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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:

http://www.ks.uiuc.edu/Research/namd/

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

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

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Journal of Computational Chemistry, 28:2618-2640, 2007. abstract, journal

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. Submitted to IBM Journal of Research and Development. 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, postscript

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.

1232 citations found March 26, 2009.

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

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

Vakhrushev, A.V., Suyetin, M.V.
Methane storage in bottle-like nanocapsules
NANOTECHNOLOGY, 20: Art. No. 125602, MAR 25 2009
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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
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Hashem, Y., Auffinger, P.
A short guide for molecular dynamics simulations of RNA systems
METHODS, 47:187-197, MAR 2009
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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
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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
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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
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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
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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
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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

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
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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
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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
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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

Poghosyan, A.H., Shahinyan, A.A.
A new parameter for validation molecular dynamics simulation (MD) data
COMPUTER PHYSICS COMMUNICATIONS, 180:238-240, FEB 2009
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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
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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
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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
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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
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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
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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
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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
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Rodriguez, J., Elola, M.D.
Encapsulation of Small Ionic Molecules within alpha-Cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 113:1423-1428, FEB 5 2009
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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

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
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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

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
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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
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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

Miao, Y.L., Ortoleva, P.J.
Molecular Dynamics/Order Parameter Extrapolation for Bionanosystem Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:423-437, FEB 2009
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Petridis, L., Smith, J.C.
A Molecular Mechanics Force Field for Lignin
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:457-467, FEB 2009
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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
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Jena, B.P.
Understanding Membrane Fusion: Combining Experimental and Simulation Studies
METHODS IN NANO CELL BIOLOGY, 90:183-+, 2008
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Goldsmith, J., Martens, C.C.
Pressure-induced water flow through model nanopores
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 11:528-533, 2009
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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
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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
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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
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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
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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
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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
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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
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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

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

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

Alexiadis, A., Kassinos, S.
Molecular Simulation of Water in Carbon Nanotubes
CHEMICAL REVIEWS, 108:5014-5034, DEC 2008
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

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

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

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

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

Orlowski, S., Nowak, W.
Topology and thermodynamics of gaseous ligands diffusion paths in human neuroglobin
BIOSYSTEMS, 94:263-266, DEC 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

Rodriguez, Y., Mezei, M., Osman, R.
The PT1-Ca2+ Gla Domain Binds to a Membrane through Two Dipalmitoylphosphatidylserines. A Computational Study
BIOCHEMISTRY, 47:13267-13278, DEC 16 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

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

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

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

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

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

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

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][EtSO4]) 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Chen, L.Y.
Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 144113, OCT 14 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Luan, B., Aksimentiev, A.
Strain softening in stretched DNA
PHYSICAL REVIEW LETTERS, 101: Art. No. 118101, SEP 12 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

Noza-Fonseca, L.M.E., 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

Ziatev, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

White, S.H., von Heijne, G.
How translocons select transmembrane helices
ANNUAL REVIEW OF BIOPHYSICS, 37:23-42, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

Alexiadis, A., Kassinos, S.
Molecular dynamic simulations of carbon nanotubes in CO2 atmosphere
CHEMICAL PHYSICS LETTERS, 460:512-516, JUL 30 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

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

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

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

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

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

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

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

Eshet, H., Bruneval, F., Parrinello, M.
New Lennard-Jones metastable phase
JOURNAL OF CHEMICAL PHYSICS, 129: Art. No. 026101, JUL 14 2008
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

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)/SM0.6-x/Chol(0.4) planar bilayers supported on SiO2 surfaces
CHEMICAL PHYSICS LETTERS, 460:289-294, JUL 20 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

Zhmakin, A.I.
Physical aspects of cryobiology
PHYSICS-USPEKHI, 51:231-252, MAR 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

I.s.k.a.n.d.a.r.s.y.a.h., 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Sotomayor, M., Schulten, K.
The allosteric role of the Ca2+ switch in adhesion and elasticity of C-cadherin
BIOPHYSICAL JOURNAL, 94:4621-4633, JUN 15 2008
abstract, full text

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

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

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

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

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

DeMarco, M.L., Woods, R.J.
Structural glycobiology: A game of snakes and ladders
GLYCOBIOLOGY, 18:426-440, JUN 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Yang, S., Roux, B.
Src kinase conformational activation: Thermodynamics, pathways, and mechanisms
PLOS COMPUTATIONAL BIOLOGY, 4: Art. No. e1000047, MAR 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Alexiadis, A., Kassinos, S.
The density of water in carbon nanotubes
CHEMICAL ENGINEERING SCIENCE, 63:2047-2056, APR 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Rodriuez-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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Kowadlo, G., Hall, N.E., Burgess, A.W.
De novo design of beta-helical polypeptides
GROWTH FACTORS, 25:168-190, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Gumbart, J., Schulten, K.
Structural determinants of lateral gate opening in the protein translocon
BIOCHEMISTRY, 46:11147-11157, OCT 2 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

De Fabritiis, G.
Performance of the Cell processor for biomolecular simulations
COMPUTER PHYSICS COMMUNICATIONS, 176:660-664, 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

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

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

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

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

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

Wang, B.Y., Kral, P.
Chemically tunable nanoscale propellers of liquids
PHYSICAL REVIEW LETTERS, 98: Art. No. 266102, JUN 29 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

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

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

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

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

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

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

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

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

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

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

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

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

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

Bulo, R.E., Donadio, D., Laio, A., Molnar, F., Rieger, J., Parrinello, M.
"Site binding" of Ca2+ ions to polyacrylates in water: A molecular dynamics study of coiling and aggregation
MACROMOLECULES, 40:3437-3442, MAY 1 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

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

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

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

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

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

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

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

Sotomayor, M., Schulten, K.
Single-molecule experiments in vitro and in silico
SCIENCE, 316:1144-1148, MAY 25 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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., 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

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

Allen, M.P.
Educational aspects of molecular simulation
MOLECULAR PHYSICS, 105:157-166, JAN-FEB 2007
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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Zanuy, D., Aleman, C.
Molecular dynamics study of complexes of poly(glutamate) and dodecyltrimethylammonium
BIOMACROMOLECULES, 8:663-671, FEB 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Treptow, W., Tarek, M.
Molecular restraints in the permeation pathway of ion channels
BIOPHYSICAL JOURNAL, 91:L26-L28, AUG 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

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

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

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

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

Henin, J., Chipot, C.
Hydrogen-bonding patterns of cholesterol in lipid membranes
CHEMICAL PHYSICS LETTERS, 425:329-335, JUL 10 2006
abstract, full text

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

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

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

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

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

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

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

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

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

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

Lyman, E., Zuckerman, D.M.
Ensemble-based convergence analysis of biomolecular trajectories
BIOPHYSICAL JOURNAL, 91:164-172, JUL 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Lagerqvist, J., Zwolak, M., Di Ventra, M.
Fast DNA sequencing via transverse electronic transport
NANO LETTERS, 6:779-782, APR 2006
abstract, full text

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

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

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

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

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

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

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

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

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

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

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

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

Spijker, P., Vaidehi, N., Freddolino, P.L., Hilbers, P.A.J., Goddard, W.A.