 2003
abstract,
full text,
TCBG publications
Asthagiri, D., Pratt, L.R., Ashbaugh, H.S.
Absolute hydration free energies of ions, ion-water clusters, and quasichemical theory
JOURNAL OF CHEMICAL PHYSICS, 119:2702-2708, AUG 1 2003
abstract,
full text
O'Brien, L.A., James, P.D., Othman, M., Berber, E., Cameron, C., Notley, C.R.P., Hegadorn, C.A., Sutherland, J.J., Hough, C., Rivard, G.E., O'Shaunessey, D., Lillicarp, D.
Founder von Willebrand factor haplotype associated with type 1 von Willebrand disease
BLOOD, 102:549-557, JUL 15 2003
abstract,
full text
Bird, L.E., Ren, J., Wright, A., Leslie, K.D., Degreve, B., Balzarini, J., Stammers, D.K.
Crystal structure of varicella zoster virus thymidine kinase
JOURNAL OF BIOLOGICAL CHEMISTRY, 278:24680-24687, JUL 4 2003
abstract,
full text
Zhu, F.Q., Schulten, K.
Water and proton conduction through carbon nanotubes as models for biological channels
BIOPHYSICAL JOURNAL, 85:236-244, JUL 2003
abstract,
full text,
TCBG publications
Grayson, P., Tajkhorshid, E., Schulten, K.
Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics
BIOPHYSICAL JOURNAL, 85:36-48, JUL 2003
abstract,
full text,
TCBG publications
Mozziconacci, J., Victor, J.M.
Nucleosome gaping supports a functional structure for the 30nm chromatin fiber
JOURNAL OF STRUCTURAL BIOLOGY, 143:72-76, JUL 2003
abstract,
full text
Amaro, R., Tajkhorshid, E., Luthey-Schulten, Z.
Developing an energy landscape for the novel function of a (beta/alpha)(8) barrel: Ammonia conduction through HisF
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 100:7599-7604, JUN 24 2003
abstract,
full text
Phillips, S.C., Gledhill, R.J., Essex, J.W., Edge, C.M.
Application of the Hilbert-Huang transform to the analysis of molecular dynamics simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 107:4869-4876, JUN 19 2003
abstract,
full text
Costantino, G., Macchiarulo, A., Entrena-Guadix, A., Camaioni, E., Pellicciari, R.
Binding mode of 6ECDCA, a potent bile acid agonist of the Farnesoid X Receptor (FXR)
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 13:1865-1868, JUN 2 2003
abstract,
full text
Abdali, S., Jensen, M.O., Bohr, H.
Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations
JOURNAL OF PHYSICS-CONDENSED MATTER, 15:S1853-S1860, MAY 14 2003
abstract,
full text
Moran, O., Traverso, S., Elia, L., Pusch, M.
Molecular Modeling of p-chlorophenoxyacetic acid binding to the CLC-0 channels
BIOCHEMISTRY, 42:5176-5185, MAY 13 2003
abstract,
full text
Lesyng, B., Bala, P., Erwin, D.
EUROGRID - European computational grid testbed
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 63:590-596, MAY 2003
abstract,
full text
Bayas, M.V., Schulten, K., Leckband, D.
Forced detachment of the CD2-CD58 complex
BIOPHYSICAL JOURNAL, 84:2223-2233, APR 2003
abstract,
full text,
TCBG publications
Phillips, S.C., Swain, M.T., Wiley, A.P., Essex, J.W., Edge, C.M.
Reversible digitally filtered molecular dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 107:2098-2110, MAR 6 2003
abstract,
full text
Anishkin, A., Gendel, V., Sharifi, N.A., Chiang, C.S., Shirinian, L., Guy, H.R., Sukharev, S.
On the conformation of the COOH-terminal domain of the large mechanosensitive channel MscL
JOURNAL OF GENERAL PHYSIOLOGY, 121:227-244, MAR 2003
abstract,
full text
Jensen, T.R., Jensen, M.O., Reitzel, N., Balashev, K., Peters, G.H., Kjaer, K., Bjornholm, T.
Water in contact with extended hydrophobic surfaces: Direct evidence of weak dewetting
PHYSICAL REVIEW LETTERS, 90: Art. No. 086101, FEB 28 2003
abstract,
full text
Barash, D., Yang, L.J., Qian, X.L., Schlick, T.
Inherent speedup limitations in multiple time step/Particle Mesh Ewald algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 24:77-88, JAN 15 2003
abstract,
full text
Wong, T.C.
Membrane structure of the human immunodeficiency virus gp41 fusion peptide by molecular dynamics simulation II. The glycine mutants
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1609:45-54, JAN 10 2003
abstract,
full text
Nielsen, B.G., Jensen, M.O., Bohr, H.G.
The probability distribution of side-chain conformations in [Leu] and [Met]enkephalin determines the potency and selectivity to mu and delta opiate receptors
BIOPOLYMERS, 71:577-592, 2003
abstract,
full text
Tajkhorshid, E., Aksimentiev, A., Balabin, I., Gao, M., Isralewitz, B., Phillips, J.C., Zhu, F.Q., Schulten, K.
Large scale simulation of protein mechanics and function
PROTEIN SIMULATIONS, 66:195-+, 2003
full text,
TCBG publications
Kale, L.V., Kumar, S., Zheng, G.B., Lee, C.W.
Scaling molecular dynamics to 3000 processors with projections: A performance analysis case study
COMPUTATIONAL SCIENCE - ICCS 2003, PT IV, PROCEEDINGS, 2660:23-32, 2003
abstract,
full text
Pytlinski, J., Skorwider, L., Benedyczak, K., Wronski, M., Bala, P., Huber, V.
Uniform access to the distributed resources for the computational chemistry using UNICORE
COMPUTATIONAL SCIENCE - ICCS 2003, PT II, PROCEEDINGS, 2658:307-315, 2003
abstract,
full text
Bhandarkar, M., Kale, L.V.
An interface model for parallel components
LANGUAGES AND COMPILERS FOR PARALLEL COMPUTING, 2624:209-222, 2003
abstract,
full text
Ma, Q., Izaguirre, J.A., Skeel, R.D.
Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 24:1951-1973, 2003
abstract,
full text
Ma, Q., Izaguirre, J.A.
Targeted mollified impulse: A multiscale stochastic integrator for long molecular dynamics simulations
MULTISCALE MODELING & SIMULATION, 2:1-21, 2003
abstract,
full text
Beaurain, F., Laguerre, M.
MD studies of the DIS/DIS kissing complex solution and x-ray structures
OLIGONUCLEOTIDES, 13:501-514, 2003
abstract,
full text
Teodoro, M.L., Phillips, G.N., Kavraki, L.E.
Understanding protein flexibility through dimensionality reduction
JOURNAL OF COMPUTATIONAL BIOLOGY, 10:617-634, 2003
abstract,
full text
Kaneko, W., Nomoto, A., Watanabe, Y., Nakamura, S., Shimizu, K.
Design and implementation of a parallel programming environment based on distributed shared arrays
HIGH PERFORMANCE COMPUTING, 2858:402-411, 2003
abstract,
full text
Matthey, T., Ko, A., Izaguirre, J.A.
PROTOMOL: A molecular dynamics research framework for algorithmic development
COMPUTATIONAL SICENCE - ICCS 2003, PT III, PROCEEDINGS, 2659:50-59, 2003
abstract,
full text
DeSouza, J., Kale, L.V.
Jade: A parallel message-driven Java
COMPUTATIONAL SICENCE - ICCS 2003, PT III, PROCEEDINGS, 2659:760-769, 2003
abstract,
full text
Skeel, R.D., Izaguirre, J.A.
An impulse integrator for Langevin dynamics
MOLECULAR PHYSICS, 100:3885-3891, DEC 20 2002
abstract,
full text
Morrow, T.I., Maginn, E.J.
Molecular dynamics study of the ionic liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate
JOURNAL OF PHYSICAL CHEMISTRY B, 106:12807-12813, DEC 12 2002
abstract,
full text
Tang, P., Xu, Y.
Large-scale molecular dynamics simulations of general anesthetic effects on the ion channel in the fully hydrated membrane: The implication of molecular mechanisms of general anesthesia
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99:16035-16040, DEC 10 2002
abstract,
full text
Saam, J., Tajkhorshid, E., Hayashi, S., Schulten, K.
Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin
BIOPHYSICAL JOURNAL, 83:3097-3112, DEC 2002
abstract,
full text,
TCBG publications
Gao, M., Wilmanns, M., Schulten, K.
Steered molecular dynamics studies of titin I1 domain unfolding
BIOPHYSICAL JOURNAL, 83:3435-3445, DEC 2002
abstract,
full text,
TCBG publications
Zhang, L.L., Zhang, J.H., Zhou, L.X.
Dynamical transition of myoglobin and Cu/Zn superoxide dismutase revealed by molecular dynamics simulation
CHINESE PHYSICS LETTERS, 19:1788-1791, DEC 2002
abstract,
full text
Mustata, G.I., Briggs, J.M.
A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 16:935-953, DEC 2002
abstract,
full text
Gao, M., Craig, D., Vogel, V., Schulten, K.
Identifying unfolding intermediates of FN-III10 by steered molecular dynamics
JOURNAL OF MOLECULAR BIOLOGY, 323:939-950, NOV 8 2002
abstract,
full text,
TCBG publications
Lupo, J.A., Wang, Z.Q., McKenney, A.M., Pachter, R., Mattson, W.
A large scale molecular dynamics simulation code using the fast multipole algorithm (FMD): performance and application
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 21:89-99, OCT 2002
abstract,
full text
Rothbard, J.B., Kreider, E., Vandeusen, C.L., Wright, L., Wylie, B.L., Wender, P.A.
Arginine-rich molecular transporters for drug delivery: Role of backbone spacing in cellular uptake
JOURNAL OF MEDICINAL CHEMISTRY, 45:3612-3618, AUG 15 2002
abstract,
full text
Zhu, F.Q., Tajkhorshid, E., Schulten, K.
Pressure-induced water transport in membrane channels studied by molecular dynamics
BIOPHYSICAL JOURNAL, 83:154-160, JUL 2002
abstract,
full text,
TCBG publications
Thomas, W.E., Trintchina, E., Forero, M., Vogel, V., Sokurenko, E.V.
Bacterial adhesion to target cells enhanced by shear force
CELL, 109:913-923, JUN 28 2002
abstract,
full text
Yeh, I.C., Hummer, G.
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 124:6563-6568, JUN 12 2002
abstract,
full text
Jensen, M.O., Park, S., Tajkhorshid, E., Schulten, K.
Energetics of glycerol conduction through aquaglyceroporin GlpF
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99:6731-6736, MAY 14 2002
abstract,
full text,
TCBG publications
Skeel, R.D., Tezcan, I., Hardy, D.J.
Multiple grid methods for classical molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 23:673-684, APR 30 2002
abstract,
full text
Tajkhorshid, E., Nollert, P., Jensen, M.O., Miercke, L.J.W., O'Connell, J., Stroud, R.M., Schulten, K.
Control of the selectivity of the aquaporin water channel family by global orientational tuning
SCIENCE, 296:525-530, APR 19 2002
abstract,
full text,
TCBG publications
Lakshminarasimhulu, P., Madura, J.D.
A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape
COMPUTER PHYSICS COMMUNICATIONS, 144:141-153, APR 1 2002
abstract,
full text
Kosztin, I., Bruinsma, R., O'Lague, P., Schulten, K.
Mechanical force generation by G proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 99:3575-3580, MAR 19 2002
abstract,
full text,
TCBG publications
Damjanovic, A., Kosztin, I., Kleinekathofer, U., Schulten, K.
Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study
PHYSICAL REVIEW E, 65: Art. No. 031919, MAR 2002
abstract,
full text,
TCBG publications
Krammer, A., Craig, D., Thomas, W.E., Schulten, K., Vogel, V.
A structural model for force regulated integrin binding to fibronectin's RGD-synergy site
MATRIX BIOLOGY, 21:139-147, MAR 2002
abstract,
full text,
TCBG publications
Mazevet, S., Collins, L.A., Kress, J.D.
Evolution of ultracold neutral plasmas
PHYSICAL REVIEW LETTERS, 88: Art. No. 055001, FEB 4 2002
abstract,
full text
Huber, T., Rajamoorthi, K., Kurze, V.F., Beyer, K., Brown, M.F.
Structure of docosahexaenoic acid-containing phospholipid bilayers as studied by H-2 NMR and molecular dynamics simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 124:298-309, JAN 16 2002
abstract,
full text
Gao, M., Lu, H., Schulten, K.
Unfolding of titin domains studied by molecular dynamics simulations
JOURNAL OF MUSCLE RESEARCH AND CELL MOTILITY, 23:513-521, 2002
abstract,
full text,
TCBG publications
Braun, R., Sarikaya, M., Schulten, K.
Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics
JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION, 13:747-757, 2002
abstract,
full text,
TCBG publications
Skeel, R.D., Hardy, D.J.
Practical construction of modified Hamiltonians
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 23:1172-1188, DEC 18 2001
abstract,
full text
Gumbiowski, K., Cherepanov, D., Muller, M., Panke, O., Promto, P., Winkler, S., Junge, W., Engelbrecht, S.
F-ATPase: Forced full rotation of the rotor despite covalent cross-link with the stator
JOURNAL OF BIOLOGICAL CHEMISTRY, 276:42287-42292, NOV 9 2001
abstract,
full text
Jensen, M.O., Tajkhorshid, E., Schulten, K.
The mechanism of glycerol conduction in aquaglyceroporins
STRUCTURE, 9:1083-1093, NOV 2001
abstract,
full text,
TCBG publications
Dixit, S.B., Chipot, C.
Can absolute free energies of association be estimated from molecular mechanical simulations? The biotin-streptavidin system revisited
JOURNAL OF PHYSICAL CHEMISTRY A, 105:9795-9799, OCT 25 2001
abstract,
full text
Gao, M., Lu, H., Schulten, K.
Simulated refolding of stretched titin immunoglobulin domains
BIOPHYSICAL JOURNAL, 81:2268-2277, OCT 2001
abstract,
full text,
TCBG publications
Koumanov, A., Karshikoff, A., Friis, E.P., Borchert, T.V.
Conformational averaging in pK calculations: Improvement and limitations in prediction of ionization properties of proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 105:9339-9344, SEP 27 2001
abstract,
full text
Zhu, F.Q., Tajkhorshid, E., Schulten, K.
Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer
FEBS LETTERS, 504:212-218, AUG 31 2001
abstract,
full text,
TCBG publications
Cherepanov, D.A., Mulkidjanian, A.Y.
Proton transfer in Azotobacter vinelandii ferredoxin I: entatic Lys84 operates as elastic counterbalance for the proton-carrying Asp15
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1505:179-184, JUN 1 2001
abstract,
full text
Gullingsrud, J., Kosztin, D., Schulten, K.
Structural determinants of MscL gating studied by molecular dynamics simulations
BIOPHYSICAL JOURNAL, 80:2074-2081, MAY 2001
abstract,
full text,
TCBG publications
Baudry, J., Tajkhorshid, E., Molnar, F., Phillips, J., Schulten, K.
Molecular dynamics study of bacteriorhodopsin and the purple membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 105:905-918, FEB 8 2001
abstract,
full text,
TCBG publications
Izaguirre, J.A., Catarello, D.P., Wozniak, J.M., Skeel, R.D.
Langevin stabilization of molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 114:2090-2098, FEB 1 2001
abstract,
full text
Elmer, S., Pande, V.S.
A new twist on the helix-coil transition: A non-biological helix with protein-like intermediates and traps
JOURNAL OF PHYSICAL CHEMISTRY B, 105:482-485, JAN 18 2001
abstract,
full text
Straatsma, T.P., McCammon, J.A.
Load balancing of molecular dynamics simulation with NWChem
IBM SYSTEMS JOURNAL, 40:328-341, 2001
abstract,
full text
Bhandarkar, M., Kale, L.V., de Sturler, E., Hoeflinger, J.
Adaptive load balancing for MPI programs
COMPUTATIONAL SCIENCE -- ICCS 200, PROCEEDINGS PT 2, 2074:108-117, 2001
abstract,
full text
Isralewitz, B., Baudry, J., Gullingsrud, J., Kosztin, D., Schulten, K.
Steered molecular dynamics investigations of protein function
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 19:13-25, 2001
abstract,
full text,
TCBG publications
Wang, Z.Q., Lupo, J.A., Patnaik, S., Pachter, R.
Large scale molecular dynamics simulations of a 4-n-pentyl-4 '-cyanobiphenyl (5CB) liquid crystalline model in the bulk and as a droplet
COMPUTATIONAL AND THEORETICAL POLYMER SCIENCE, 11:375-387, 2001
abstract,
full text
Bhandarkar, M.A., Kale, L.V.
A parallel framework for explicit FEM
HIGH PERFORMANCE COMPUTING - HIPC 2000, PROCEEDINGS, 1970:385-394, 2001
abstract,
full text
Xu, D., Xu, Y., Uberbacher, E.C.
Computational Tools For Protein Modeling
CURRENT PROTEIN & PEPTIDE SCIENCE, 1:1-21, JUL 2000
abstract,
full text
Heffelfinger, G.S.
Parallel atomistic simulations
COMPUTER PHYSICS COMMUNICATIONS, 128:219-237, JUN 2000
abstract,
full text
Heath, M.T., Dick, W.A.
Virtual prototyping of solid propellant rockets
COMPUTING IN SCIENCE & ENGINEERING, 2:21-32, MAR-APR 2000
abstract,
full text
Bryant, Z., Pande, V.S., Rokhsar, D.S.
Mechanical unfolding of a beta-hairpin using molecular dynamics
BIOPHYSICAL JOURNAL, 78:584-589, FEB 2000
abstract,
full text
Schlick, T., Skeel, R.D., Brunger, A.T., Kale, L.V., Board, J.A., Hermans, J., Schulten, K.
Algorithmic challenges in computational molecular biophysics
JOURNAL OF COMPUTATIONAL PHYSICS, 151:9-48, MAY 1 1999
abstract,
full text,
TCBG publications