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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

Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Terry Jones, Laxmikant V. Kale, and James C.Phillips.
Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6.
In Proceedings of the 2012 ACM/IEEE Conference on Supercomputing (SC12), 2012.
abstract, conference

Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kale, James C.Phillips, and Chris Harrison.
Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime.
In Proceedings of the 2011 ACM/IEEE Conference on Supercomputing (SC11), 2011.
abstract, conference

Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell, Jr., Klaus Schulten, and Benoit Roux.
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD.
J. Phys. Chem. Lett., Vol. 2, pp. 87-92, 2011.
abstract, journal

Abhinav Bhatele, Laxmikant V. Kale and Sameer Kumar.
Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications.
In Proceedings of 23rd ACM International Conference on Supercomputing (ICS), 2009.
abstract

James C. Phillips, John E. Stone, and Klaus Schulten.
Adapting a message-driven parallel application to GPU-accelerated clusters.
In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC08), 2008.
abstract, conference

Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale.
Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms.
In Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008.
abstract

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

Klaus Schulten, James C. Phillips, Laxmikant V. Kale, Abhinav Bhatele.
Biomolecular modeling in the era of petascale computing.
In Petascale Computing: Algorithms and Applications, pp. 165-181, D. Bader, Ed., Chapman & Hall / CRC Press, New York, 2008.
abstract

Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, and Laxmikant V. Kale.
Scalable Molecular Dynamics with NAMD on Blue Gene/L.
IBM Journal of Research and Development, Volume 52, No. 1/2, 2007.
abstract

K.Y. Sanbonmatsu and C.-S. Tung.
High performance computing in biology: Multimillion atom simulations of nanoscale systems.
Journal of Structural Biology, 157:470-480, 2007.
journal

Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus Schulten.
Managing biomolecular simulations in a grid environment with NAMD-G.
Proceedings of the 2006 TeraGrid Conference, 2006. In Press.
abstract

Sameer Kumar, Chao Huang, Gheorghe Almasi, and Laxmikant V. Kale.
Achieving Strong Scaling with NAMD on Blue Gene/L.
Proceedings of IEEE International Parallel & Distributed Processing Symposium 2006, 2006.
abstract

Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng.
Biomolecular modeling using parallel supercomputers.
In S. Aluru, editor, Handbook of computational molecular biology, pp. 34.1-34.43. Taylor and Francis, 2005.
abstract

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten.
Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal

Joachim Hein, Fiona Reid, Lorna Smith, Ian Bush, Martyn Guest, and Paul Sherwood.
On the performance of molecular dynamics applications on current high-end systems.
Phil. Trans. R. Soc. A, 363:1987-1998, 2005.
journal

James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kalé.
NAMD: Biomolecular Simulation on Thousands of Processors.
Proceedings of the IEEE/ACM SC2002 Conference. IEEE Press, 2002. Technical Paper 277.
abstract, pdf

Robert K. Brunner, James C. Phillips, Laxmikant V. Kalé.
Scalable Molecular Dynamics for Large Biomolecular Systems.
Proceedings of the IEEE/ACM SC2000 Conference. IEEE Press, 2000. Technical Paper 271.
abstract, pdf

R. Sharma, M. Zeller, V. I. Pavlovic, T. S. Huang, Z. Lo, S. Chu, Y. Zhao, J. Phillips, and K. Schulten.
Speech/Gesture Interface to a Visual Computing Environment.
IEEE Computer Graphics and Applications, March/April 2000, 29-37.
abstract,

Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten.
NAMD2: Greater scalability for parallel molecular dynamics.
Journal of Computational Physics, 151:283-312, 1999.
abstract

Robert Brunner, Laxmikant Kalé, and James Phillips.
Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code.
In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.

James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten.
Avoiding algorithmic obfuscation in a message-driven parallel MD code.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, 4:472-482, 1999. Springer-Verlag.
abstract

L. V. Kalé, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki.
NAMD: A Case Study in Multilingual Parallel Programming.
In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert D. Skeel, and Klaus Schulten.
NAMD-A parallel, object-oriented molecular dynamics program.
International Journal of Supercomputer Applications and High Performance Computing, 10:251-268, 1996.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
Computational Physics Communications, 91:111-134, 1995.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kalé, Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
In S.N. Atluri, G. Yagawa, and T.A. Cruse, editors, Computational Mechanics 95, volume 1, pages 476-481, 1995.
abstract

Papers Citing NAMD

The "full text" links lead to Google Scholar searches for the article. We do not provide copies of these articles ourselves. Articles by TCBG members are available in the TCBG Publications Database.

3907 citations found May 25, 2013.

GhattyVenkataKrishna, P.K., Chavali, N., Uberbacher, E.C.
Flexibility of active-site gorge aromatic residues and non-gorge aromatic residues in acetylcholinesterase
CHEMICAL PAPERS, 67:677-681, JUL 2013
abstract, full text

Polyakov, A.Y., Lyutyy, T.V., Denisov, S., Reva, V.V., Hanggi, P.
Large-scale ferrofluid simulations on graphics processing units
COMPUTER PHYSICS COMMUNICATIONS, 184:1483-1489, JUN 2013
abstract, full text

Geng, W.H., Jacob, F.
A GPU-accelerated direct-sum boundary integral Poisson-Boltzmann solver
COMPUTER PHYSICS COMMUNICATIONS, 184:1490-1496, JUN 2013
abstract, full text

Jin, H.B., Kang, Y., Zhang, J., Wu, T., Wang, Q.
Interaction between tissue-type plasminogen activator and ligands grafted onto hydrogel
MOLECULAR SIMULATION, 39:513-520, MAY 1 2013
abstract, full text

Lejal, N., Tarus, B., Bouguyon, E., Chenavas, S., Bertho, N., Delmas, B., Ruigrok, R.W.H., Di Primo, C., Slama-Schwok, A.
Structure-Based Discovery of the Novel Antiviral Properties of Naproxen against the Nucleoprotein of Influenza A Virus
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 57:2231-2242, MAY 2013
abstract, full text

Vilos, C., Morales, F.A., Solar, P.A., Herrera, N.S., Gonzalez-Nilo, F.D., Aguayo, D.A., Mendoza, H.L., Comer, J., Bravo, M.L., Gonzalez, P.A., Kato, S., Cuello, M.A., Alonso, C., Bravo, E.J., Bustamante, E.I., Owen, G.I., Velasquez, L.A.
Paclitaxel-PHBV nanoparticles and their toxicity to endometrial and primary ovarian cancer cells
BIOMATERIALS, 34:4098-4108, MAY 2013
abstract, full text

Ozcan, A., Olmez, E.O., Alakent, B.
Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:788-804, MAY 2013
abstract, full text

Ermakova, E., Miller, M.C., Nesmelova, I.V., Lopez-Merino, L., Berbis, M.A., Nesmelov, Y., Tkachev, Y.V., Lagartera, L., Daragan, V.A., Andre, S., Canada, F.J., Jimenez-Barbero, J., Solis, D., Gabius, H.J., Mayo, K.H.
Lactose binding to human galectin-7 (p53-induced gene 1) induces long-range effects through the protein resulting in increased dimer stability and evidence for positive cooperativity
GLYCOBIOLOGY, 23:508-523, MAY 2013
abstract, full text

Florian, P.E., Macovei, A., Lazar, C., Milac, A.L., Sokolowska, I., Darie, C.C., Evans, R.W., Roseanu, A., Branza-Nichita, N.
Characterization of the anti-HBV activity of HLP123, a human lactoferrin-derived peptide
JOURNAL OF MEDICAL VIROLOGY, 85:780-788, MAY 2013
abstract, full text

Hofmeyer, T., Schmelz, S., Degiacomi, M.T., Dal Peraro, M., Daneschdar, M., Scrima, A., van den Heuvel, J., Heinz, D.W., Kolmar, H.
Arranged Sevenfold: Structural Insights into the C-Terminal Oligomerization Domain of Human C4b-Binding Protein
JOURNAL OF MOLECULAR BIOLOGY, 425:1302-1317, APR 26 2013
abstract, full text

McCullagh, M., Voth, G.A.
Unraveling the Role of the Protein Environment for [FeFe]-Hydrogenase: A New Application of Coarse-Graining
JOURNAL OF PHYSICAL CHEMISTRY B, 117:4062-4071, APR 18 2013
abstract, full text

Amaral, M., Levy, C., Heyes, D.J., Lafite, P., Outeiro, T.F., Giorgini, F., Leys, D., Scrutton, N.S.
Structural basis of kynurenine 3-monooxygenase inhibition
NATURE, 496:382-+, APR 18 2013
abstract, full text

Fontani, G., Gaspari, R., Spencer, N.D., Passerone, D., Crockett, R.
Adsorption and Friction Behavior of Amphiphilic Polymers on Hydrophobic Surfaces
LANGMUIR, 29:4760-4771, APR 16 2013
abstract, full text

Li, N., Mao, D.B., Lu, S.Q., Tong, C.F., Zhang, Y., Long, M.
Distinct Binding Affinities of Mac-1 and LFA-1 in Neutrophil Activation
JOURNAL OF IMMUNOLOGY, 190:4371-4381, APR 15 2013
abstract, full text

Yu, S., Huang, H., Iliuk, A., Wang, W.H., Jayasundera, K.B., Tao, W.A., Post, C.B., Geahlen, R.L.
Syk Inhibits the Activity of Protein Kinase A by Phosphorylating Tyrosine 330 of the Catalytic Subunit
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:10870-10881, APR 12 2013
abstract, full text

Fan, J., Saunders, M.G., Haddadian, E.J., Freed, K.F., De La Cruz, E.M., Voth, G.A.
Molecular Origins of Cofilin-Linked Changes in Actin Filament Mechanics
JOURNAL OF MOLECULAR BIOLOGY, 425:1225-1240, APR 12 2013
abstract, full text

Vashisth, H., Skiniotis, G., Brooks, C.L.
Enhanced Sampling and Overfitting Analyses in Structural Refinement of Nucleic Acids into Electron Microscopy Maps
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3738-3746, APR 11 2013
abstract, full text

Stock, L., Delemotte, L., Carnevale, V., Treptow, W., Klein, M.L.
Conduction in a Biological Sodium Selective Channel
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3782-3789, APR 11 2013
abstract, full text

Zhao, L., Li, W.Z., Tian, P.
Reconciling Mediating and Slaving Roles of Water in Protein Conformational Dynamics
PLOS ONE, 8: Art. No. e60553, APR 11 2013
abstract, full text

Zimbron, J.M., Heinisch, T., Schmid, M., Hamels, D., Nogueira, E.S., Schirmer, T., Ward, T.R.
A Dual Anchoring Strategy for the Localization and Activation of Artificial Metalloenzymes Based on the Biotin-Streptavidin Technology
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:5384-5388, APR 10 2013
abstract, full text

Kumar, E.A., Chen, Q.Y., Kizhake, S., Kolar, C., Kang, M., Chang, C.E.A., Borgstahl, G.E.O., Natarajan, A.
The paradox of conformational constraint in the design of Cbl(TKB)-binding peptides
SCIENTIFIC REPORTS, 3: Art. No. 1639, APR 10 2013
abstract, full text

Liu, Y., Esser, L., Interlandi, G., Kisiela, D.I., Tchesnokova, V., Thomas, W.E., Sokurenko, E., Xia, D., Savarino, S.J.
Tight Conformational Coupling between the Domains of the Enterotoxigenic Escherichia coli Fimbrial Adhesin CfaE Regulates Binding State Transition
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:9993-10001, APR 5 2013
abstract, full text

Shkurti, A., Orsi, M., Macii, E., Ficarra, E., Acquaviva, A.
Acceleration of coarse grain molecular dynamics on GPU architectures
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:803-818, APR 5 2013
abstract, full text

Nowosielski, M., Hoffmann, M., Kuron, A., Korycka-Machala, M., Dziadek, J.
The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics dagger
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:750-756, APR 5 2013
abstract, full text

Gao, J.K., Shi, W.J., Ye, J., Wang, X.Q., Hirao, H., Zhao, Y.
QM/MM Modeling of Environmental Effects on Electronic Transitions of the FMO Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3488-3495, APR 4 2013
abstract, full text

Neumann, A., Baginski, M., Winczewski, S., Czub, J.
The Effect of Sterols on Amphotericin B Self-Aggregation in a Lipid Bilayer as Revealed by Free Energy Simulations
BIOPHYSICAL JOURNAL, 104:1485-1494, APR 2 2013
abstract, full text

Janosi, L., Ceccarelli, M.
The Gating Mechanism of the Human Aquaporin 5 Revealed by Molecular Dynamics Simulations
PLOS ONE, 8: Art. No. e59897, APR 2 2013
abstract, full text

Felix, J., Elegheert, J., Gutsche, I., Shkumatov, A.V., Wen, Y.R., Bracke, N., Pannecoucke, E., Vandenberghe, I., Devreese, B., Svergun, D.I., Pauwels, E., Vergauwen, B., Savvides, S.N.
Human IL-34 and CSF-1 Establish Structurally Similar Extracellular Assemblies with Their Common Hematopoietic Receptor
STRUCTURE, 21:528-539, APR 2 2013
abstract, full text

Plummer, A., Thompson, M.K., Franzen, S.
Role of Polarity of the Distal Pocket in the Control of Inhibitor Binding in Dehaloperoxidase-Hemoglobin
BIOCHEMISTRY, 52:2218-2227, APR 2 2013
abstract, full text

Emileh, A., Tuzer, F., Yeh, H., Umashankara, M., Moreira, D.R.M., LaLonde, J.M., Bewley, C.A., Abrams, C.F., Chaiken, I.M.
A Model of Peptide Triazole Entry Inhibitor Binding to HIV-1 gp120 and the Mechanism of Bridging Sheet Disruption
BIOCHEMISTRY, 52:2245-2261, APR 2 2013
abstract, full text

Longhi, G., Ceselli, A., Fornili, S.L., Abbate, S., Ceraulo, L., Liveri, V.T.
Molecular dynamics of electrosprayed water nanodroplets containing sodium bis(2-ethylhexyl)sulfosuccinate
JOURNAL OF MASS SPECTROMETRY, 48:478-486, APR 2013
abstract, full text

Patmanidis, I., Glykos, N.M.
As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 41:68-71, APR 2013
abstract, full text

Pietra, F.
On the Pathways of Biologically Relevant Diatomic Gases through Proteins. Dioxygen and Heme Oxygenase from the Perspective of Molecular Dynamics
CHEMISTRY & BIODIVERSITY, 10:556-568, APR 2013
abstract, full text

Azcune, I., Balentova, E., Sagartzazu-Aizpurua, M., Santos, J.I., Miranda, J.I., Fratila, R.M., Aizpurua, J.M.
Modulating Lectin Inhibition with N-Glycosyl-1,2,3-triazole Scaffolds
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 12, 2434-2444, APR 2013
abstract, full text

Roberts, M.L., Kino, T., Nicolaides, N.C., Hurt, D.E., Katsantoni, E., Sertedaki, A., Komianou, F., Kassiou, K., Chrousos, G.P., Charmandari, E.
A Novel Point Mutation in the DNA-Binding Domain (DBD) of the Human Glucocorticoid Receptor Causes Primary Generalized Glucocorticoid Resistance by Disrupting the Hydrophobic Structure of its DBD
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM, 98:E790-E795, APR 2013
abstract, full text

Gordon, D., Chen, R., Chung, S.H.
COMPUTATIONAL METHODS OF STUDYING THE BINDING OF TOXINS FROM VENOMOUS ANIMALS TO BIOLOGICAL ION CHANNELS: THEORY AND APPLICATIONS
PHYSIOLOGICAL REVIEWS, 93:767-802, APR 2013
abstract, full text

Shi, J.P., Zhao, J., Yang, F., Wang, J.P.
Femtosecond Two-Dimensional Infrared Spectroscopy of N-Ethypropionamide
ACTA PHYSICO-CHIMICA SINICA, 29:695-700, APR 2013
abstract, full text

Nevidimov, A.V., Razumov, V.F.
Molecular dynamics simulation of reverse micelles: A search for the most efficient strategy
COLLOID JOURNAL, 75:191-197, APR 2013
abstract, full text

Mahmood, M.I., Liu, X.L., Neya, S., Hoshino, T.
Influence of Lipid Composition on the Structural Stability of G-Protein Coupled Receptor
CHEMICAL & PHARMACEUTICAL BULLETIN, 61:426-437, APR 2013
abstract, full text

Krammer, E.M., Homble, F., Prevost, M.
Molecular origin of VDAC selectivity towards inorganic ions: A combined molecular and Brownian dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:1284-1292, APR 2013
abstract, full text

Pronk, S., Pall, S., Schulz, R., Larsson, P., Bjelkmar, P., Apostolov, R., Shirts, M.R., Smith, J.C., Kasson, P.M., van der Spoel, D., Hess, B., Lindahl, E.
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
BIOINFORMATICS, 29:845-854, APR 1 2013
abstract, full text

Oliveira, B.L., Moreira, I.S., Fernandes, P.A., Ramos, M.J., Santos, I., Correia, J.D.G.
Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms
JOURNAL OF MOLECULAR MODELING, 19:1537-1551, APR 2013
abstract, full text

Randjelovic, J., Eric, S., Savic, V.
Computational study and peptide inhibitors design for the CDK9 - cyclin T1 complex
JOURNAL OF MOLECULAR MODELING, 19:1711-1725, APR 2013
abstract, full text

Sukalovic, V., Soskic, V., Sencanski, M., Andric, D., Kostic-Rajacic, S.
Determination of key receptor-ligand interactions of dopaminergic arylpiperazines and the dopamine D2 receptor homology model
JOURNAL OF MOLECULAR MODELING, 19:1751-1762, APR 2013
abstract, full text

Yatawara, A., Wilson, J.L., Taylor, L., Polgar, P., Mierke, D.F.
C-terminus of ET A/ETB receptors regulate endothelin-1 signal transmission
JOURNAL OF PEPTIDE SCIENCE, 19:257-262, APR 2013
abstract, full text

Ramirez-Duran, L.A., Rosales-Hernandez, M.C., Hernandez-Rodriguez, M., Mendieta-Wejebe, J.E., Trujillo-Ferrara, J., Correa-Basurto, J.
Mapping Myeloperoxidase to Identify its Promiscuity Properties Using Docking and Molecular Dynamics Simulations
CURRENT PHARMACEUTICAL DESIGN, 19:2204-2215, APR 2013
abstract, full text

Mao, L., Yang, Y.L.
Targeting the Nuclear Transport Machinery by Rational Drug Design
CURRENT PHARMACEUTICAL DESIGN, 19:2318-2325, APR 2013
abstract, full text

Lai-Kee-Him, J., Schellenberger, P., Dumas, C., Richard, E., Trapani, S., Komar, V., Demangeat, G., Ritzenthaler, C., Bron, P.
The backbone model of the Arabis mosaic virus reveals new insights into functional domains of Nepovirus capsid
JOURNAL OF STRUCTURAL BIOLOGY, 182:1-9, APR 2013
abstract, full text

Chapman, M.S., Trzynka, A., Chapman, B.K.
Atomic modeling of cryo-electron microscopy reconstructions - Joint refinement of model and imaging parameters
JOURNAL OF STRUCTURAL BIOLOGY, 182:10-21, APR 2013
abstract, full text

Pulawski, W., Filipek, S., Zwolinska, A., Debinski, A., Krzysko, K., Garduno-Juarez, R., Viswanathan, S., Renugopalakrishnan, V.
Low-temperature molecular dynamics simulations of horse heart cytochrome c and comparison with inelastic neutron scattering data
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 42:291-300, APR 2013
abstract, full text

Zhang, Z.Y., Liu, M., Li, B.P., Wang, Y.L., Yue, J.J., Liang, L., Sun, J.Z.
Exploring the mechanism of a regulatory SNP of KLK3 by molecular dynamics simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:426-440, APR 1 2013
abstract, full text

Sun, C., Tang, T., Uludag, H.
A molecular dynamics simulation study on the effect of lipid substitution on polyethylenimine mediated siRNA complexation
BIOMATERIALS, 34:2822-2833, APR 2013
abstract, full text

Halverson, J.D., Brandes, T., Lenz, O., Arnold, A., Bevc, S., Starchenko, V., Kremer, K., Stuehn, T., Reith, D.
ESPResSo++: A modern multiscale simulation package for soft matter systems
COMPUTER PHYSICS COMMUNICATIONS, 184:1129-1149, APR 2013
abstract, full text

Hu, G.D., Qi, L.S., Dou, X.H., Wang, J.H.
The influences of protonation state of histidine on aromatic/arginine region of aquaporin-1 protein
MOLECULAR SIMULATION, 39:261-269, APR 1 2013
abstract, full text

Garate, J.A., Oostenbrink, C.
Lipid a from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:658-674, APR 2013
abstract, full text

Raczynski, P., Gorny, K., Pabiszczak, M., Gburski, Z.
Nanoindentation of biomembrane by carbon nanotubes - MD simulation
COMPUTATIONAL MATERIALS SCIENCE, 70:13-18, APR 2013
abstract, full text

Qiu, W.Z., Nguyen, T.C., Skafidas, E.
Modeling and Estimating Simulated DNA Nanopore Translocation Signals
IEEE SENSORS JOURNAL, 13:1216-1222, APR 2013
abstract, full text

Hor, L., Dobson, R.C.J., Downton, M.T., Wagner, J., Hutton, C.A., Perugini, M.A.
Dimerization of Bacterial Diaminopimelate Epimerase Is Essential for Catalysis
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:9238-9248, MAR 29 2013
abstract, full text

Wang, L.Y., Dumont, R.S., Dickson, J.M.
Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes
JOURNAL OF CHEMICAL PHYSICS, 138: Art. No. 124701, MAR 28 2013
abstract, full text

Gross, A.S., Bell, A.T., Chu, J.W.
Preferential Interactions between Lithium Chloride and Glucan Chains in N,N-Dimethylacetamide Drive Cellulose Dissolution
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3280-3286, MAR 28 2013
abstract, full text

Bernini, C., Andruniow, T., Olivucci, M., Pogni, R., Basosi, R., Sinicropi, A.
Effects of the Protein Environment on the Spectral Properties of Tryptophan Radicals in Pseudomonas aeruginosa Azurin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:4822-4833, MAR 27 2013
abstract, full text

Song, Y., Peng, W., Liu, K., Yang, P., Zhang, W.K., Zhang, X.
Exploring the Folding Pattern of a Polymer Chain in a Single Crystal by Combining Single-Molecule Force Spectroscopy and Steered Molecular Dynamics Simulations
LANGMUIR, 29:3853-3857, MAR 26 2013
abstract, full text

Kumar, A., Cocco, E., Atzori, L., Marrosu, M.G., Pieroni, E.
Structural and Dynamical Insights on HLA-DR2 Complexes That Confer Susceptibility to Multiple Sclerosis in Sardinia: A Molecular Dynamics Simulation Study
PLOS ONE, 8: Art. No. e59711, MAR 26 2013
abstract, full text

Mirza, I.A., Burk, D.L., Xiong, B., Iwaki, H., Hasegawa, Y., Grosse, S., Lau, P.C.K., Berghuis, A.M.
Structural Analysis of a Novel Cyclohexylamine Oxidase from Brevibacterium oxydans IH-35A
PLOS ONE, 8: Art. No. e60072, MAR 26 2013
abstract, full text

Tsutakawa, S.E., Shin, D.S., Mol, C.D., Izumi, T., Arvai, A.S., Mantha, A.K., Szczesny, B., Ivanov, I.N., Hosfield, D.J., Maiti, B., Pique, M.E., Frankel, K.A., Hitomi, K., Cunningham, R.P., Mitra, S., Tainer, J.A.
Conserved Structural Chemistry for Incision Activity in Structurally Non-homologous Apurinic/Apyrimidinic Endonuclease APE1 and Endonuclease IV DNA Repair Enzymes
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:8445-8455, MAR 22 2013
abstract, full text

Glass, D.C., Krishnan, M., Smith, J.C., Baudry, J.
Three Entropic Classes of Side Chain in a Globular Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 117:3127-3134, MAR 21 2013
abstract, full text

Das, A., Chakrabarti, J., Ghosh, M.
Conformational Contribution to Thermodynamics of Binding in Protein-Peptide Complexes through Microscopic Simulation
BIOPHYSICAL JOURNAL, 104:1274-1284, MAR 19 2013
abstract, full text

Genchev, G.Z., Kobayashi, T., Lu, H.
Calcium Induced Regulation of Skeletal Troponin - Computational Insights from Molecular Dynamics Simulations
PLOS ONE, 8: Art. No. e58313, MAR 15 2013
abstract, full text

Gorny, K., Dendzik, Z., Pabiszczak, M., Gburski, Z.
Non-Debye dipolar relaxation of ethylene glycol embedded in ZSM-5 zeolite host matrix - Computer simulation study
JOURNAL OF NON-CRYSTALLINE SOLIDS, 364:28-33, MAR 15 2013
abstract, full text

Ikeda, A., Ishikawa, M., Aono, R., Kikuchi, J., Akiyama, M., Shinoda, W.
Regioselective Recognition of a [60]Fullerene-Bisadduct by Cyclodextrin
JOURNAL OF ORGANIC CHEMISTRY, 78:2534-2541, MAR 15 2013
abstract, full text

Prates, E.T., Stankovic, I., Silveira, R.L., Liberato, M.V., Henrique-Silva, F., Pereira, N., Polikarpov, I., Skaf, M.S.
X-ray Structure and Molecular Dynamics Simulations of Endoglucanase 3 from Trichoderma harzianum: Structural Organization and Substrate Recognition by Endoglucanases That Lack Cellulose Binding Module
PLOS ONE, 8: Art. No. e59069, MAR 14 2013
abstract, full text

Hom, K., Heinzl, G.A., Eakanunkul, S., Lopes, P.E.M., Xue, F.T., MacKerell, A.D., Wilks, A.
Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) of P. aeruginosa
JOURNAL OF MEDICINAL CHEMISTRY, 56:2097-2109, MAR 14 2013
abstract, full text

Komuro, Y., Miyashita, N., Mori, T., Muneyuki, E., Saitoh, T., Kohda, D., Sugita, Y.
Energetics of the Presequence-Binding Poses in Mitochondrial Protein Import Through Tom20
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2864-2871, MAR 14 2013
abstract, full text

Morrow, C.P., Yazaydin, A.O., Krishnan, M., Bowers, G.M., Kalinichev, A.G., Kirkpatrick, R.J.
Structure, Energetics, and Dynamics of Smectite Clay Interlayer Hydration: Molecular Dynamics and Metadynamics Investigation of Na-Hectorite
JOURNAL OF PHYSICAL CHEMISTRY C, 117:5172-5187, MAR 14 2013
abstract, full text

Chuev, G.N., Vyalov, I., Georgi, N.
Extraction of atom-atom bridge and direct correlation functions from molecular simulations: A test for ambient water
CHEMICAL PHYSICS LETTERS, 561:175-178, MAR 13 2013
abstract, full text

Lee, C.K., Hua, C.C., Chen, S.A.
Phase Transition and Gels in Conjugated Polymer Solutions
MACROMOLECULES, 46:1932-1938, MAR 12 2013
abstract, full text

Das, A., Plotkin, S.S.
Mechanical Probes of SOD1 Predict Systematic Trends in Metal and Dimer Affinity of ALS-Associated Mutants
JOURNAL OF MOLECULAR BIOLOGY, 425:850-874, MAR 11 2013
abstract, full text

Patel, P., Clarke, C., Barraclough, D.L., Jowitt, T.A., Rudland, P.S., Barraclough, R., Lian, L.Y.
Metastasis-Promoting Anterior Gradient 2 Protein Has a Dimeric Thioredoxin Fold Structure and a Role in Cell Adhesion
JOURNAL OF MOLECULAR BIOLOGY, 425:929-943, MAR 11 2013
abstract, full text

Clavier, A., Kraszewski, S., Ramseyer, C., Picaud, F.
Insertion kinetics of small nucleotides through single walled carbon nanotube
JOURNAL OF BIOTECHNOLOGY, 164:13-18, MAR 10 2013
abstract, full text

Machado, L.D., Legoas, S.B., Soares, J.S., Shadmi, N., Jorio, A., Joselevich, E., Galvao, D.S.
Dynamics of the Formation of Carbon Nanotube Serpentines
PHYSICAL REVIEW LETTERS, 110: Art. No. 105502, MAR 8 2013
abstract, full text

Karachevtsev, M.V., Gladchenko, G.O., Plokhotnichenko, A.M., Leontiev, V.S., Karachevtsev, V.A.
Adsorption of Biopolymers on SWCNT: Ordered Poly(rC) and Disordered Poly(rI)
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2636-2644, MAR 7 2013
abstract, full text

Burney, P.R., Pfaendtner, J.
Structural and Dynamic Features of Candida rugosa Lipase 1 in Water, Octane, Toluene, and Ionic Liquids BMIM-PF6 and BMIM-NO3
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2662-2670, MAR 7 2013
abstract, full text

Harada, R., Tochio, N., Kigawa, T., Sugita, Y., Feig, M.
Reduced Native State Stability in Crowded Cellular Environment Due to Protein-Protein Interactions
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:3696-3701, MAR 6 2013
abstract, full text

Geng, R.S., Sotomayor, M., Kinder, K.J., Gopal, S.R., Gerka-Stuyt, J., Chen, D.H.C., Hardisty-Hughes, R.E., Ball, G., Parker, A., Gaudet, R., Furness, D., Brown, S.D., Corey, D.P., Alagramam, K.N.
Noddy, a Mouse Harboring a Missense Mutation in Protocadherin-15, Reveals the Impact of Disrupting a Critical Interaction Site between Tip-Link Cadherins in Inner Ear Hair Cells
JOURNAL OF NEUROSCIENCE, 33:4395-4404, MAR 6 2013
abstract, full text

Stock, L., Souza, C., Treptow, W.
Structural Basis for Activation of Voltage-Gated Cation Channels
BIOCHEMISTRY, 52:1501-1513, MAR 5 2013
abstract, full text

Mahdavi, S., Kuyucak, S.
Why the Drosophila Shaker K+ Channel Is Not a Good Model for Ligand Binding to Voltage-Gated Kv1 Channels
BIOCHEMISTRY, 52:1631-1640, MAR 5 2013
abstract, full text

Mijajlovic, M., Penna, M.J., Biggs, M.J.
Free Energy of Adsorption for a Peptide at a Liquid/Solid Interface via Nonequilibrium Molecular Dynamics
LANGMUIR, 29:2919-2926, MAR 5 2013
abstract, full text

Bier, D., Rose, R., Bravo-Rodriguez, K., Bartel, M., Ramirez-Anguita, J.M., Dutt, S., Wilch, C., Klarner, F.G., Sanchez-Garcia, E., Schrader, T., Ottmann, C.
Molecular tweezers modulate 14-3-3 protein-protein interactions
NATURE CHEMISTRY, 5:234-239, MAR 2013
abstract, full text

Zhang, X., Xia, M.D., Li, Y., Liu, H.H., Jiang, X., Ren, W.L., Wu, J.P., DeCaen, P., Yu, F., Huang, S., He, J.H., Clapham, D.E., Yan, N., Gong, H.P.
Analysis of the selectivity filter of the voltage-gated sodium channel NavRh
CELL RESEARCH, 23:409-422, MAR 2013
abstract, full text

Thibault, J.C., Facelli, J.C., Cheatham, T.E.
iBIOMES: Managing and Sharing Biomolecular Simulation Data in a Distributed Environment
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:726-736, MAR 2013
abstract, full text

Jin, A.J., Lafer, E.M., Peng, J.Q., Smith, P.D., Nossal, R.
Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy
METHODS, 59:316-327, MAR 1 2013
abstract, full text

Mehrbod, M., Mofrad, M.R.K.
Localized Lipid Packing of Transmembrane Domains Impedes Integrin Clustering
PLOS COMPUTATIONAL BIOLOGY, 9: Art. No. e1002948, MAR 2013
abstract, full text

Rashid, M.H., Mahdavi, S., Kuyucak, S.
Computational Studies of Marine Toxins Targeting Ion Channels
MARINE DRUGS, 11:848-869, MAR 2013
abstract, full text

Paasche, A., Schirmeister, T., Engels, B.
Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1765-1777, MAR 2013
abstract, full text

Gracia, E., Farre, D., Cortes, A., Ferrer-Costa, C., Orozco, M., Mallol, J., Lluis, C., Canela, E.I., McCormick, P.J., Franco, R., Fanelli, F., Casado, V.
The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors
FASEB JOURNAL, 27:1048-1061, MAR 2013
abstract, full text

Wu, Q.Y., Li, F., Guo, H.Y., Cao, J., Chen, C., Chen, W., Zeng, L.Y., Li, Z.Y., Wang, X.Y., Xu, K.L.
Disrupting of E79 and K138 interaction is responsible for human muscle creatine kinase deficiency diseases
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 54:216-224, MAR 2013
abstract, full text

Chang, C.M., Jalbout, A.F.
Theoretical Design of Free Radical "Sponges" in DNA
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 10:591-593, MAR 2013
abstract, full text

Gao, Y., Olsen, K.W.
Molecular Dynamics of Drug Crystal Dissolution: Simulation of Acetaminophen Form I in Water
MOLECULAR PHARMACEUTICS, 10:905-917, MAR 2013
abstract, full text

Galaz, S., Morales-Quintana, L., Moya-Leon, M.A., Herrera, R.
Structural analysis of the alcohol acyltransferase protein family from Cucumismelo shows that enzyme activity depends on an essential solvent channel
FEBS JOURNAL, 280:1344-1357, MAR 2013
abstract, full text

Morris, K.L., Rodger, A., Hicks, M.R., Debulpaep, M., Schymkowitz, J., Rousseau, F., Serpell, L.C.
Exploring the sequence-structure relationship for amyloid peptides
BIOCHEMICAL JOURNAL, 450:275-283, MAR 1 2013
abstract, full text

Mifsud, J., Ravaud, S., Krammer, E.M., Chipot, C., Kunji, E.R.S., Pebay-Peyroula, E., Dehez, F.
The substrate specificity of the human ADP/ATP carrier AAC1
MOLECULAR MEMBRANE BIOLOGY, 30:160-168, MAR 2013
abstract, full text

Atkinson, S.C., Dogovski, C., Downton, M.T., Czabotar, P.E., Dobson, R.C.J., Gerrard, J.A., Wagner, J., Perugini, M.A.
Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition
PLANT MOLECULAR BIOLOGY, 81:431-446, MAR 2013
abstract, full text

Buck, P.M., Kumar, S., Singh, S.K.
Insights into the potential aggregation liabilities of the b12 Fab fragment via elevated temperature molecular dynamics
PROTEIN ENGINEERING DESIGN & SELECTION, 26:195-205, MAR 2013
abstract, full text

Ward, K.E., Bhardwaj, N., Vora, M., Chalfant, C.E., Lu, H., Stahelin, R.V.
The molecular basis of ceramide-1-phosphate recognition by C2 domains
JOURNAL OF LIPID RESEARCH, 54:636-648, MAR 2013
abstract, full text

Escaffre, O., Le Nouen, C., Amelot, M., Ambroggio, X., Ogden, K.M., Guionie, O., Toquin, D., Muller, H., Islam, M.R., Eterradossi, N.
Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus
JOURNAL OF VIROLOGY, 87:2767-2780, MAR 2013
abstract, full text

Xin, Y.N., Zhao, Y.Q., Lin, Z.H., Jiang, X.J., Xuan, S.Y., Huang, J.F.
Molecular dynamics simulation of PNPLA3 I148M polymorphism reveals reduced substrate access to the catalytic cavity
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:406-414, MAR 2013
abstract, full text

Lei, D.S., Zhang, X., Jiang, S.B., Cai, Z.D., Rames, M.J., Zhang, L., Ren, G., Zhang, S.L.
Structural features of cholesteryl ester transfer protein: A molecular dynamics simulation study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:415-425, MAR 2013
abstract, full text

Wang, X.L., Kumar, S., Buck, P.M., Singh, S.K.
Impact of deglycosylation and thermal stress on conformational stability of a full length murine igG2a monoclonal antibody: Observations from molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:443-460, MAR 2013
abstract, full text

Olson, M.A., Lee, M.S.
Structure refinement of protein model decoys requires accurate side-chain placement
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:469-478, MAR 2013
abstract, full text

Cerutti, D.S., Rice, J.E., Swope, W.C., Case, D.A.
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2328-2338, FEB 28 2013
abstract, full text

Karatasos, K.
Self-Association and Complexation of the Anti-Cancer Drug Doxorubicin with PEGylated Hyperbranched Polyesters in an Aqueous Environment
JOURNAL OF PHYSICAL CHEMISTRY B, 117:2564-2575, FEB 28 2013
abstract, full text

Kang, S.G., Huynh, T., Xia, Z., Zhang, Y., Fang, H.P., Wei, G.H., Zhou, R.H.
Hydrophobic Interaction Drives Surface-Assisted Epitaxial Assembly of Amyloid-like Peptides
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:3150-3157, FEB 27 2013
abstract, full text

Gonzalez, W., Zuniga, L., Cid, L.P., Arevalo, B., Niemeyer, M.I., Sepulveda, F.V.
An Extracellular Ion Pathway Plays a Central Role in the Cooperative Gating of a K-2P K+ Channel by Extracellular pH
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:5984-5991, FEB 22 2013
abstract, full text

Takemura, K., Burri, R.R., Ishikawa, T., Ishikura, T., Sakuraba, S., Matubayasi, N., Kuwata, K., Kitao, A.
Free-energy analysis of lysozyme-triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation
CHEMICAL PHYSICS LETTERS, 559:94-98, FEB 20 2013
abstract, full text

Ricci, M., Spijker, P., Stellacci, F., Molinari, J.F., Voitchovsky, K.
Direct Visualization of Single Ions in the Stern Layer of Calcite
LANGMUIR, 29:2207-2216, FEB 19 2013
abstract, full text

Ren, S.K., Sato, R., Hasegawa, K., Ohta, H., Masuda, S.
A Predicted Structure for the PixD-PixE Complex Determined by Homology Modeling, Docking Simulations, and a Mutagenesis Study
BIOCHEMISTRY, 52:1272-1279, FEB 19 2013
abstract, full text

GhattyVenkataKrishna, P.K., Alekozai, E.M., Beckham, G.T., Schulz, R., Crowley, M.F., Uberbacher, E.C., Cheng, X.L.
Initial Recognition of a Cellodextrin Chain in the Cellulose-Binding Tunnel May Affect Cellobiohydrolase Directional Specificity
BIOPHYSICAL JOURNAL, 104:904-912, FEB 19 2013
abstract, full text

Cai, W.S., Chipot, C.
Frontiers in High-Performance, Large-Scale Molecular Dynamics. 35 Years of Molecular-Dynamics Simulations of Biological Systems
ACTA CHIMICA SINICA, 71:159-168, FEB 15 2013
abstract, full text

Surdutovich, E., Yakubovich, A.V., Solov'yov, A.V.
Biodamage via shock waves initiated by irradiation with ions
SCIENTIFIC REPORTS, 3: Art. No. 1289, FEB 15 2013
abstract, full text

Zimnicka, M., Chung, T.W., Moss, C.L., Turecek, F.
Perturbing Peptide Cation-Radical Electronic States by Thioxoamide Groups: Formation, Dissociations, and Energetics of Thioxopeptide Cation-Radicals
JOURNAL OF PHYSICAL CHEMISTRY A, 117:1265-1275, FEB 14 2013
abstract, full text

Peters, G.H., Wang, C.H., Cruys-Bagger, N., Velardez, G.F., Madsen, J.J., Westh, P.
Binding of Serotonin to Lipid Membranes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:2164-2171, FEB 13 2013
abstract, full text

Mowrey, D., Cheng, M.H., Liu, L.T., Willenbring, D., Lu, X.H., Wymore, T., Xu, Y., Tang, P.
Asymmetric Ligand Binding Facilitates Conformational Transitions in Pentameric Ligand-Gated Ion Channels
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:2172-2180, FEB 13 2013
abstract, full text

Gumbart, J.C., Teo, I., Roux, B., Schulten, K.
Reconciling the Roles of Kinetic and Thermodynamic Factors in Membrane-Protein Insertion
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:2291-2297, FEB 13 2013
abstract, full text, TCBG publications

Krems, M., Di Ventra, M.
Ionic Coulomb blockade in nanopores
JOURNAL OF PHYSICS-CONDENSED MATTER, 25: Art. No. 065101, FEB 13 2013
abstract, full text

Liang, G.Z., Zhao, J., Yu, X., Zheng, J.
Comparative Molecular Dynamics Study of Human Islet Amyloid Polypeptide (IAPP) and Rat IAPP Oligomers
BIOCHEMISTRY, 52:1089-1100, FEB 12 2013
abstract, full text

Fogolari, F., Corazza, A., Esposito, G.
Generalized Born forces: Surface integral formulation
JOURNAL OF CHEMICAL PHYSICS, 138: Art. No. 054112, FEB 7 2013
abstract, full text

Hilder, T.A., Chung, S.H.
Conduction and Block of Inward Rectifier K+ Channels: Predicted Structure of a Potent Blocker of Kir2.1
BIOCHEMISTRY, 52:967-974, FEB 5 2013
abstract, full text

Yang, L., Ahmed, A., Sandler, S.I.
Comparison of two simulation methods to compute solvation free energies and partition coefficients
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:284-293, FEB 5 2013
abstract, full text

Popov, A.V., Vorobjev, Y.N., Zharkov, D.O.
MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:319-325, FEB 5 2013
abstract, full text

Ferreira, L.G., dos Santos, R.N., Andricopulo, A.D.
Structure-Based Drug Design Studies on a Series of Aldolase Inhibitors
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 24:201-211, FEB 2013
abstract, full text

Hilder, T.A., Chung, S.H.
Conductance properties of the inwardly rectifying channel, Kir3.2: Molecular and Brownian dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:471-478, FEB 2013
abstract, full text

Witte, K., Olausson, B.E.S., Walrant, A., Alves, I.D., Vogel, A.
Structure and dynamics of the two amphipathic arginine-rich peptides RW9 and RL9 in a lipid environment investigated by solid-state NMR and MD simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1828:824-833, FEB 2013
abstract, full text

Karoulia, Z., Papadopoulos, G., Nomikos, M., Thanassoulas, A., Papadopoulou, T.C., Nounesis, G., Kontou, M., Stathopoulos, C., Leonidas, D.D.
Studies on the Essential Intramolecular Interaction Between the A1 and A2 Domains of von Willebrand Factor
PROTEIN AND PEPTIDE LETTERS, 20:231-240, FEB 2013
abstract, full text

Jung, S.G., Schlick, T.
Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site
NUCLEIC ACIDS RESEARCH, 41:1483-1495, FEB 2013
abstract, full text

Thomas, M., Jayatilaka, D., Corry, B.
How does overcoordination create ion selectivity?
BIOPHYSICAL CHEMISTRY, 172:37-42, FEB 2013
abstract, full text

Lane, T.J., Shukla, D., Beauchamp, K.A., Pande, V.S.
To milliseconds and beyond: challenges in the simulation of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 23:58-65, FEB 2013
abstract, full text

Feng, Z.W., Hou, T.J., Li, Y.Y.
Docking and MD study of histamine H4R based on the crystal structure of H1R
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 39:1-12, FEB 2013
abstract, full text

Caballero, J., Poblete, H., Navarro, C., Alzate-Morales, J.H.
Association of nicotinic acid with a poly(amidoamine) dendrimer studied by molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 39:71-78, FEB 2013
abstract, full text

Thomas, M., Jayatilaka, D., Corry, B.
An Entropic Mechanism of Generating Selective Ion Binding in Macromolecules
PLOS COMPUTATIONAL BIOLOGY, 9: Art. No. e1002914, FEB 2013
abstract, full text

Koldso, H., Christiansen, A.B., Sinning, S., Schiott, B.
Comparative Modeling of the Human Monoamine Transporters: Similarities in Substrate Binding
ACS CHEMICAL NEUROSCIENCE, 4:295-309, FEB 2013
abstract, full text

Velikonja, A., Perutkova, S., Gongadze, E., Kramar, P., Polak, A., Macek-Lebar, A., Iglic, A.
Monovalent Ions and Water Dipoles in Contact with Dipolar Zwitterionic Lipid Headgroups-Theory and MD Simulations
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 14:2846-2861, FEB 2013
abstract, full text

Nagagarajan, S., Xue, F.T., MacKerell, A.D.
Impact of Substrate Protonation and Tautomerization States on Interactions with the Active Site of Arginase I
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:452-460, FEB 2013
abstract, full text

Sundermann, U., Bravo-Rodriguez, K., Klopries, S., Kushnir, S., Gomez, H., Sanchez-Garcia, E., Schulz, F.
Enzyme-Directed Mutasynthesis: A Combined Experimental and Theoretical Approach to Substrate Recognition of a Polyketide Synthase
ACS CHEMICAL BIOLOGY, 8:443-450, FEB 2013
abstract, full text

Wei, C.Y., Pohorille, A.
Permeation of Aldopentoses and Nucleosides Through Fatty Acid and Phospholipid Membranes: Implications to the Origins of Life
ASTROBIOLOGY, 13:177-188, FEB 2013
abstract, full text

Comer, J., Chipot, C., Gonzalez-Nilo, F.D.
Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:876-882, FEB 2013
abstract, full text

Lapelosa, M., Abrams, C.F.
A Computational Study of Water and CO Migration Sites and Channels Inside Myoglobin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1265-1271, FEB 2013
abstract, full text

Mirjalili, V., Feig, M.
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:1294-1303, FEB 2013
abstract, full text

Chen, R., Chung, S.H.
Effect of Gating Modifier Toxins on Membrane Thickness: Implications for Toxin Effect on Gramicidin and Mechanosensitive Channels
TOXINS, 5:456-471, FEB 2013
abstract, full text

Nemkevich, A., Spackman, M.A., Corry, B.
Simulations of Guest Transport in Clathrates of Dianin's Compound and Hydroquinone
CHEMISTRY-A EUROPEAN JOURNAL, 19:2676-2684, FEB 2013
abstract, full text

Grimm, C., Meyer, T., Czapla, S., Nikolaus, J., Scheidt, H.A., Vogel, A., Herrmann, A., Wessig, P., Huster, D., Muller, P.
Structure and Dynamics of Molecular Rods in Membranes: Application of a Spin-Labeled Rod
CHEMISTRY-A EUROPEAN JOURNAL, 19:2703-2710, FEB 2013
abstract, full text

Hofheinz, K., Kakularam, K.R., Adel, S., Anton, M., Polymarasetty, A., Reddanna, P., Kuhn, H., Horn, T.
Conversion of pro-inflammatory murine Alox5 into an anti-inflammatory 15S-lipoxygenating enzyme by multiple mutations of sequence determinants
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 530:40-47, FEB 1 2013
abstract, full text

Wang, L., Li, Q., Wu, L.F., Liu, S.W., Zhang, Y., Yang, X., Zhu, P.P., Zhang, H.L., Zhang, K., Lou, J.Z., Liu, P.S., Tong, L., Sun, F., Fan, Z.S.
Identification of SERPINB1 As a Physiological Inhibitor of Human Granzyme H
JOURNAL OF IMMUNOLOGY, 190:1319-1330, FEB 1 2013
abstract, full text

Ballut, L., Sapay, N., Chautard, E., Imberty, A., Ricard-Blum, S.
Mapping of heparin/heparan sulfate binding sites on alpha v beta 3 integrin by molecular docking
JOURNAL OF MOLECULAR RECOGNITION, 26:76-85, FEB 2013
abstract, full text

Wang, S., Zhao, W.J., Liu, H.H., Gong, H.P., Yan, Y.B.
Increasing beta B1-crystallin sensitivity to proteolysis caused by the congenital cataract-microcornea syndrome mutation S129R
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1832:302-311, FEB 2013
abstract, full text

Bhatti, G., Jayanthi, L., VandeVord, P., Gebremichael, Y.
Computational investigation of the key factors affecting the second stage activation mechanisms of domain II m-calpain
JOURNAL OF MOLECULAR MODELING, 19:779-792, FEB 2013
abstract, full text

Toubar, R.A., Zhmurov, A., Barsegov, V., Marx, K.A.
Comparative simulation studies of native and single-site mutant human beta-defensin-1 peptides
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 31:174-194, FEB 1 2013
abstract, full text

Chaudhari, S.R., Mogurampelly, S., Suryaprakash, N.
Engagement of CF3 Group in N-H center dot center dot center dot F-C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 117:1123-1129, JAN 31 2013
abstract, full text

Pester, O., Barrett, P.J., Hornburg, D., Hornburg, P., Probstle, R., Widmaier, S., Kutzner, C., Durrbaum, M., Kapurniotu, A., Sanders, C.R., Scharnagl, C., Langosch, D.
The Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix Provides a Rationale for the Sequential Cleavage Mechanism of gamma-Secretase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:1317-1329, JAN 30 2013
abstract, full text

Hsu, Y.H., Bucher, D., Cao, J., Li, S., Yang, S.W., Kokotos, G., Woods, V.L., McCammon, J.A., Dennis, E.A.
Fluoroketone Inhibition of Ca2+-Independent Phospholipase A(2) through Binding Pocket Association Defined by Hydrogen/Deuterium Exchange and Molecular Dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:1330-1337, JAN 30 2013
abstract, full text

Xia, Z., Huynh, T., Ren, P.Y., Zhou, R.H.
Large Domain Motions in Ago Protein Controlled by the Guide DNA-Strand Seed Region Determine the Ago-DNA-mRNA Complex Recognition Process
PLOS ONE, 8: Art. No. e54620, JAN 29 2013
abstract, full text

Pal, S., Bandyopadhyay, S.
Importance of Protein Conformational Motions and Electrostatic Anchoring Sites on the Dynamics and Hydrogen Bond Properties of Hydration Water
LANGMUIR, 29:1162-1173, JAN 29 2013
abstract, full text

Barucha-Kraszewska, J., Kraszewski, S., Ramseyer, C.
Will C-Laurdan Dethrone Laurdan in Fluorescent Solvent Relaxation Techniques for Lipid Membrane Studies?
LANGMUIR, 29:1174-1182, JAN 29 2013
abstract, full text

Lin, Y.L., Meng, Y.L., Jiang, W., Roux, B.
Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:1664-1669, JAN 29 2013
abstract, full text

Shaikh, S.A., Li, J., Enkavi, G., Wen, P.C., Huang, Z.J., Tajkhorshid, E.
Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations
BIOCHEMISTRY, 52:569-587, JAN 29 2013
abstract, full text

Kamiya, M., Kato, H.E., Ishitani, R., Nureki, O., Hayashi, S.
Structural and spectral characterizations of C1C2 channelrhodopsin and its mutants by molecular simulations
CHEMICAL PHYSICS LETTERS, 556:266-271, JAN 29 2013
abstract, full text

Saito, H., Iwayama, M., Mizukami, T., Kang, J., Tateno, M., Nagao, H.
Molecular dynamics study on binding free energy of Azurin-Cytochrome c551 complex
CHEMICAL PHYSICS LETTERS, 556:297-302, JAN 29 2013
abstract, full text

Kim, S.Y., Colpitts, C.C., Wiedemann, G., Jepson, C., Rahimi, M., Rothwell, J.R., McInnes, A.D., Hasebe, M., Reski, R., Sterenberg, B.T., Suh, D.Y.
Physcomitrella PpORS, Basal to Plant Type III Polyketide Synthases in Phylogenetic Trees, Is a Very Long Chain 2 '-Oxoalkylresorcinol Synthase
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:2767-2777, JAN 25 2013
abstract, full text

Ovchinnikov, V., Cecchini, M., Karplus, M.
A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences
JOURNAL OF PHYSICAL CHEMISTRY B, 117:750-762, JAN 24 2013
abstract, full text

Wang, X.Q., Hirao, H.
ONIOM (DFT:MM) Study of the Catalytic Mechanism of myo-Inositol Monophosphatase: Essential Role of Water in Enzyme Catalysis in the Two-Metal Mechanism
JOURNAL OF PHYSICAL CHEMISTRY B, 117:833-842, JAN 24 2013
abstract, full text

Anastasio, N.C., Gilbertson, S.R., Bubar, M.J., Agarkov, A., Stutz, S.J., Jeng, Y., Bremer, N.M., Smith, T.D., Fox, R.G., Swinford, S.E., Seitz, P.K., Charendoff, M.N., Craft, J.W., Laezza, F.M., Watson, C.S., Briggs, J.M., Cunningham, K.A.
Peptide Inhibitors Disrupt the Serotonin 5-HT2C Receptor Interaction with Phosphatase and Tensin Homolog to Allosterically Modulate Cellular Signaling and Behavior
JOURNAL OF NEUROSCIENCE, 33:1615-1630, JAN 23 2013
abstract, full text

Lai, Y., Diao, J.J., Liu, Y.X., Ishitsuka, Y., Su, Z.L., Schulten, K., Ha, T., Shin, Y.K.
Fusion pore formation and expansion induced by Ca2+ and synaptotagmin 1
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:1333-1338, JAN 22 2013
abstract, full text, TCBG publications

Liu, Y.T., Zhu, F.Q.
Collective Diffusion Model for Ion Conduction through Microscopic Channels
BIOPHYSICAL JOURNAL, 104:368-376, JAN 22 2013
abstract, full text

Vazquez, F.X., Unger, V.M., Voth, G.A.
Autoinhibition of Endophilin in Solution via Interdomain Interactions
BIOPHYSICAL JOURNAL, 104:396-403, JAN 22 2013
abstract, full text

Schkolnik, G., Utesch, T., Zhao, J.J., Jiang, S., Thompson, M.K., Mroginski, M.A., Hildebrandt, P., Franzen, S.
Catalytic efficiency of dehaloperoxidase A is controlled by electrostatics - application of the vibrational Stark effect to understand enzyme kinetics
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 430:1011-1015, JAN 18 2013
abstract, full text

Faller, C.E., Reilly, K.A., Hills, R.D., Guvench, O.
Peptide Backbone Sampling Convergence with the Adaptive Biasing Force Algorithm
JOURNAL OF PHYSICAL CHEMISTRY B, 117:518-526, JAN 17 2013
abstract, full text

Wang, J.W., Zhao, Y.Q., Wang, Y.J., Huang, J.F.
Molecular dynamics simulations and statistical coupling analysis reveal functional coevolution network of oncogenic mutations in the CDKN2A-CDK6 complex
FEBS LETTERS, 587:136-141, JAN 16 2013
abstract, full text

Imhof, P., Zahran, M.
The Effect of a G:T Mispair on the Dynamics of DNA
PLOS ONE, 8: Art. No. e53305, JAN 15 2013
abstract, full text

Utesch, T., Millo, D., Castro, M.A., Hildebrandt, P., Zebger, I., Mroginski, M.A.
Effect of the Protonation Degree of a Self-Assembled Monolayer on the Immobilization Dynamics of a [NiFe] Hydrogenase
LANGMUIR, 29:673-682, JAN 15 2013
abstract, full text

Zhu, L., Zhong, X.W., Chen, S.R.W., Banavali, N., Liu, Z.
Modeling a Ryanodine Receptor N-terminal Domain Connecting the Central Vestibule and the Corner Clamp Region
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:903-914, JAN 11 2013
abstract, full text

Bagai, S., Sun, C.B., Tang, T.
Potential of Mean Force of Polyethylenimine-Mediated DNA Attraction
JOURNAL OF PHYSICAL CHEMISTRY B, 117:49-56, JAN 10 2013
abstract, full text

Gabrieli, A., Sant, M., Demontis, P., Suffritti, G.B.
Development and Optimization of a New Force Field for Flexible Aluminosilicates, Enabling Fast Molecular Dynamics Simulations on Parallel Architectures
JOURNAL OF PHYSICAL CHEMISTRY C, 117:503-509, JAN 10 2013
abstract, full text

Uttarwar, R.G., Potoff, J., Huang, Y.L.
Study on Interfacial Interaction between Polymer and Nanoparticle in a Nanocoating Matrix: A MARTINI Coarse-Graining Method
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 52:73-82, JAN 9 2013
abstract, full text

Cheng, J.J., Karri, S., Grauffel, C., Wang, F., Reuter, N., Roberts, M.F., Wintrode, P.L., Gershenson, A.
Does Changing the Predicted Dynamics of a Phospholipase C Alter Activity and Membrane Binding?
BIOPHYSICAL JOURNAL, 104:185-195, JAN 8 2013
abstract, full text

Severin, P.M.D., Zou, X.Q., Schulten, K., Gaub, H.E.
Effects of Cytosine Hydroxymethylation on DNA Strand Separation
BIOPHYSICAL JOURNAL, 104:208-215, JAN 8 2013
abstract, full text, TCBG publications

Ziervogel, B.K., Roux, B.
The Binding of Antibiotics in OmpF Porin
STRUCTURE, 21:76-87, JAN 8 2013
abstract, full text

Zhang, J.L., Zheng, Q.C., Li, Z.Q., Zhang, H.X.
How Does (E)-2-(Acetamidomethylene)succinate Bind to Its Hydrolase? From the Binding Process to the Final Result
PLOS ONE, 8: Art. No. e53811, JAN 7 2013
abstract, full text

da Silva, L.P., da Silva, J.C.G.E.
Analysis of the performance of DFT functionals in the study of light emission by oxyluciferin analogs
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 113:45-51, JAN 5 2013
abstract, full text

Hilbers, F., Junge, W., Sielaff, H.
The Torque of Rotary F-ATPase Can Unfold Subunit Gamma If Rotor and Stator Are Cross-Linked
PLOS ONE, 8: Art. No. e53754, JAN 3 2013
abstract, full text

Balme, S., Picaud, F., Kraszewski, S., Dejardin, P., Janot, J.M., Lepoitevin, M., Capomanes, J., Ramseyer, C., Henn, F.
Controlling potassium selectivity and proton blocking in a hybrid biological/solid-state polymer nanoporous membrane
NANOSCALE, 5:3961-3968, 2013
abstract, full text

Akdag, I.O., Ozkirimli, E.
The Uptake Mechanism of the Cell-Penetrating pVEC Peptide
JOURNAL OF CHEMISTRY, Art. No. 851915, 2013
abstract, full text

Bhatnagar, N., Kamath, G., Potoff, J.J.
Prediction of 1-octanol-water and air-water partition coefficients for nitro-aromatic compounds from molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:6467-6474, 2013
abstract, full text

Ortoleva, P., Singharoy, A., Pankavich, S.
Hierarchical multiscale modeling of macromolecules and their assemblies
SOFT MATTER, 9:4319-4335, 2013
abstract, full text

Burkhardt, J.B., Skelton, A.A., Fried, J.R.
The water-channel forming ability of heptapeptide-based anion channels: insights from molecular dynamics simulations
SOFT MATTER, 9:4444-4454, 2013
abstract, full text

Wassman, C.D., Baronio, R., Demir, O., Wallentine, B.D., Chen, C.K., Hall, L.V., Salehi, F., Lin, D.W., Chung, B.P., Hatfield, G.W., Chamberlin, A.R., Luecke, H., Lathrop, R.H., Kaiser, P., Amaro, R.E.
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
NATURE COMMUNICATIONS, 4: Art. No. 1407, JAN 2013
abstract, full text

Kang, S.G., Huynh, T., Zhou, R.H.
Metallofullerenol Gd@C-82(OH)(22) distracts the proline-rich-motif from putative binding on the SH3 domain
NANOSCALE, 5:2703-2712, 2013
abstract, full text

Pandey, S., Baker, G.A., Sze, L., Pandey, S., Kamath, G., Zhao, H., Baker, S.N.
Ionic liquids containing fluorinated beta-diketonate anions: synthesis, characterization and potential applications
NEW JOURNAL OF CHEMISTRY, 37:909-919, 2013
abstract, full text

Moussa, S.G., Stern, A.C., Raff, J.D., Dilbeck, C.W., Tobias, D.J., Finlayson-Pitts, B.J.
Experimental and theoretical studies of the interaction of gas phase nitric acid and water with a self-assembled monolayer
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:448-458, 2013
abstract, full text

Sezer, D.
Computation of DNP coupling factors of a nitroxide radical in toluene: seamless combination of MD simulations and analytical calculations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:526-540, 2013
abstract, full text

Ormeno, D., Romero, F., Lopez-Fenner, J., Avila, A., Martinez-Torres, A., Parodi, J.
Ethanol Reduces Amyloid Aggregation In Vitro and Prevents Toxicity in Cell Lines
ARCHIVES OF MEDICAL RESEARCH, 44:1-7, JAN 2013
abstract, full text

Zhang, L.M., Wang, Z.L., Lu, Z.X., Shen, H., Huang, J., Zhao, Q.H., Liu, M., He, N.Y., Zhang, Z.J.
PEGylated reduced graphene oxide as a superior ssRNA delivery system
JOURNAL OF MATERIALS CHEMISTRY B, 1:749-755, 2013
abstract, full text

Chen, L.Y.
Glycerol inhibits water permeation through Plasmodium Falciparum aquaglyceroporin
JOURNAL OF STRUCTURAL BIOLOGY, 181:71-76, JAN 2013
abstract, full text

Prigozhin, M.B., Gruebele, M.
Microsecond folding experiments and simulations: a match is made
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:3372-3388, 2013
abstract, full text

Rahaman, O., Melchionna, S., Laage, D., Sterpone, F.
The effect of protein composition on hydration dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:3570-3576, 2013
abstract, full text

Carlson, J., Baxter, S.A., Dreau, D., Nesmelova, I.V.
The heterodimerization of platelet-derived chemokines
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:158-168, JAN 2013
abstract, full text

Zhang, Y.B., Chen, L.Y.
In silico study of Aquaporin V: Effects and affinity of the central pore-occluding lipid
BIOPHYSICAL CHEMISTRY, 171:24-30, JAN 2013
abstract, full text

Moran, O., Grottesi, A., Chadbum, A.J., Tammaro, P.
Parametrisation of the free energy of ATP binding to wild-type and mutant Kir6.2 potassium channels
BIOPHYSICAL CHEMISTRY, 171:76-83, JAN 2013
abstract, full text

Lemmin, T., Soto, C.S., Clinthorne, G., DeGrado, W.F., Dal Peraro, M.
Assembly of the Transmembrane Domain of E. coli PhoQ Histidine Kinase: Implications for Signal Transduction from Molecular Simulations
PLOS COMPUTATIONAL BIOLOGY, 9: Art. No. e1002878, JAN 2013
abstract, full text

Pujato, M., MacCarthy, T., Fiser, A., Bergman, A.
The Underlying Molecular and Network Level Mechanisms in the Evolution of Robustness in Gene Regulatory Networks
PLOS COMPUTATIONAL BIOLOGY, 9: Art. No. e1002865, JAN 2013
abstract, full text

Yu, H., Schulten, K.
Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations
PLOS COMPUTATIONAL BIOLOGY, 9: Art. No. e1002892, JAN 2013
abstract, full text, TCBG publications

Pavan, G.M., Barducci, A., Albertazzi, L., Parrinello, M.
Combining metadynamics simulation and experiments to characterize dendrimers in solution
SOFT MATTER, 9:2593-2597, 2013
abstract, full text

Pietra, F.
On the Pathways for CO Egress from Carboxy Human Cytoglobin. A Molecular-Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 10:86-95, JAN 2013
abstract, full text

Sadiq, S.K., Guixa-Gonzalez, R., Dainese, E., Pastor, M., De Fabritiis, G., Selent, J.
Molecular Modeling and Simulation of Membrane Lipid-Mediated Effects on GPCRs
CURRENT MEDICINAL CHEMISTRY, 20:22-38, JAN 2013
abstract, full text

Luo, Y., Jiang, W., Yu, H.B., MacKerell, A.D., Roux, B.
Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field
FARADAY DISCUSSIONS, 160:135-149, 2013
abstract, full text

Sukenik, S., Sapir, L., Gilman-Politi, R., Harries, D.
Diversity in the mechanisms of cosolute action on biomolecular processes
FARADAY DISCUSSIONS, 160:225-237, 2013
abstract, full text

Ferraro, D.J., Bhave, S.R., Kotipatruni, R.P., Hunn, J.C., Wildman, S.A., Hong, C., Dadey, D.Y.A., Muhoro, L.K., Jaboin, J.J., Thotala, D., Hallahan, D.E.
High-throughput identification of putative receptors for cancer-binding peptides using biopanning and microarray analysis
INTEGRATIVE BIOLOGY, 5:342-350, 2013
abstract, full text

Wiktor, M., Morin, S., Sass, H.J., Kebbel, F., Grzesiek, S.
Biophysical and structural investigation of bacterially expressed and engineered CCR5, a G protein-coupled receptor
JOURNAL OF BIOMOLECULAR NMR, 55:79-95, JAN 2013
abstract, full text

Arrar, M., de Oliveira, C.A.F., Fajer, M., Sinko, W., McCammon, J.A.
w-REXAMD: A Hamiltonian Replica Exchange Approach to Improve Free Energy Calculations for Systems with Kinetically Trapped Conformations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:18-23, JAN 2013
abstract, full text

Lee, T.S., Radak, B.K., Pabis, A., York, D.M.
A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:153-164, JAN 2013
abstract, full text

Eastman, P., Friedrichs, M.S., Chodera, J.D., Radmer, R.J., Bruns, C.M., Ku, J.P., Beauchamp, K.A., Lane, T.J., Wang, L.P., Shukla, D., Tye, T., Houston, M., Stich, T., Klein, C., Shirts, M.R., Pande, V.S.
OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:461-469, JAN 2013
abstract, full text

Lemmin, T., Bovigny, C., Lancon, D., Dal Peraro, M.
Cardiolipin Models for Molecular Simulations of Bacterial and Mitochondrial Membranes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:670-678, JAN 2013
abstract, full text

Gumbart, J.C., Roux, B., Chipot, C.
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:794-802, JAN 2013
abstract, full text

Grebner, C., Kastner, J., Thiel, W., Engels, B.
A New Tabu-Search-Based Algorithm for Solvation of Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:814-821, JAN 2013
abstract, full text

Jang, H., Connelly, L., Arce, F.T., Ramachandran, S., Kagan, B.L., Lal, R., Nussinov, R.
Mechanisms for the Insertion of Toxic, Fibril-like beta-Amyloid Oligomers into the Membrane
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:822-833, JAN 2013
abstract, full text

Jain, V., Hilton, B., Lin, B., Patnaik, S., Liang, F.T., Darian, E., Zou, Y., MacKerell, A.D., Cho, B.P.
Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor
NUCLEIC ACIDS RESEARCH, 41:869-880, JAN 2013
abstract, full text

Wang, X., Xu, F.T., Liu, J.S., Gao, B.Q., Liu, Y.X., Zhai, Y.J., Ma, J., Zhang, K., Baker, T.S., Schulten, K., Zheng, D., Pang, H., Sun, F.
Atomic Model of Rabbit Hemorrhagic Disease Virus by Cryo-Electron Microscopy and Crystallography
PLOS PATHOGENS, 9: Art. No. e1003132, JAN 2013
abstract, full text, TCBG publications

Zanuy, D., Teixeira-Dias, B., del Valle, L.J., Poater, J., Sola, M., Aleman, C.
Examining the formation of specific interactions between poly(3,4-ethylenedioxythiophene) and nucleotide bases
RSC ADVANCES, 3:2639-2649, 2013
abstract, full text

Fawcett, T.M., Irausquin, S.J., Simin, M., Valafar, H.
An artificial neural network approach to improving the correlation between protein energetics and the backbone structure
PROTEOMICS, 13:230-238, JAN 2013
abstract, full text

Goncalves, M.B., Dreyer, J., Lupieri, P., Barrera-Patino, C., Ippoliti, E., Webb, M.R., Corrie, J.E.T., Carloni, P.
Structural prediction of a rhodamine-based biosensor and comparison with biophysical data
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:2177-2183, 2013
abstract, full text

Elgabarty, H., Schmieder, P., Sebastiani, D.
Unraveling the existence of dynamic water channels in light-harvesting proteins: alpha-C-phycocyanobilin in vitro
CHEMICAL SCIENCE, 4:755-763, 2013
abstract, full text

Cui, Y.L., Zhang, J.L., Zheng, Q.C., Niu, R.J., Xu, Y., Zhang, H.X., Sun, C.C.
Structural and Dynamic Basis of Human Cytochrome P4507B1: A Survey of Substrate Selectivity and Major Active Site Access Channels
CHEMISTRY-A EUROPEAN JOURNAL, 19:548-556, JAN 2013
abstract, full text

Grouzmann, E., Gualtierotti, J.B., Gerber-Lemaire, S., Abid, K., Brakch, N., Pedretti, A., Testa, B., Vistoli, G.
Lack of Enantioselectivity in the SULT1A3-catalyzed Sulfoconjugation of Normetanephrine Enantiomers: An In Vitro and Computational Study
CHIRALITY, 25:28-34, JAN 2013
abstract, full text

Textor, L.C., Colussi, F., Silveira, R.L., Serpa, V., de Mello, B.L., Muniz, J.R.C., Squina, F.M., Pereira, N., Skaf, M.S., Polikarpov, I.
Joint X-ray crystallographic and molecular dynamics study of cellobiohydrolase I from Trichoderma harzianum: deciphering the structural features of cellobiohydrolase catalytic activity
FEBS JOURNAL, 280:56-69, JAN 2013
abstract, full text

Halder, P., Taraphder, S.
Modeling the structure and proton transfer pathways of the mutant His-107-Tyr of human carbonic anhydrase II
JOURNAL OF MOLECULAR MODELING, 19:289-298, JAN 2013
abstract, full text

Liu, Y.T., Agrawal, N.J., Radhakrishnan, R.
A flexible-protein molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK-3 beta, and CDK2/Cyclin A protein kinases
JOURNAL OF MOLECULAR MODELING, 19:371-382, JAN 2013
abstract, full text

Arias, H.R., Fedorov, N.B., Benson, L.C., Lippiello, P.M., Gatto, G.J., Feuerbach, D., Ortells, M.O.
Functional and Structural Interaction of (-)-Reboxetine with the Human alpha 4 beta 2 Nicotinic Acetylcholine Receptor
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS, 344:113-123, JAN 2013
abstract, full text

Li, Y.L., Guo, H.
Atomistic simulations of an antimicrobial molecule interacting with a model bacterial membrane
THEORETICAL CHEMISTRY ACCOUNTS, 132: Art. No. 1303, JAN 2013
abstract, full text

Tillman, T., Cheng, M.H., Chen, Q., Tang, P., Xu, Y.
Reversal of ion-charge selectivity renders the pentameric ligand-gated ion channel GLIC insensitive to anaesthetics
BIOCHEMICAL JOURNAL, 449:61-68, JAN 1 2013
abstract, full text

Swift, R.V., Amaro, R.E.
Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?
CHEMICAL BIOLOGY & DRUG DESIGN, 81:61-71, JAN 2013
abstract, full text

Wan, H., Hu, J.P., Tian, X.H., Chang, S.
Molecular dynamics simulations of wild type and mutants of human complement receptor 2 complexed with C3d
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:1241-1251, 2013
abstract, full text

Davis, B.C., Thorpe, I.F.
Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:40-52, JAN 2013
abstract, full text

Romanowska, J., Reuter, N., Trylska, J.
Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 81:63-80, JAN 2013
abstract, full text

Jana, A.K., Jose, J.C., Sengupta, N.
Critical roles of key domains in complete adsorption of A beta peptide on single-walled carbon nanotubes: insights with point mutations and MD simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 15:837-844, 2013
abstract, full text

Bertran, O., Zhang, B.Z., Schluter, A.D., Halperin, A., Kroger, M., Aleman, C.
Computer simulation of dendronized polymers: organization and characterization at the atomistic level
RSC ADVANCES, 3:126-140, 2013
abstract, full text

Thiele, D., Kraszewski, S., Balme, S., Picaud, F., Janot, J.M., Dejardin, P.
Structure and ionic selectivity of a hybrid polyene/artificial polymer solid state membrane
SOFT MATTER, 9:684-691, 2013
abstract, full text

Cho, K.R., Salter, E.A., De Yoreo, J.J., Wierzbicki, A., Elhadj, S., Huang, Y., Qiu, S.R.
Growth inhibition of calcium oxalate monohydrate crystal by linear aspartic acid enantiomers investigated by in situ atomic force microscopy
CRYSTENGCOMM, 15:54-64, 2013
abstract, full text

Witkowski, M., Oleksiak, A., Piontek, T., Weglarz, J.
Practical power consumption estimation for real life HPC applications
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING AND ESCIENCE, 29:208-217, JAN 2013
abstract, full text

Causa, F., Della Moglie, R., Iaccino, E., Mimmi, S., Marasco, D., Scognamiglio, P.L., Battista, E., Palmieri, C., Cosenza, C., Sanguigno, L., Quinto, I., Scala, G., Netti, P.A.
Evolutionary screening and adsorption behavior of engineered M13 bacteriophage and derived dodecapeptide for selective decoration of gold interfaces
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 389:220-229, JAN 1 2013
abstract, full text

Votapka, L.W., Czapla, L., Zhenirovskyy, M., Amaro, R.E.
DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 13:256-268, JAN 2013
abstract, full text

Isin, B., Estiu, G., Wiest, O., Oltvai, Z.N.
Identifying Ligand Binding Conformations of the beta 2-Adrenergic Receptor by Using Its Agonists as Computational Probes
PLOS ONE, 7: Art. No. e50186, DEC 31 2012
abstract, full text

Yamaguchi, Y., Nishima, W., Re, S.Y., Sugita, Y.
Confident identification of isomeric N-glycan structures by combined ion mobility mass spectrometry and hydrophilic interaction liquid chromatography
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 26:2877-2884, DEC 30 2012
abstract, full text

Grauffel, C., Abboud, A., Liszczak, G., Marmorstein, R., Arnesen, T., Reuter, N.
Specificity and Versatility of Substrate Binding Sites in Four Catalytic Domains of Human N-Terminal Acetyltransferases
PLOS ONE, 7: Art. No. e52642, DEC 28 2012
abstract, full text

Edens, L.E., Brozik, J.A., Keller, D.J.
Coarse-Grained Model DNA: Structure, Sequences, Stems, Circles, Hairpins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14735-14743, DEC 27 2012
abstract, full text

Pan, J.J., Cheng, X.L., Heberle, F.A., Mostofian, B., Kucerka, N., Drazba, P., Katsaras, J.
Interactions between Ether Phospholipids and Cholesterol As Determined by Scattering and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14829-14838, DEC 27 2012
abstract, full text

Cembran, A., Masterson, L.R., McClendon, C.L., Taylor, S.S., Gao, J.L., Veglia, G.
Conformational Equilibrium of N-Myristoylated cAMP-Dependent Protein Kinase A by Molecular Dynamics Simulations
BIOCHEMISTRY, 51:10186-10196, DEC 25 2012
abstract, full text

Sodt, A.J., Pastor, R.W.
The tension of a curved surface from simulation
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 234101, DEC 21 2012
abstract, full text

Sahu, B.S., Obbineni, J.M., Sahu, G., Allu, P.K.R., Subramanian, L., Sonawane, P.J., Singh, P.K., Sasi, B.K., Senapati, S., Maji, S.K., Bera, A.K., Gomathi, B.S., Mullasari, A.S., Mahapatra, N.R.
Functional Genetic Variants of the Catecholamine-Release-Inhibitory Peptide Catestatin in an Indian Population ALLELE-SPECIFIC EFFECTS ON METABOLIC TRAITS
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:43840-43852, DEC 21 2012
abstract, full text

Kotsyubynskyy, D., Zerbetto, M., Soltesova, M., Engstrom, O., Pendrill, R., Kowalewski, J., Widmalm, G., Polimeno, A.
Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. 2. Interpretation of Complex Dynamics in Linear Oligosaccharides
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14541-14555, DEC 20 2012
abstract, full text

Gaborek, T.J., Chipot, C., Madura, J.D.
Conformational Free-Energy Landscapes for a Peptide in Saline Environments
BIOPHYSICAL JOURNAL, 103:2513-2520, DEC 19 2012
abstract, full text

Kitam, V.O., Maksymchuk, O.V., Chashchyn, M.O.
The possible mechanisms of CYP2E1 interactions with HSP90 and the influence of ethanol on them
BMC STRUCTURAL BIOLOGY, 12: Art. No. 33, DEC 17 2012
abstract, full text

Turecek, F., Moss, C.L., Chung, T.W.
Correlating ETD fragment ion intensities with peptide ion conformational and electronic structure
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 330:207-219, DEC 15 2012
abstract, full text

Saito, H., Iwayama, M., Takagi, H., Nishimura, M., Miyakawa, T., Kawaguchi, K., Takasu, M., Mizukami, T., Nagao, H.
Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:3834-3839, DEC 15 2012
abstract, full text

Strunk, T., Wolf, M., Brieg, M., Klenin, K., Biewer, A., Tristram, F., Ernst, M., Kleine, P.J., Heilmann, N., Kondov, I., Wenzel, W.
SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2602-2613, DEC 15 2012
abstract, full text

Barakat, K.H., Jordheim, L.P., Perez-Pineiro, R., Wishart, D., Dumontet, C., Tuszynski, J.A.
Virtual Screening and Biological Evaluation of Inhibitors Targeting the XPA-ERCC1 Interaction
PLOS ONE, 7: Art. No. e51329, DEC 14 2012
abstract, full text

Miller, K.A., Williams, L.H., Rose, E., Kuiper, M., Dahl, H.H.M., Manji, S.S.M.
Inner Ear Morphology Is Perturbed in Two Novel Mouse Models of Recessive Deafness
PLOS ONE, 7: Art. No. e51284, DEC 12 2012
abstract, full text

Vargiu, A.V., Nikaido, H.
Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:20637-20642, DEC 11 2012
abstract, full text

Kang, S.G., Huynh, T., Zhou, R.H.
Non-destructive Inhibition of Metallofullerenol Gd@C-82(OH)(22) on WW domain: Implication on Signal Transduction Pathway
SCIENTIFIC REPORTS, 2: Art. No. 957, DEC 11 2012
abstract, full text

Rui, H., Rivera, M., Im, W.
Protein Dynamics and Ion Traffic in Bacterioferritin
BIOCHEMISTRY, 51:9900-9910, DEC 11 2012
abstract, full text

Takemura, K., Guo, H., Sakuraba, S., Matubayasi, N., Kitao, A.
Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 215105, DEC 7 2012
abstract, full text

Rippers, Y., Horch, M., Hildebrandt, P., Zebger, I., Mroginski, M.A.
Revealing the Absolute Configuration of the CO and CN- Ligands at the Active Site of a [NiFe] Hydrogenase
CHEMPHYSCHEM, 13:3852-3856, DEC 7 2012
abstract, full text

Modi, N., Benz, R., Hancock, R.E.W., Kleinekathofer, U.
Modeling the Ion Selectivity of the Phosphate Specific Channel OprP
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:3639-3645, DEC 6 2012
abstract, full text

Haspel, N., Laurent, A.D., Zanuy, D., Nussinov, R., Aleman, C., Puiggali, J., Revilla-Lopez, G.
Conformational Exploration of Two Peptides and Their Hybrid Polymer Conjugates: Potentialities As Self-Aggregating Materials
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13941-13952, DEC 6 2012
abstract, full text

Mula, S., McConnell, M.D., Ching, A., Zhao, N., Gordon, H.L., Hastings, G., Redding, K.E., van der Est, A.
Introduction of a Hydrogen Bond between Phylloquinone PhQ(A) and a Threonine Side-Chain OH Group in Photosystem I
JOURNAL OF PHYSICAL CHEMISTRY B, 116:14008-14016, DEC 6 2012
abstract, full text

Sotomayor, M., Weihofen, W.A., Gaudet, R., Corey, D.P.
Structure of a force-conveying cadherin bond essential for inner-ear mechanotransduction
NATURE, 492:128-+, DEC 6 2012
abstract, full text

Fujimoto, Y.K., Green, D.F.
Carbohydrate Recognition by the Antiviral Lectin Cyanovirin-N
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:19639-19651, DEC 5 2012
abstract, full text

Lockhart, C., Klimov, D.K.
Molecular Interactions of Alzheimer's Biomarker FDDNP with A beta Peptide
BIOPHYSICAL JOURNAL, 103:2341-2351, DEC 5 2012
abstract, full text

Tyka, M.D., Jung, K., Baker, D.
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2483-+, DEC 5 2012
abstract, full text

Kirkpatrick, A., Heo, J., Abrol, R., Goddard, W.A.
Predicted structure of agonist-bound glucagon-like peptide 1 receptor, a class B G protein-coupled receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:19988-19993, DEC 4 2012
abstract, full text

Chen, R., Robinson, A., Chung, S.H.
Binding of Hanatoxin to the Voltage Sensor of Kv2.1
TOXINS, 4:1552-1564, DEC 2012
abstract, full text

Wu, Q.Y., Li, F., Guo, H.Y., Cao, J., Chen, C., Chen, W., Zhao, K., Zeng, L.Y., Han, Z.X., Li, Z.Y., Wang, X.Y., Xu, K.L.
Amino acid residue E543 in JAK2 C618R is a potential therapeutic target for myeloproliferative disorders caused by JAK2 C618R mutation
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 528:57-66, DEC 1 2012
abstract, full text

Cho, K.R., Salter, E.A., De Yoreo, J.J., Wierzbicki, A., Elhadj, S., Huang, Y., Qiu, S.R.
Impact of Chiral Molecules on the Formation of Biominerals: A Calcium Oxalate Monohydrate Example
CRYSTAL GROWTH & DESIGN, 12:5939-5947, DEC 2012
abstract, full text

Maienschein-Cline, M., Dinner, A.R., Hlavacek, W.S., Mu, F.P.
Improved predictions of transcription factor binding sites using physicochemical features of DNA
NUCLEIC ACIDS RESEARCH, 40: Art. No. e175, DEC 2012
abstract, full text

Abolbashari, M.H., Ameli, S.
Mechanical unfolding of titin I27 domain: Nanoscale simulation of mechanical properties based on virial theorem via steered molecular dynamics technique
SCIENTIA IRANICA, 19:1526-1533, DEC 2012
abstract, full text

Pietra, F.
On 3LEZ, a Deep-Sea Halophilic Protein with in vitro Class-A beta-Lactamase Activity: Molecular-Dynamics, Docking, and Reactivity Simulations
CHEMISTRY & BIODIVERSITY, 9:2659-2684, DEC 2012
abstract, full text

Lacroix, J.J., Pless, S.A., Maragliano, L., Campos, F.V., Galpin, J.D., Ahern, C.A., Roux, B., Bezanilla, F.
Intermediate state trapping of a voltage sensor
JOURNAL OF GENERAL PHYSIOLOGY, 140:635-652, DEC 2012
abstract, full text

Mwaura, J., Tao, Z., James, H., Albers, T., Schwartz, A., Grewer, C.
Protonation State of a Conserved Acidic Amino Acid Involved in Na+ Binding to the Glutamate Transporter EAAC1
ACS CHEMICAL NEUROSCIENCE, 3:1073-1083, DEC 2012
abstract, full text

Gentile, F., Moretti, M., Limongi, T., Falqui, A., Bertoni, G., Scarpellini, A., Santoriello, S., Maragliano, L., Zaccaria, R.P., di Fabrizio, E.
Direct Imaging of DNA Fibers: The Visage of Double Helix
NANO LETTERS, 12:6453-6458, DEC 2012
abstract, full text

Ferreira-Cerca, S., Sagar, V., Schafer, T., Diop, M., Wesseling, A.M., Lu, H.Y., Chai, E., Hurt, E., LaRonde-LeBlanc, N.
ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 19:1316-+, DEC 2012
abstract, full text

Kappel, K., Wereszczynski, J., Clubb, R.T., McCammon, J.A.
The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations
PROTEIN SCIENCE, 21:1858-1871, DEC 2012
abstract, full text

Sotomayor-Zarate, R., Quirozi, G., Araya, K.A., Abarea, J., Ibanez, M.R., Montecinos, A., Guajardo, C., Nunez, G., Fierro, A., Moya, P.R., Iturriaga-Vasquez, P., Gomez-Molina, C., Gysling, K., Reyes-Parada, M.
4-Methylthioamphetamine Increases Dopamine in the Rat Striatum and has Rewarding Effects In Vivo
BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY, 111:371-379, DEC 2012
abstract, full text

Salvi, M., Trashi, E., Cozza, G., Franchin, C., Arrigoni, G., Pinna, L.A.
Investigation on PLK2 and PLK3 substrate recognition
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1824:1366-1373, DEC 2012
abstract, full text

Shenoy, S.S., Nanda, H., Losche, M.
Membrane association of the PTEN tumor suppressor: Electrostatic interaction with phosphatidylserine-containing bilayers and regulatory role of the C-terminal tail
JOURNAL OF STRUCTURAL BIOLOGY, 180:394-408, DEC 2012
abstract, full text

Venkateshwari, S., Veluraja, K.
Molecular Modelling and Molecular Dynamics studies of GD1A, GD1B and their complexes with BoNT/B - Perspectives in interaction and specificity
JOURNAL OF STRUCTURAL BIOLOGY, 180:497-508, DEC 2012
abstract, full text

Yogesh, R., Behera, R.N.
Molecular Dynamics Simulations of Micellization of Alkyl Ethoxylate
ASIAN JOURNAL OF CHEMISTRY, 24:5785-5788, DEC 2012
abstract, full text

Li, M.S., Mai, B.K.
Steered Molecular Dynamics-A Promising Tool for Drug Design
CURRENT BIOINFORMATICS, 7:342-351, DEC 2012
abstract, full text

Feng, Z.W., Hou, T.J., Li, Y.Y.
Selectivity and activation of dopamine D3R from molecular dynamics
JOURNAL OF MOLECULAR MODELING, 18:5051-5063, DEC 2012
abstract, full text

Atilgan, C., Inanc, I., Atilgan, A.R.
On modifying properties of polymeric melts by nanoscopic particles
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 50:1653-1662, DEC 1 2012
abstract, full text

Srivastava, A., Ben Halevi, R., Veksler, A., Granek, R.
Tensorial elastic network model for protein dynamics: Integration of the anisotropic network model with bond-bending and twist elasticities
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2692-2700, DEC 2012
abstract, full text

Simonson, T., Satpati, P.
Nucleotide recognition by the initiation factor aIF5B: Free energy simulations of a neoclassical GTPase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2742-2757, DEC 2012
abstract, full text

Gur, M., Erman, B.
Quasi-harmonic fluctuations of two bound peptides
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2769-2779, DEC 2012
abstract, full text

Prakash, P., Sayyed-Ahmad, A., Zhou, Y., Volk, D.E., Gorenstein, D.G., Dial, E., Lichtenberger, L.M., Gorfe, A.A.
Aggregation behavior of ibuprofen, cholic acid and dodecylphosphocholine micelles
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:3040-3047, DEC 2012
abstract, full text

Zhao, J., Luo, Y., Jang, H.B., Yu, X., Wei, G.H., Nussinov, R., Zheng, J.
Probing ion channel activity of human islet amyloid polypeptide (amylin)
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:3121-3130, DEC 2012
abstract, full text

Wang, S., Tu, Y.S., Wan, R.Z., Fang, H.P.
Evaporation of Tiny Water Aggregation on Solid Surfaces with Different Wetting Properties
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13863-13867, NOV 29 2012
abstract, full text

Hansen, F.Y., Peters, G.H., Taub, H., Miskowiec, A.
Diffusion of water and selected atoms in DMPC lipid bilayer membranes
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 204910, NOV 28 2012
abstract, full text

Timko, J., Kuyucak, S.
Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 205106, NOV 28 2012
abstract, full text

Matsunaga, Y., Koike, R., Ota, M., Tame, J.R.H., Kidera, A.
Influence of Structural Symmetry on Protein Dynamics
PLOS ONE, 7: Art. No. e50011, NOV 26 2012
abstract, full text

Rosenhouse-Dantsker, A., Noskov, S., Han, H.Z., Adney, S.K., Tang, Q.Y., Rodriguez-Menchaca, A.A., Kowalsky, G.B., Petrou, V.I., Osborn, C.V., Logothetis, D.E., Levitan, I.
Distant Cytosolic Residues Mediate a Two-way Molecular Switch That Controls the Modulation of Inwardly Rectifying Potassium (Kir) Channels by Cholesterol and Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P-2)
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:40266-40278, NOV 23 2012
abstract, full text

Martin, L.S., Cerda, F., Jimenez, V., Fuentealba, J., Munoz, B., Aguayo, L.G., Guzman, L.
Inhibition of the Ethanol-induced Potentiation of alpha 1 Glycine Receptor by a Small Peptide That Interferes with G beta gamma Binding
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:40713-40721, NOV 23 2012
abstract, full text

Cheng, M.H., Coalson, R.D.
Energetics and Ion permeation Characteristics in a Glutamate-Gated Chloride (GluCl) Receptor Channel
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13637-13643, NOV 22 2012
abstract, full text

Furini, S., Domene, C.
Nonselective Conduction in a Mutated NaK Channel with Three Cation-Binding Sites
BIOPHYSICAL JOURNAL, 103:2106-2114, NOV 21 2012
abstract, full text

Miao, Y.L., Yi, Z., Cantrell, C., Glass, D.C., Baudry, J., Jain, N., Smith, J.C.
Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR, and Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 103:2167-2176, NOV 21 2012
abstract, full text

Collu, F., Vargiu, A.V., Dreier, J., Cascella, M., Ruggerone, P.
Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:19146-19158, NOV 21 2012
abstract, full text

de Victoria, A.L., Tamamis, P., Kieslich, C.A., Morikis, D.
Insights into the Structure, Correlated Motions, and Electrostatic Properties of Two HIV-1 gp120 V3 Loops
PLOS ONE, 7: Art. No. e49925, NOV 19 2012
abstract, full text

Faure, E., Starek, G., McGuire, H., Berneche, S., Blunck, R.
A Limited 4 angstrom Radial Displacement of the S4-S5 Linker Is Sufficient for Internal Gate Closing in Kv Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 287: DOI 10.1074/jbc.M112.415497, NOV 16 2012
abstract, full text

Mayer, F., Leone, V., Langer, J.D., Faraldo-Gomez, J.D., Muller, V.
A c Subunit with Four Transmembrane Helices and One Ion (Na+)-binding Site in an Archaeal ATP Synthase IMPLICATIONS FOR c RING FUNCTION AND STRUCTURE
JOURNAL OF BIOLOGICAL CHEMISTRY, 287: DOI 10.1074/jbc.M112.411223, NOV 16 2012
abstract, full text

Pennington, M.W., Rashid, M.H., Tajhya, R.B., Beeton, C., Kuyucak, S., Norton, R.S.
A C-terminally amidated analogue of ShK is a potent and selective blocker of the voltage-gated potassium channel Kv1.3
FEBS LETTERS, 586:3996-4001, NOV 16 2012
abstract, full text

Luan, B.Q., Wang, D.Q., Zhou, R.H., Harrer, S., Peng, H.B., Stolovitzky, G.
Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol
NANOTECHNOLOGY, 23: Art. No. 455102, NOV 16 2012
abstract, full text

Ngo, V.A., Kalia, R.K., Nakano, A., Vashishta, P.
Molecular Mechanism of Flip-Flop in Triple-Layer Oleic-Acid Membrane: Correlation between Oleic Acid and Water
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13416-13423, NOV 15 2012
abstract, full text

Zhao, K.W., Wu, H.Y.
Size Effects of Pore Density and Solute Size on Water Osmosis through Nanoporous Membrane
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13459-13466, NOV 15 2012
abstract, full text

Solov'yov, I.A., Yakubovich, A.V., Nikolaev, P.V., Volkovets, I., Solov'yov, A.V.
MesoBioNano exploreruA universal program for multiscale computer simulations of complex molecular structure and dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2412-2439, NOV 15 2012
abstract, full text

Flatt, J.W., Fox, T.L., Makarova, N., Blackwell, J.L., Dmitriev, I.P., Kashentseva, E.A., Curiel, D.T., Stewart, P.L.
CryoEM Visualization of an Adenovirus Capsid-Incorporated HIV Antigen
PLOS ONE, 7: Art. No. e49607, NOV 14 2012
abstract, full text

Pasquino, R., Zhang, B., Sigel, R., Yu, H., Ottiger, M., Bertran, O., Aleman, C., Schluter, A.D., Vlassopoulos, D.
Linear Viscoelastic Response of Dendronized Polymers
MACROMOLECULES, 45:8813-8823, NOV 13 2012
abstract, full text

Burgess, D.E., Bartos, D.C., Reloj, A.R., Campbell, K.S., Johnson, J.N., Tester, D.J., Ackerman, M.J., Fressart, V., Denjoy, I., Guicheney, P., Moss, A.J., Ohno, S., Horie, M., Delisle, B.P.
High-Risk Long QT Syndrome Mutations in the Kv7.1 (KCNQ1) Pore Disrupt the Molecular Basis for Rapid K+ Permeation
BIOCHEMISTRY, 51:9076-9085, NOV 13 2012
abstract, full text

Navaratnarajah, C.K., Negi, S., Braun, W., Cattaneo, R.
Membrane Fusion Triggering THREE MODULES WITH DIFFERENT STRUCTURE AND FUNCTION IN THE UPPER HALF OF THE MEASLES VIRUS ATTACHMENT PROTEIN STALK
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:38543-38551, NOV 9 2012
abstract, full text

Shim, J.Y., Bertalovitz, A.C., Kendall, D.A.
Probing the Interaction of SR141716A with the CB1 Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:38741-38754, NOV 9 2012
abstract, full text

Lai, C.L., Jao, C.C., Lyman, E., Gallop, J.L., Peter, B.J., McMahon, H.T., Langen, R., Voth, G.A.
Membrane Binding and Self-Association of the Epsin N-Terminal Homology Domain
JOURNAL OF MOLECULAR BIOLOGY, 423:800-817, NOV 9 2012
abstract, full text

Rogaski, B., Klauda, J.B.
Membrane-Binding Mechanism of a Peripheral Membrane Protein through Microsecond Molecular Dynamics Simulations
JOURNAL OF MOLECULAR BIOLOGY, 423:847-861, NOV 9 2012
abstract, full text

Zerbetto, M., Kotsyubynskyy, D., Kowalewski, J., Widmalm, G., Polimeno, A.
Stochastic Modeling of Flexible Biomolecules Applied to NMR Relaxation. I. Internal Dynamics of Cyclodextrins: gamma-Cyclodextrin as a Case Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:13159-13171, NOV 8 2012
abstract, full text

Zhang, Y., Lou, J.Z.
The Ca2+ Influence on Calmodulin Unfolding Pathway: A Steered Molecular Dynamics Simulation Study
PLOS ONE, 7: Art. No. e49013, NOV 7 2012
abstract, full text

Andersson, M., Bondar, A.N., Freites, J.A., Tobias, D.J., Kaback, H.R., White, S.H.
Proton-Coupled Dynamics in Lactose Permease
STRUCTURE, 20:1893-1904, NOV 7 2012
abstract, full text

Kubiak-Ossowska, K., Mulheran, P.A.
Protein Diffusion and Long-Term Adsorption States at Charged Solid Surfaces
LANGMUIR, 28:15577-15585, NOV 6 2012
abstract, full text

Kang, P., Qin, W., Zheng, Z.M., Dong, C.Q., Yang, Y.P.
Theoretical study on the mechanisms of cellulose dissolution and precipitation in the phosphoric acid-acetone process
CARBOHYDRATE POLYMERS, 90:1771-1778, NOV 6 2012
abstract, full text

Ceccarini, L., Masetti, M., Cavalli, A., Recanatini, M.
Ion Conduction through the hERG Potassium Channel
PLOS ONE, 7: Art. No. e49017, NOV 2 2012
abstract, full text

Ghemtio, L., Perez-Nueno, V.I., Leroux, V., Asses, Y., Souchet, M., Mavridis, L., Maigret, B., Ritchie, D.W.
Recent Trends and Applications in 3D Virtual Screening
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING, 15:749-769, NOV 2012
abstract, full text

Kekenes-Huskey, P.M., Lindert, S., McCammon, J.A.
Molecular Basis of Calcium-Sensitizing and Desensitizing Mutations of the Human Cardiac Troponin C Regulatory Domain: A Multi-Scale Simulation Study
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002777, NOV 2012
abstract, full text

Zhang, D.D., Liu, G.Q., Xue, J.Y., Lou, J.Z., Nierhaus, K.H., Gong, W.M., Qin, Y.
Common chaperone activity in the G-domain of trGTPase protects L11-L12 interaction on the ribosome
NUCLEIC ACIDS RESEARCH, 40:10851-10865, NOV 2012
abstract, full text

Plsikova, J., Janovec, L., Koval, J., Ungvarsky, J., Mikes, J., Jendzelovsky, R., Fedorocko, P., Imrich, J., Kristian, P., Kasparkova, J., Brabec, V., Kozurkova, M.
3,6-Bis(3-alkylguanidino)acridines as DNA-intercalating antitumor agents
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 57:283-295, NOV 2012
abstract, full text

Simard, J., Ammi, M., Auvray, M.
Collaborative Strategies for the Search of 3-D Targets in Molecular Environments
IEEE TRANSACTIONS ON SYSTEMS MAN AND CYBERNETICS PART C-APPLICATIONS AND REVIEWS, 42:1555-1565, NOV 2012
abstract, full text

Zheng, Y., Gun'ko, V.M., Howell, C.A., Sandeman, S.R., Phillips, G.J., Kozynchenko, O.P., Tennison, S.R., Ivanov, A.E., Mikhalovsky, S.V.
Composites with Macroporous Poly(vinyl alcohol) Cryogels with Attached Activated Carbon Microparticles with Controlled Accessibility of a Surface
ACS APPLIED MATERIALS & INTERFACES, 4:5936-5944, NOV 2012
abstract, full text

Mohebbi, A.
Prediction of specific heat and thermal conductivity of nanofluids by a combined equilibrium and non-equilibrium molecular dynamics simulation
JOURNAL OF MOLECULAR LIQUIDS, 175:51-58, NOV 2012
abstract, full text

Zhao, H.T., Huang, D.Z., Caflisch, A.
Discovery of Tyrosine Kinase Inhibitors by Docking into an Inactive Kinase Conformation Generated by Molecular Dynamics
CHEMMEDCHEM, 7:1983-1990, NOV 2012
abstract, full text

Wan, S.Z., Coveney, P.V.
Regulation of JAK2 Activation by Janus Homology 2: Evidence from Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2992-3000, NOV 2012
abstract, full text

Louet, M., Charlier, L., Martinez, J., Floquet, N.
Dissociation of Membrane-Anchored Heterotrimeric G-Protein Induced by G(alpha) Subunit Binding to GTP
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:3022-3027, NOV 2012
abstract, full text

Han, W., Schulten, K.
Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4413-4424, NOV 2012
abstract, full text, TCBG publications

Piggot, T.J., Pineiro, A., Khalid, S.
Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4593-4609, NOV 2012
abstract, full text

Ruymgaart, A.P., Elber, R.
Revisiting Molecular Dynamics on a CPU/GPU System: Water Kernel and SHAKE Parallelization
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4624-4636, NOV 2012
abstract, full text

Jiang, W., Luo, Y., Maragliano, L., Roux, B.
Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4672-4680, NOV 2012
abstract, full text

Ozer, G., Quirk, S., Hernandez, R.
Thermodynamics of Decaalanine Stretching in Water Obtained by Adaptive Steered Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:4837-4844, NOV 2012
abstract, full text

Lockhart, C., Kim, S., Klimov, D.K.
Explicit Solvent Molecular Dynamics Simulations of A beta Peptide Interacting with Ibuprofen Ligands
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12922-12932, NOV 1 2012
abstract, full text

Calligari, P., Abergel, D.
Toward the Characterization of Fractional Stochastic Processes Underlying Methyl Dynamics in Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12955-12965, NOV 1 2012
abstract, full text

Lin, P.H., Tsai, C.W., Wu, J.W., Ruaan, R.C., Chen, W.Y.
Molecular dynamics simulation of the induced-fit binding process of DNA aptamer and L-argininamide
BIOTECHNOLOGY JOURNAL, 7: DOI 10.1002/biot.201200003, NOV 2012
abstract, full text

Stauch, B., Orts, J., Carlomagno, T.
The description of protein internal motions aids selection of ligand binding poses by the INPHARMA method
JOURNAL OF BIOMOLECULAR NMR, 54:245-256, NOV 2012
abstract, full text

Unzueta, U., Ferrer-Miralles, N., Cedano, J., Xu, Z.K., Pesarrodona, M., Saccardo, P., Garcia-Fruitos, E., Domingo-Espin, J., Kumar, P., Gupta, K.C., Mangues, R., Villaverde, A., Vazquez, E.
Non-amyloidogenic peptide tags for the regulatable self-assembling of protein-only nanoparticles
BIOMATERIALS, 33:8714-8722, NOV 2012
abstract, full text

Suplatov, D.A., Besenmatter, W., Svedas, V.K., Svendsen, A.
Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities
PROTEIN ENGINEERING DESIGN & SELECTION, 25:689-697, NOV 2012
abstract, full text

Nandi, T.K., Bairagya, H.R., Mishra, D.K., Mukhopadhyay, B.P., Banerjee, A.
Structural and Putative Functional Role of Conserved Water Molecular Cluster in the X-ray Structures of Plant Thiol Proteases: A Molecular Dynamics Simulation Study
JOURNAL OF CHEMICAL CRYSTALLOGRAPHY, 42:1105-1118, NOV 2012
abstract, full text

del Val, C., White, S.H., Bondar, A.N.
Ser/Thr Motifs in Transmembrane Proteins: Conservation Patterns and Effects on Local Protein Structure and Dynamics
JOURNAL OF MEMBRANE BIOLOGY, 245:717-730, NOV 2012
abstract, full text

Lee, C.J., Wu, S., Bartolotti, L.J., Pedersen, L.G.
Molecular dynamic simulations of the binary complex of human tissue factor (TF1-242) and factor VIIa (TF1-242/FVIIa) on a 4:1 POPC/POPS lipid bilayer
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 10:2402-2405, NOV 2012
full text

Lestard, M.E.D., Diaz, S.B., Tuttolomondo, M.E., Cortez, S.S., Puiatti, M., Pierini, A.B., Ben Altabef, A.
Interaction of S-methyl methanethiosulfonate with DPPC bilayer
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 97:479-489, NOV 2012
abstract, full text

Broadley, S.G., Gumbart, J.C., Weber, B.W., Marakalala, M.J., Steenkamp, D.J., Sewell, B.T.
A new crystal form of MshB from Mycobacterium tuberculosis with glycerol and acetate in the active site suggests the catalytic mechanism
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 68:1450-1459, NOV 2012
abstract, full text

Liu, H.M., Roberts, J.A., Moore, D., Anderson, B., Pallansch, M.A., Pevear, D.C., Collett, M.S., Oberste, M.S.
Characterization of Poliovirus Variants Selected for Resistance to the Antiviral Compound V-073
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 56:5568-5574, NOV 2012
abstract, full text

Tuszynski, J.A., Craddock, T.J.A., Mane, J.Y., Barakat, K., Tseng, C.Y., Gajewski, M., Winter, P., Alisaraie, L., Patterson, J., Carpenter, E., Wang, W.W., Deyholos, M.K., Li, L.J., Sun, X., Zhang, Y., Wong, G.K.S.
Modeling the Yew Tree Tubulin and a Comparison of its Interaction with Paclitaxel to Human Tubulin
PHARMACEUTICAL RESEARCH, 29:3007-3021, NOV 2012
abstract, full text

Caulfield, T., Devkota, B.
Motion of transfer RNA from the A/T state into the A-site using docking and simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2489-2500, NOV 2012
abstract, full text

Losasso, V., Schiffer, S., Barth, S., Carloni, P.
Design of human granzyme B variants resistant to serpin B9
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2514-2522, NOV 2012
abstract, full text

Qiu, H., Shen, R., Guo, W.L.
Ion solvation and structural stability in a sodium channel investigated by molecular dynamics calculations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2529-2535, NOV 2012
abstract, full text

Tsai, H.H.G., Lai, W.X., Lin, H.D., Lee, J.B., Juang, W.F., Tseng, W.H.
Molecular dynamics simulation of cation-phospholipid clustering in phospholipid bilayers: Possible role in stalk formation during membrane fusion
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2742-2755, NOV 2012
abstract, full text

Kraszewski, S., Picaud, F., Elhechmi, I., Gharbi, T., Ramseyer, C.
How long a functionalized carbon nanotube can passively penetrate a lipid membrane
CARBON, 50:5301-5308, NOV 2012
abstract, full text

Paris, G., Kraszewski, S., Ramseyer, C., Enescu, M.
About the structural role of disulfide bridges in serum albumins: Evidence from protein simulated unfolding
BIOPOLYMERS, 97:889-898, NOV 2012
abstract, full text

Bellacchio, E.
In silico analysis of the two tandem somatomedin B domains of ENPP1 reveals hints on the homodimerization of the protein
JOURNAL OF CELLULAR PHYSIOLOGY, 227:3566-3574, NOV 2012
abstract, full text

Solov'yov, I.A., Domratcheva, T., Shahi, A.R.M., Schulten, K.
Decrypting Cryptochrome: Revealing the Molecular Identity of the Photoactivation Reaction
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:18046-18052, OCT 31 2012
abstract, full text, TCBG publications

Khafizov, K., Perez, C., Koshy, C., Quick, M., Fendler, K., Ziegler, C., Forrest, L.R.
Investigation of the sodium-binding sites in the sodium-coupled betaine transporter BetP
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E3035-E3044, OCT 30 2012
abstract, full text

Marek, P.J., Patsalo, V., Green, D.F., Raleigh, D.P.
Ionic Strength Effects on Amyloid Formation by Amylin Are a Complicated Interplay among Debye Screening, Ion Selectivity, and Hofmeister Effects
BIOCHEMISTRY, 51:8478-8490, OCT 30 2012
abstract, full text

Nikolova, E.N., Bascom, G.D., Andricioaei, I., Al-Hashimi, H.M.
Probing Sequence-Specific DNA Flexibility in A-Tracts and Pyrimidine-Purine Steps by Nuclear Magnetic Resonance C-13 Relaxation and Molecular Dynamics Simulations
BIOCHEMISTRY, 51:8654-8664, OCT 30 2012
abstract, full text

Tam, H.H., Asthagiri, D., Paulaitis, M.E.
Coordination state probabilities and the solvation free energy of Zn2+ in aqueous methanol solutions
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 164504, OCT 28 2012
abstract, full text

Das, D., Samanta, D., Hasan, S., Das, A., Bhattacharya, A., Dasgupta, S., Chakrabarti, A., Ghorai, P., Das Gupta, C.
Identical RNA-Protein Interactions in Vivo and in Vitro and a Scheme of Folding the Newly Synthesized Proteins by Ribosomes
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:37508-37521, OCT 26 2012
abstract, full text

Rodriguez-Rodriguez, E.R., Ledezma-Candanoza, L.M., Contreras-Ferrat, L.G., Olamendi-Portugal, T., Possani, L.D., Becerril, B., Riano-Umbarila, L.
A Single Mutation in Framework 2 of the Heavy Variable Domain Improves the Properties of a Diabody and a Related Single-Chain Antibody
JOURNAL OF MOLECULAR BIOLOGY, 423:337-350, OCT 26 2012
abstract, full text

Favia, A.D., Habrant, D., Scarpelli, R., Migliore, M., Albani, C., Bertozzi, S.M., Dionisi, M., Tarozzo, G., Piomelli, D., Cavalli, A., De Vivo, M.
Identification and Characterization of Carprofen as a Multitarget Fatty Acid Amide Hydrolase/Cyclooxygenase Inhibitor
JOURNAL OF MEDICINAL CHEMISTRY, 55:8807-8826, OCT 25 2012
abstract, full text

Banas, P., Sklenovsky, P., Wedekind, J.E., Sponer, J., Otyepka, M.
Molecular Mechanism of preQ(1) Riboswitch Action: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12721-12734, OCT 25 2012
abstract, full text

Interlandi, G., Ling, M.H., Tu, A.Y., Chung, D.W., Thomas, W.E.
Structural Basis of Type 2A von Willebrand Disease Investigated by Molecular Dynamics Simulations and Experiments
PLOS ONE, 7: Art. No. e45207, OCT 23 2012
abstract, full text

Hill, E.H., Stratton, K., Whitten, D.G., Evans, D.G.
Molecular Dynamics Simulation Study of the Interaction of Cationic Biocides with Lipid Bilayers: Aggregation Effects and Bilayer Damage
LANGMUIR, 28:14849-14854, OCT 23 2012
abstract, full text

Abderemane-Ali, F., Es-Salah-Lamoureux, Z., Delemotte, L., Kasimova, M.A., Labro, A.J., Snyders, D.J., Fedida, D., Tarek, M., Baro, I., Loussouarn, G.
Dual Effect of Phosphatidyl (4,5)-Bisphosphate PIP2 on Shaker K+ Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:36158-36167, OCT 19 2012
abstract, full text

Payne, C.M., Baban, J., Horn, S.J., Backe, P.H., Arvai, A.S., Dalhus, B., Bjoras, M., Eijsink, V.G.H., Sorlie, M., Beckham, G.T., Vaaje-Kolstad, G.
Hallmarks of Processivity in Glycoside Hydrolases from Crystallographic and Computational Studies of the Serratia marcescens Chitinases
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:36322-36330, OCT 19 2012
abstract, full text

Laurent, A.D., Mironov, V.A., Chapagain, P.P., Nemukhin, A.V., Krylov, A.I.
Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12426-12440, OCT 18 2012
abstract, full text

Fisette, O., Gagne, S., Lague, P.
Molecular Dynamics of Class A beta-lactamases-Effects of Substrate Binding
BIOPHYSICAL JOURNAL, 103:1790-1801, OCT 17 2012
abstract, full text

Gkionis, K., Rungger, I., Sanvito, S., Schwingenschlogl, U.
Protocol for classical molecular dynamics simulations of nano-junctions in solution
JOURNAL OF APPLIED PHYSICS, 112: Art. No. 083714, OCT 15 2012
abstract, full text

Hadi-Alijanvand, H., Proctor, E.A., Goliaei, B., Dokholyan, N.V., Moosavi-Movahedi, A.A.
Thermal Unfolding Pathway of PHD2 Catalytic Domain in Three Different PHD2 Species: Computational Approaches
PLOS ONE, 7: Art. No. e47061, OCT 15 2012
abstract, full text

Ylilauri, M., Pentikainen, O.T.
Structural Mechanism of N-Methyl-D-Aspartate Receptor Type 1 Partial Agonism
PLOS ONE, 7: Art. No. e47604, OCT 15 2012
abstract, full text

Martini, M.F., Pickholz, M.
Molecular dynamics study of uncharged bupivacaine enantiomers in phospholipid bilayers
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:3341-3345, OCT 15 2012
abstract, full text

Marais, P., Kenwood, J., Smith, K.C., Kuttel, M.M., Gain, J.
Efficient compression of molecular dynamics trajectory files
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:2131-2141, OCT 15 2012
abstract, full text

El-Hendawy, M.M., Garate, J.A., English, N.J., O'Reilly, S., Mooney, D.A.
Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 145103, OCT 14 2012
abstract, full text

Jover, J., Haslam, A.J., Galindo, A., Jackson, G., Muller, E.A.
Pseudo hard-sphere potential for use in continuous molecular-dynamics simulation of spherical and chain molecules
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 144505, OCT 14 2012
abstract, full text

Yu, C., Lou, J.Z., Wu, J.J., Pan, L.F., Feng, W., Zhang, M.J.
Membrane-induced Lever Arm Expansion Allows Myosin VI to Walk with Large and Variable Step Sizes
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:35021-35035, OCT 12 2012
abstract, full text

Dillon, S.L., Williamson, D.M., Elferich, J., Radler, D., Joshi, R., Thomas, G., Shinde, U.
Propeptides Are Sufficient to Regulate Organelle-Specific pH-Dependent Activation of Furin and Proprotein Convertase 1/3
JOURNAL OF MOLECULAR BIOLOGY, 423:47-62, OCT 12 2012
abstract, full text

Giambasu, G.M., Lee, T.S., Scott, W.G., York, D.M.
Mapping L1 Ligase Ribozyme Conformational Switch
JOURNAL OF MOLECULAR BIOLOGY, 423:106-122, OCT 12 2012
abstract, full text

Zhao, J.J., de Serrano, V., Dumarieh, R., Thompson, M., Ghiladi, R.A., Franzen, S.
The Role of the Distal Histidine in H2O2 Activation and Heme Protection in both Peroxidase and Globin Functions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12065-12077, OCT 11 2012
abstract, full text

Canchi, D.R., Jayasimha, P., Rau, D.C., Makhatadze, G.I., Garcia, A.E.
Molecular Mechanism for the Preferential Exclusion of TMAO from Protein Surfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12095-12104, OCT 11 2012
abstract, full text

Liu, Y.Z., Wu, M., Feng, X.Z., Shao, X.G., Cai, W.S.
Adsorption Behavior of Hydrophobin Proteins on Polydimethylsiloxane Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 116:12227-12234, OCT 11 2012
abstract, full text

Chen, R., Chung, S.H.
Structural Basis of the Selective Block of Kv1.2 by Maurotoxin from Computer Simulations
PLOS ONE, 7: Art. No. e47253, OCT 10 2012
abstract, full text

Deng, L., Broom, A., Kitova, E.N., Richards, M.R., Zheng, R.B., Shoemaker, G.K., Meiering, E.M., Klassen, J.S.
Kinetic Stability of the Streptavidin-Biotin Interaction Enhanced in the Gas Phase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:16586-16596, OCT 10 2012
abstract, full text

Larue, R., Gupta, K., Wuensch, C., Shkriabai, N., Kessl, J.J., Danhart, E., Feng, L., Taltynov, O., Christ, F., Van Duyne, G.D., Debyser, Z., Foster, M.P., Kvaratskhelia, M.
Interaction of the HIV-1 Intasome with Transportin 3 Protein (TNPO3 or TRN-SR2)
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:34044-34058, OCT 5 2012
abstract, full text

Priyadarzini, T.R.K., Selvin, J.F.A., Gromiha, M.M., Fukui, K., Veluraja, K.
Theoretical Investigation on the Binding Specificity of Sialyldisaccharides with Hemagglutinins of Influenza A Virus by Molecular Dynamics Simulations
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:34547-34557, OCT 5 2012
abstract, full text

Shen, R., Guo, W.L.
Mechanism for Variable Selectivity and Conductance in Mutated NaK Channels
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:2887-2891, OCT 4 2012
abstract, full text

Koyama, M., Nishimasu, H., Ishitani, R., Nureki, O.
Molecular Dynamics Simulation of Autotaxin: Roles of the Nuclease-like Domain and the Glycan Modification
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11798-11808, OCT 4 2012
abstract, full text

Halder, S., Bhattacharyya, D.
Structural Variations of Single and Tandem Mismatches in RNA Duplexes: A Joint MD Simulation and Crystal Structure Database Analysis
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11845-11856, OCT 4 2012
abstract, full text

Averett, R.D., Menn, B., Lee, E.H., Helms, C.C., Barker, T., Guthold, M.
A Modular Fibrinogen Model that Captures the Stress-Strain Behavior of Fibrin Fibers
BIOPHYSICAL JOURNAL, 103:1537-1544, OCT 3 2012
abstract, full text

Khelashvili, G., Galli, A., Weinstein, H.
Phosphatidylinositol 4,5-Biphosphate (PIP2) Lipids Regulate the Phosphorylation of Syntaxin N-Terminus by Modulating Both Its Position and Local Structure
BIOCHEMISTRY, 51:7685-7698, OCT 2 2012
abstract, full text

Chen, R., Chung, S.H.
Binding Modes and Functional Surface of Anti-mammalian Scorpion alpha-Toxins to Sodium Channels
BIOCHEMISTRY, 51:7775-7782, OCT 2 2012
abstract, full text

Sencanski, M.V., Sukalovic, V.B., Dosen-Micovic, L.I., Soskic, V., Andric, D.B., Roglic, G.M., Kostic-Rajacic, S.V.
MODELING INTERACTIONS OF alpha(1A) ADRENERGIC RECEPTOR AND DIFFERENT ARYLPIPERAZINE LIGANDS
DIGEST JOURNAL OF NANOMATERIALS AND BIOSTRUCTURES, 7:1767-1777, OCT-DEC 2012
abstract, full text

Hilder, T.A., Pace, R.J., Chung, S.H.
Computational Design of a Carbon Nanotube Fluorofullerene Biosensor
SENSORS, 12:13720-13735, OCT 2012
abstract, full text

Chen, Y., Cruz-Chu, E.R., Woodard, J.C., Gartia, M.R., Schulten, K., Liu, L.
Electrically Induced Conformational Change of Peptides on Metallic Nanosurfaces
ACS NANO, 6:8847-8856, OCT 2012
abstract, full text, TCBG publications

Kang, S.G., Li, H., Huynh, T., Zhang, F.C., Xia, Z., Zhang, Y., Zhou, R.H.
Molecular Mechanism of Surface-Assisted Epitaxial Self-Assembly of Amyloid-like Peptides
ACS NANO, 6:9276-9282, OCT 2012
abstract, full text

Montero-Alejo, V., Acosta-Alba, J., Perdomo-Morales, R., Perera, E., Hernandez-Rodriguez, E.W., Estrada, M.P., Porto-Verdecia, M.
Defensin like peptide from Panulirus argus relates structurally with beta defensin from vertebrates
FISH & SHELLFISH IMMUNOLOGY, 33:872-879, OCT 2012
abstract, full text

Singharoy, A., Joshi, H., Ortoleva, P.J.
Multiscale Macromolecular Simulation: Role of Evolving Ensembles
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2638-2649, OCT 2012
abstract, full text

Schmidt, T.H., Kandt, C.
LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2657-2669, OCT 2012
abstract, full text

Shang, Z.G., Sigworth, F.J.
Hydration-layer models for cryo-EM image simulation
JOURNAL OF STRUCTURAL BIOLOGY, 180:10-16, OCT 2012
abstract, full text

Zeng, Y.Y., Larson, S.B., Heitsch, C.E., McPherson, A., Harvey, S.C.
A model for the structure of satellite tobacco mosaic virus
JOURNAL OF STRUCTURAL BIOLOGY, 180:110-116, OCT 2012
abstract, full text

Harvey, M.J., De Fabritiis, G.
High-throughput molecular dynamics: the powerful new tool for drug discovery
DRUG DISCOVERY TODAY, 17:1059-1062, OCT 2012
abstract, full text

Kim, H.W., McIntosh, J.M.
alpha 6 nAChR subunit residues that confer alpha-conotoxin BuIA selectivity
FASEB JOURNAL, 26:4102-4110, OCT 2012
abstract, full text

Kramar, P., Delemotte, L., Lebar, A.M., Kotulska, M., Tarek, M., Miklavcic, D.
Molecular-Level Characterization of Lipid Membrane Electroporation using Linearly Rising Current
JOURNAL OF MEMBRANE BIOLOGY, 245:651-659, OCT 2012
abstract, full text

Torzilli, P.A., Bourne, J.W., Cigler, T., Vincent, C.T.
A new paradigm for mechanobiological mechanisms in tumor metastasis
SEMINARS IN CANCER BIOLOGY, 22:385-395, OCT 2012
abstract, full text

Ozorowski, G., Ryan, C.M., Whitelegge, J.P., Luecke, H.
Withaferin A binds covalently to the N-terminal domain of annexin A2
BIOLOGICAL CHEMISTRY, 393:1151-1163, OCT 2012
abstract, full text

Zhu, F.Q., Hummer, G.
Theory and Simulation of Ion Conduction in the Pentameric GLIC Channel
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3759-3768, OCT 2012
abstract, full text

Kekenes-Huskey, P.M., Metzger, V.T., Grant, B.J., McCammon, J.A.
Calcium binding and allosteric signaling mechanisms for the sarcoplasmic reticulum Ca2+ATPase
PROTEIN SCIENCE, 21:1429-1443, OCT 2012
abstract, full text

Landstrom, J., Persson, K., Rademacher, C., Lundborg, M., Wakarchuk, W., Peters, T., Widmalm, G.
Small molecules containing hetero-bicyclic ring systems compete with UDP-Glc for binding to WaaG glycosyltransferase
GLYCOCONJUGATE JOURNAL, 29:491-502, OCT 2012
abstract, full text

Fackeldey, K., Klimm, M., Weber, M.
A coarse graining method for the dimension reduction of the state space of biomolecules
JOURNAL OF MATHEMATICAL CHEMISTRY, 50:2623-2635, OCT 2012
abstract, full text

Tan, Q.L., Qin, W., Chen, Q.L., Dong, C.Q., Li, W.Y., Yang, Y.P.
Synergetic effect of ZrO2 on the oxidation-reduction reaction of Fe2O3 during chemical looping combustion
APPLIED SURFACE SCIENCE, 258:10022-10027, OCT 1 2012
abstract, full text

Jana, S., Dalapati, S., Ghosh, S., Guchhait, N.
Potential charge transfer probe induced conformational changes of model plasma protein human serum albumin: Spectroscopic, molecular docking, and molecular dynamics simulation study
BIOPOLYMERS, 97:766-777, OCT 2012
abstract, full text

Bardhan, J.P., Jungwirth, P., Makowski, L.
Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 124101, SEP 28 2012
abstract, full text

Holland, B.W., Gray, C.G., Tomberli, B.
Calculating diffusion and permeability coefficients with the oscillating forward-reverse method
PHYSICAL REVIEW E, 86: Art. No. 036707, SEP 27 2012
abstract, full text

Chagovets, V.V., Kosevich, M.V., Stepanian, S.G., Boryak, O.A., Shelkovsky, V.S., Orlov, V.V., Leontiev, V.S., Pokrovskiy, V.A., Adamowicz, L., Karachevtsev, V.A.
Noncovalent Interaction of Methylene Blue with Carbon Nanotubes: Theoretical and Mass Spectrometry Characterization
JOURNAL OF PHYSICAL CHEMISTRY C, 116:20579-20590, SEP 27 2012
abstract, full text

Baxa, M.C., Haddadian, E.J., Jha, A.K., Freed, K.F., Sosnick, T.R.
Context and Force Field Dependence of the Loss of Protein Backbone Entropy upon Folding Using Realistic Denatured and Native State Ensembles
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:15929-15936, SEP 26 2012
abstract, full text

Zheng, X.G., Wu, C.J., Ponder, J.W., Marshall, G.R.
Molecular Dynamics of beta-Hairpin Models of Epigenetic Recognition Motifs
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:15970-15978, SEP 26 2012
abstract, full text

Zhou, A.D., Abu-Baker, S., Sahu, I.D., Liu, L.S., McCarrick, R.M., Dabney-Smith, C., Lorigan, G.A.
Determining alpha-Helical and beta-Sheet Secondary Structures via Pulsed Electron Spin Resonance Spectroscopy
BIOCHEMISTRY, 51:7417-7419, SEP 25 2012
abstract, full text

Rubach, J.K., Cui, G., Schneck, J.L., Taylor, A.N., Zhao, B.G., Smallwood, A., Nevins, N., Wisnoski, D., Thrall, S.H., Meek, T.D.
The Amino-Acid Substituents of Dipeptide Substrates of Cathepsin C Can Determine the Rate-Limiting Steps of Catalysis
BIOCHEMISTRY, 51:7551-7568, SEP 25 2012
abstract, full text

Tsai, C.W., Chen, W.Y., Ruaan, R.C.
Retention Prediction of Peptide Diastereomers in Reversed-Phase Liquid Chromatography Assisted by Molecular Dynamics Simulation
LANGMUIR, 28:13601-13608, SEP 25 2012
abstract, full text

Apte-Sengupta, S., Negi, S., Leonard, V.H.J., Oezguen, N., Navaratnarajah, C.K., Braun, W., Cattaneo, R.
Base of the Measles Virus Fusion Trimer Head Receives the Signal That Triggers Membrane Fusion
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:33026-33035, SEP 21 2012
abstract, full text

Moscoso, C., Vergara-Jaque, A., Marquez-Miranda, V., Sepulveda, R.V., Valencia, I., Diaz-Franulic, I., Gonzalez-Nilo, F., Naranjo, D.
K+ Conduction and Mg2+ Blockade in a Shaker Kv-Channel Single Point Mutant with an Unusually High Conductance
BIOPHYSICAL JOURNAL, 103:1198-1207, SEP 19 2012
abstract, full text

Fan, J., Saunders, M.G., Voth, G.A.
Coarse-Graining Provides Insights on the Essential Nature of Heterogeneity in Actin Filaments
BIOPHYSICAL JOURNAL, 103:1334-1342, SEP 19 2012
abstract, full text

Zheng, W.J., Tekpinar, M.
Structure-Based Simulations of the Trans location Mechanism of the Hepatitis C Virus NS3 Helicase along Single-Stranded Nucleic Acid
BIOPHYSICAL JOURNAL, 103:1343-1353, SEP 19 2012
abstract, full text

Vagenende, V., Trout, B.L.
Quantitative Characterization of Local Protein Solvation To Predict Solvent Effects on Protein Structure
BIOPHYSICAL JOURNAL, 103:1354-1362, SEP 19 2012
abstract, full text

Zomot, E., Bahar, I.
A Conformational Switch in a Partially Unwound Helix Selectively Determines the Pathway for Substrate Release from the Carnitine/gamma-Butyrobetaine Antiporter CaiT
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:31823-31832, SEP 14 2012
abstract, full text

Minh, D.D.L.
Implicit ligand theory: Rigorous binding free energies and thermodynamic expectations from molecular docking
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 104106, SEP 14 2012
abstract, full text

Carpenter, T.S., Lau, E.Y., Lightstone, F.C.
A Role for Loop F in Modulating GABA Binding Affinity in the GABA(A) Receptor
JOURNAL OF MOLECULAR BIOLOGY, 422:310-323, SEP 14 2012
abstract, full text

Ngo, V.A., Kalia, R.K., Nakano, A., Vashishta, P.
Supercrystals of DNA-Functionalized Gold Nanoparticles: A Million-Atom Molecular Dynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 116:19579-19585, SEP 13 2012
abstract, full text

Nagata, T., Fedorov, D.G., Sawada, T., Kitaura, K.
Analysis of Solute-Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to a Solvated Griffithsin-Carbohydrate Complex
JOURNAL OF PHYSICAL CHEMISTRY A, 116:9088-9099, SEP 13 2012
abstract, full text

Liu, L.S., Sahu, I.D., Mayo, D.J., McCarrick, R.M., Troxel, K., Zhou, A.D., Shockley, E., Lorigan, G.A.
Enhancement of Electron Spin Echo Envelope Modulation Spectroscopic Methods to Investigate the Secondary Structure of Membrane Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11041-11045, SEP 13 2012
abstract, full text

MacMillan, A.C., McIntire, T.M., Freites, J.A., Tobias, D.J., Nizkorodov, S.A.
Interaction of Water Vapor with the Surfaces of Imidazolium-Based Ionic Liquid Nanoparticles and Thin Films
JOURNAL OF PHYSICAL CHEMISTRY B, 116:11255-11265, SEP 13 2012
abstract, full text

Abi, T.G., Taraphder, S.
Proton transfer reactions in carbon nanotubes endohedrally functionalized with selected polar amino acid sidechains
CHEMICAL PHYSICS, 405:107-116, SEP 11 2012
abstract, full text

Liu, Y.Z., Cai, W.S., Shao, X.G.
Molecular Dynamics Simulation of Hydrophobin Proteins on the Surface of Single-walled Carbon Nanotubes
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 33:2013-2018, SEP 10 2012
abstract, full text

Luan, B.Q., Zhou, R.H.
Nanopore-Based Sensors for Detecting Toxicity of a Carbon Nanotube to Proteins
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:2337-2341, SEP 6 2012
abstract, full text

Fujita, T., Brookes, J.C., Saikin, S.K., Aspuru-Guzik, A.
Memory-Assisted Exciton Diffusion in the Chlorosome Light-Harvesting Antenna of Green Sulfur Bacteria
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:2357-2361, SEP 6 2012
abstract, full text

Eilers, M., Goncalves, J.A., Abuja, S., Kirkup, C., Hirshfeld, A., Simmerling, C., Reeves, P.J., Sheves, M., Smith, S.O.
Structural Transitions of Transmembrane Helix 6 in the Formation of Metarhodopsin I
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10477-10489, SEP 6 2012
abstract, full text

Schlamadinger, D.E., Wang, Y., McCammon, J.A., Kim, J.E.
Spectroscopic and Computational Study of Melittin, Cecropin A, and the Hybrid Peptide CM15
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10600-10608, SEP 6 2012
abstract, full text

Ghane, T., Brancolini, G., Varsano, D., Di Felice, R.
Optical Properties of Triplex DNA from Time-Dependent Density Functional Theory
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10693-10702, SEP 6 2012
abstract, full text

Platania, C.B.M., Salomone, S., Leggio, G.M., Drago, F., Bucolo, C.
Homology Modeling of Dopamine D-2 and D-3 Receptors: Molecular Dynamics Refinement and Docking Evaluation
PLOS ONE, 7: Art. No. e44316, SEP 6 2012
abstract, full text

Topol, I., Collins, J., Mironov, V., Savitsky, A., Nemukhin, A.
Modeling absorption of the kindling fluorescent protein with the neutral form of the chromophore
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:2947-2951, SEP 5 2012
abstract, full text

Vashisth, H., Skiniotis, G., Brooks, C.L.
Using Enhanced Sampling and Structural Restraints to Refine Atomic Structures into Low-Resolution Electron Microscopy Maps
STRUCTURE, 20:1453-1462, SEP 5 2012
abstract, full text

Zhao, C.F., Stolzenberg, S., Gracia, L., Weinstein, H., Noskov, S., Shi, L.
Ion-Controlled Conformational Dynamics in the Outward-Open Transition from an Occluded State of LeuT
BIOPHYSICAL JOURNAL, 103:878-888, SEP 5 2012
abstract, full text

Alcaino, J., Fuentealba, M., Cabrera, R., Baeza, M., Cifuentes, V.
Modeling the Interfacial Interactions between CrtS and CrtR from Xanthophyllomyces dendrorhous, a P450 System Involved in Astaxanthin Production
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 60:8640-8647, SEP 5 2012
abstract, full text

Nichols, S.E., Swift, R.V., Amaro, R.E.
Rational Prediction with Molecular Dynamics for Hit Identification
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 12:2002-2012, SEP 2012
abstract, full text

Merchant, B.A., Madura, J.D.
Insights from molecular dynamics: The binding site of cocaine in the dopamine transporter and permeation pathways of substrates in the leucine and dopamine transporters
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 38:1-12, SEP 2012
abstract, full text

Ai, R.Z., Chang, C.E.A.
Ligand-specific homology modeling of human cannabinoid (CB1) receptor
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 38:155-164, SEP 2012
abstract, full text

Roberts, J.A., Kuiper, M.J., Thorley, B.R., Smooker, P.M., Hung, A.
Investigation of a predicted N-terminal amphipathic et-helix using atomistic molecular dynamics simulation of a complete prototype poliovirus virion
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 38:165-173, SEP 2012
abstract, full text

Tarasov, D.S., Ibragimova, M.Y., Izotova, E.D., Akberova, N.I., Zhdanov, R.I.
Molecular dynamics and free energy of binding of oleic acid to DNA in aqueous solutions
DOKLADY BIOCHEMISTRY AND BIOPHYSICS, 446:223-228, SEP 2012
full text

Hamulakova, S., Janovec, L., Hrabinova, M., Kristian, P., Kuca, K., Banasova, M., Imrich, J.
Synthesis, design and biological evaluation of novel highly potent tacrine congeners for the treatment of Alzheimer's disease
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 55:23-31, SEP 2012
abstract, full text

Wang, H., Zhang, P.W., Schutte, C.
On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3243-3256, SEP 2012
abstract, full text

Best, R.B., Zhu, X., Shim, J., Lopes, P.E.M., Mittal, J., Feig, M., MacKerell, A.D.
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone phi, psi and Side-Chain chi(1) and chi(2) Dihedral Angles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3257-3273, SEP 2012
abstract, full text

Weber, V., Asthagiri, D.
Regularizing Binding Energy Distributions and the Hydration Free Energy of Protein Cytochrome C from All-Atom Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:3409-3415, SEP 2012
abstract, full text

Delemotte, L., Tarek, M.
Molecular Dynamics Simulations of Lipid Membrane Electroporation
JOURNAL OF MEMBRANE BIOLOGY, 245:531-543, SEP 2012
abstract, full text

Chandler, D.E., Penin, F., Schulten, K., Chipot, C.
The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002702, SEP 2012
abstract, full text, TCBG publications

Kurkcuoglu, Z., Bakan, A., Kocaman, D., Bahar, I., Doruker, P.
Coupling between Catalytic Loop Motions and Enzyme Global Dynamics
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002705, SEP 2012
abstract, full text

Langeslay, D.J., Young, R.P., Beni, S., Beecher, C.N., Mueller, L.J., Larive, C.K.
Sulfamate proton solvent exchange in heparin oligosaccharides: Evidence for a persistent hydrogen bond in the antithrombin-binding pentasaccharide Arixtra
GLYCOBIOLOGY, 22:1173-1182, SEP 2012
abstract, full text

Sun, C.B., Tang, T., Uludag, H.
Probing the Effects of Lipid Substitution on Polycation Mediated DNA Aggregation: A Molecular Dynamics Simulations Study
BIOMACROMOLECULES, 13:2982-2988, SEP 2012
abstract, full text

Banerjee, A.K., Arora, N., Murty, U.S.N.
Aspartate carbamoyltransferase of Plasmodium falciparum as a potential drug target for designing anti-malarial chemotherapeutic agents
MEDICINAL CHEMISTRY RESEARCH, 21:2480-2493, SEP 2012
abstract, full text

Graciano, L., Correa, J.M., Gandra, R.F., Seixas, F.A.V., Kadowaki, M.K., Sampaio, S.C., Silva, J.L.D., Osaku, C.A., Simao, R.D.G.
The cloning, expression, purification, characterization and modeled structure of Caulobacter crescentus beta-Xylosidase I
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, 28:2879-2888, SEP 2012
abstract, full text

Gushchin, I.Y., Gordeliy, V.I., Grudinin, S.
A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating
JOURNAL OF MOLECULAR MODELING, 18:4053-4060, SEP 2012
abstract, full text

Lin, Y.W., Nie, C.M., Liao, L.F.
Rational design of a nitrite reductase based on myoglobin: a molecular modeling and dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 18:4409-4415, SEP 2012
abstract, full text

Sutto, L., Marsili, S., Gervasio, F.L.
New advances in metadynamics
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2:771-779, SEP-OCT 2012
abstract, full text

Gao, W.M., Kong, L.X., Hodgson, P.
Atomic interaction of functionalized carbon nanotube-based nanofluids with a heating surface and its effect on heat transfer
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER, 55:5007-5015, SEP 2012
abstract, full text

Segrest, J.P., Jones, M.K., Catte, A., Thirumuruganandham, S.P.
Validation of previous computer models and MD simulations of discoidal HDL by a recent crystal structure of apoA-I
JOURNAL OF LIPID RESEARCH, 53:1851-1863, SEP 2012
abstract, full text

Spijker, P., Anciaux, G., Molinari, J.F.
The effect of loading on surface roughness at the atomistic level
COMPUTATIONAL MECHANICS, 50:273-283, SEP 2012
abstract, full text

Barber, A.F., Carnevale, V., Raju, S.G., Amaral, C., Treptow, W., Klein, M.L.
Hinge-bending motions in the pore domain of a bacterial voltage-gated sodium channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2120-2125, SEP 2012
abstract, full text

Reddy, A.S., Warshaviak, D.T., Chachisvilis, M.
Effect of membrane tension on the physical properties of DOPC lipid bilayer membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:2271-2281, SEP 2012
abstract, full text

Vassiliev, S., Zaraiskaya, T., Bruce, D.
Exploring the energetics of water permeation in photosystem II by multiple steered molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1817:1671-1678, SEP 2012
abstract, full text

Chan, K.Y., Trabuco, L.G., Schreiner, E., Schulten, K.
Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method
BIOPOLYMERS, 97:678-686, SEP 2012
abstract, full text, TCBG publications

Huang, Y.M.M., Kang, M., Chang, C.E.A.
Mechanistic Insights into Phosphopeptide-BRCT Domain Association: Preorganization, Flexibility, and Phosphate Recognition
JOURNAL OF PHYSICAL CHEMISTRY B, 116:10247-10258, AUG 30 2012
abstract, full text

Yu, X., Zheng, J.
Cholesterol Promotes the Interaction of Alzheimer beta-Amyloid Monomer with Lipid Bilayer
JOURNAL OF MOLECULAR BIOLOGY, 421:561-571, AUG 24 2012
abstract, full text

Tofoleanu, F., Buchete, N.V.
Molecular Interactions of Alzheimer's A beta Protofilaments with Lipid Membranes
JOURNAL OF MOLECULAR BIOLOGY, 421:572-586, AUG 24 2012
abstract, full text

Liu, P., Chipot, C., Shao, X.G., Cai, W.S.
How Do alpha-Cyclodextrins Self-Organize on a Polymer Chain?
JOURNAL OF PHYSICAL CHEMISTRY C, 116:17913-17918, AUG 23 2012
abstract, full text

Xiao, B.T., Tong, C.F., Jia, X.L., Guo, R., Lu, S.Q., Zhang, Y., McEver, R.P., Zhu, C., Long, M.A.
Tyrosine Replacement of PSGL-1 Reduces Association Kinetics with P- and L-Selectin on the Cell Membrane
BIOPHYSICAL JOURNAL, 103:777-785, AUG 22 2012
abstract, full text

Bojovschi, A., Liu, M.S., Sadus, R.J.
Conformational dynamics of ATP/Mg:ATP in motor proteins via data mining and molecular simulation
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 075101, AUG 21 2012
abstract, full text

Fleurat-Lessard, P., Michel, C., Bulo, R.E.
Energy extrapolation schemes for adaptive multi-scale molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 074111, AUG 21 2012
abstract, full text

Hall, B.A., Wright, D.W., Jha, S., Coveney, P.V.
Quantized Water Access to the HIV-1 Protease Active Site as a Proposed Mechanism for Cooperative Mutations in Drug Affinity
BIOCHEMISTRY, 51:6487-6489, AUG 21 2012
abstract, full text

von Castelmur, E., Struempfer, J., Franke, B., Bogomolovas, J., Barbieri, S., Qadota, H., Konarev, P.V., Svergun, D.I., Labeit, S., Benian, G.M., Schulten, K., Mayans, O.
Identification of an N-terminal inhibitory extension as the primary mechanosensory regulator of twitchin kinase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:13608-13613, AUG 21 2012
abstract, full text, TCBG publications

Qin, Z., Buehler, M.
Molecular mechanics of dihydroxyphenylalanine at a silica interface
APPLIED PHYSICS LETTERS, 101: Art. No. 083702, AUG 20 2012
abstract, full text

Kumar, P., Lehmann, J., Libchaber, A.
Kinetics of Bulge Bases in Small RNAs and the Effect of Pressure on It
PLOS ONE, 7: Art. No. e42052, AUG 20 2012
abstract, full text

Bai, M., Pang, X.Y., Lou, J.Z., Zhou, Q.J., Zhang, K., Ma, J., Li, J., Sun, F., Hsu, V.W.
Mechanistic Insights into Regulated Cargo Binding by ACAP1 Protein
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:28675-28685, AUG 17 2012
abstract, full text

Biedermannova, L., Prokop, Z., Gora, A., Chovancova, E., Kovacs, M., Damborsky, J., Wade, R.C.
A Single Mutation in a Tunnel to the Active Site Changes the Mechanism and Kinetics of Product Release in Haloalkane Dehalogenase LinB
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:29062-29074, AUG 17 2012
abstract, full text

Pacios, L.F., Gomez-Casado, C., Tordesillas, L., Palacin, A., Sanchez-Monge, R., Diaz-Perales, A.
Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1831-1844, AUG 15 2012
abstract, full text

Zhang, X.H., He, X., Baker, J., Tama, F., Chang, G., Wright, S.H.
Twelve Transmembrane Helices Form the Functional Core of Mammalian MATE1 (Multidrug and Toxin Extruder 1) Protein
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:27971-27982, AUG 10 2012
abstract, full text

Amato, A.A., Rajagopalan, S., Lin, J.Z., Carvalho, B.M., Figueira, A.C.M., Lu, J., Ayers, S.D., Mottin, M., Silveira, R.L., Souza, P.C.T., Mourao, R.H.V., Saad, M.J.A., Togashi, M., Simeoni, L.A., Abdalla, D.S.P., Skaf, M.S., Polikparpov, I., Lima, M.C.A., Galdino, S.L., Brennan, R.G., Baxter, J.D., Pitta, I.R., Webb, P., Phillips, K.J., Neves, F.A.R.
GQ-16, a Novel Peroxisome Proliferator-activated Receptor gamma (PPAR gamma) Ligand, Promotes Insulin Sensitization without Weight Gain
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:28169-28179, AUG 10 2012
abstract, full text

da Silva, L.P., Vieira, J., da Silva, J.C.G.E.
Comparative theoretical study of the binding of luciferyl-adenylate and dehydroluciferyl-adenylate to firefly luciferase
CHEMICAL PHYSICS LETTERS, 543:137-141, AUG 10 2012
abstract, full text

Turpin, E.R., Hirst, J.D.
Transformation of the dihedral corrective map for D-amino residues using the CHARMM force field
CHEMICAL PHYSICS LETTERS, 543:142-147, AUG 10 2012
abstract, full text

Akhshi, P., Acton, G., Wu, G.
Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G(3)T(4)G(4))](2) G-Quadruplex DNA Structure
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9363-9370, AUG 9 2012
abstract, full text

Stober, S.T., Abrams, C.F.
Energetics and Mechanism of the Normal-to-Amyloidogenic Isomerization of beta 2-Microglobulin: On-the-Fly String Method Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9371-9375, AUG 9 2012
abstract, full text

Klauda, J.B., Monje, V., Kim, T., Im, W.
Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9424-9431, AUG 9 2012
abstract, full text

Verde, A.V., Bolhuis, P.G., Campen, R.K.
Statics and Dynamics of Free and Hydrogen-Bonded OH Groups at the Air/Water Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 116:9467-9481, AUG 9 2012
abstract, full text

Gautieri, A., Pate, M.I., Vesentini, S., Redaelli, A., Buehler, M.J.
Hydration and distance dependence of intermolecular shearing between collagen molecules in a model microfibril
JOURNAL OF BIOMECHANICS, 45:2079-2083, AUG 9 2012
abstract, full text

Robertson, J.L., Palmer, L.G., Roux, B.
Multi-Ion Distributions in the Cytoplasmic Domain of Inward Rectifier Potassium Channels
BIOPHYSICAL JOURNAL, 103:434-443, AUG 8 2012
abstract, full text

Wright, D.W., Sadiq, S.K., De Fabritiis, G., Coveney, P.V.
Thumbs Down for HIV: Domain Level Rearrangements Do Occur in the NNRTI-Bound HIV-1 Reverse Transcriptase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:12885-12888, AUG 8 2012
abstract, full text

Marin, M.B., Ghenea, S., Spiridon, L.N., Chiritoiu, G.N., Petrescu, A.J., Petrescu, S.M.
Tyrosinase Degradation Is Prevented when EDEM1 Lacks the Intrinsically Disordered Region
PLOS ONE, 7: Art. No. e42998, AUG 8 2012
abstract, full text

Raghuraman, H., Cordero-Morales, J.F., Jogini, V., Pan, A.C., Kollewe, A., Roux, B., Perozo, E.
Mechanism of Cd2+ Coordination during Slow Inactivation in Potassium Channels
STRUCTURE, 20:1332-1342, AUG 8 2012
abstract, full text

Inada, H., Procko, E., Sotomayor, M., Gaudet, R.
Structural and Biochemical Consequences of Disease-Causing Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Channel
BIOCHEMISTRY, 51:6195-6206, AUG 7 2012
abstract, full text

Johnson, Q.R., Nellas, R.B., Shen, T.Y.
Solvent-Dependent Gating Motions of an Extremophilic Lipase from Pseudomonas aeruginosa
BIOCHEMISTRY, 51:6238-6245, AUG 7 2012
abstract, full text

Jana, M., Bandyopadhyay, S.
Restricted dynamics of water around a protein-carbohydrate complex: Computer simulation studies
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 055102, AUG 7 2012
abstract, full text

Gong, R., Wang, Y.P., Ying, T.L., Dimitrov, D.S.
Bispecific Engineered Antibody Domains (Nanoantibodies) That Interact Noncompetitively with an HIV-1 Neutralizing Epitope and FcRn
PLOS ONE, 7: Art. No. e42288, AUG 7 2012
abstract, full text

Natarajan, K., Senapati, S.
Understanding the Basis of Drug Resistance of the Mutants of alpha beta-Tubulin Dimer via Molecular Dynamics Simulations
PLOS ONE, 7: Art. No. e42351, AUG 7 2012
abstract, full text

van Eijk, M., Rynkiewicz, M.J., White, M.R., Hartshorn, K.L., Zou, X.Q., Schulten, K., Luo, D., Crouch, E.C., Cafarella, T.R., Head, J.F., Haagsman, H.P., Seaton, B.A.
A Unique Sugar-binding Site Mediates the Distinct Anti-influenza Activity of Pig Surfactant Protein D
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:26666-26677, AUG 3 2012
abstract, full text, TCBG publications

Yang, Z.X., Xiu, P., Shi, B.Y., Hua, L., Zhou, R.H.
Coherent Microscopic Picture for Urea-Induced Denaturation of Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8856-8862, AUG 2 2012
abstract, full text

Feng, Z.W., Hou, T.J., Li, Y.Y.
Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2119-2131, AUG 2012
abstract, full text

Liu, J., Fan, J.F., Cen, M., Song, X.Z., Liu, D.Y., Zhou, W.Q., Liu, Z., Yan, J.F.
Dependences of Water Permeation through Cyclic Octa-peptide Nanotubes on Channel Length and Membrane Thickness
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:2132-2138, AUG 2012
abstract, full text

Bhattacharya, S., Derrington, I.M., Pavlenok, M., Niederweis, M., Gundlach, J.H., Aksimentiev, A.
Molecular Dynamics Study of MspA Arginine Mutants Predicts Slow DNA Translocations and Ion Current Blockades Indicative of DNA Sequence
ACS NANO, 6:6960-6968, AUG 2012
abstract, full text

Pietra, F.
On CO Egress from, and Re-Uptake by, the Enzyme MauG, as a Mimic of the Acquisition of Oxidizing Agents by the pre-MADH_MauG System. A Molecular Mechanics Approach
CHEMISTRY & BIODIVERSITY, 9:1425-1435, AUG 2012
abstract, full text

Jasinski, A., Mikulska, K., Krajnik, B., Mackowski, S., Nowak, W.
Dynamics of Protein Elements of Hybrid Nanostructures - Molecular Dynamics Simulations of Light Harvesting Peridinin-Chlorophyll a-Protein Model
ACTA PHYSICA POLONICA A, 122:284-288, AUG 2012
abstract, full text

Romanowska, J., Nowinski, K.S., Trylska, J.
Determining Geometrically Stable Domains in Molecular Conformation Sets
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2588-2599, AUG 2012
abstract, full text

Liu, P., Dehez, F., Cai, W.S., Chipot, C.
A Toolkit for the Analysis of Free-Energy Perturbation Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2606-2616, AUG 2012
abstract, full text

Wong-ekkabut, J., Karttunen, M.
Assessment of Common Simulation Protocols for Simulations of Nanopores, Membrane Proteins, and Channels
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2905-2911, AUG 2012
abstract, full text

Nguyen, T.H., Arnesano, F., Scintilla, S., Rossetti, G., Ippoliti, E., Carloni, P., Natile, G.
Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2912-2920, AUG 2012
abstract, full text

VanWart, A.T., Eargle, J., Luthey-Schulten, Z., Amaro, R.E.
Exploring Residue Component Contributions to Dynamical Network Models of Allostery
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2949-2961, AUG 2012
abstract, full text

Melo, M.C.R., Bernardi, R.C., Fernandes, T.V.A., Pascutti, P.G.
GSAFold: A new application of GSA to protein structure prediction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:2305-2310, AUG 2012
abstract, full text

Garcia-Fandino, R., Bernado, P., Ayuso-Tejedor, S., Sancho, J., Orozco, M.
Defining the Nature of Thermal Intermediate in 3 State Folding Proteins: Apoflavodoxin, a Study Case
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002647, AUG 2012
abstract, full text

Pisliakov, A.V., Hino, T., Shiro, Y., Sugita, Y.
Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002674, AUG 2012
abstract, full text

Mladenovic, M., Mihailovic, M., Desanka, B.B., Vukovic, N., Sukdolak, S., Matic, S., Niciforovic, N., Mihailovic, V., Maskovic, P., Vrvic, M.M., Solujic, S.
Biochemical and pharmacological evaluation of 4-hydroxychromen-2-ones bearing polar C-3 substituents as anticoagulants
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 54:144-158, AUG 2012
abstract, full text

Fioramonte, M., dos Santos, A.M., McIlwain, S., Noble, W.S., Franchini, K.G., Gozzo, F.C.
Analysis of secondary structure in proteins by chemical cross-linking coupled to MS
PROTEOMICS, 12:2746-2752, AUG 2012
abstract, full text

Pradhan, S.M., Katti, K.S., Katti, D.R.
Structural Hierarchy Controls Deformation Behavior of Collagen
BIOMACROMOLECULES, 13:2562-2569, AUG 2012
abstract, full text

Chen, B.D., Yang, C.L., Wang, M.S., Ma, X.G.
Dynamic mechanism for encapsulating two HIV replication inhibitor peptides with carbon nanotubes
CHINESE PHYSICS B, 21: Art. No. 083103, AUG 2012
abstract, full text

Mage, M.G., Dolan, M.A., Wang, R., Boyd, L.F., Revilleza, M.J., Robinson, H., Natarajan, K., Myers, N.B., Hansen, T.H., Margulies, D.H.
The Peptide-Receptive Transition State of MHC Class I Molecules: Insight from Structure and Molecular Dynamics
JOURNAL OF IMMUNOLOGY, 189:1391-1399, AUG 1 2012
abstract, full text

Lee, O.S., Liu, Y.M., Schatz, G.C.
Molecular dynamics simulation of beta-sheet formation in self-assembled peptide amphiphile fibers
JOURNAL OF NANOPARTICLE RESEARCH, 14: Art. No. 936, AUG 2012
abstract, full text

Hu, G.D., Chen, L.Y., Wang, J.H.
Insights into the mechanisms of the selectivity filter of Escherichia coli aquaporin Z
JOURNAL OF MOLECULAR MODELING, 18:3731-3741, AUG 2012
abstract, full text

Galloux, M., Tarus, B., Blazevic, I., Fix, J., Duquerroy, S., Eleouet, J.F.
Characterization of a Viral Phosphoprotein Binding Site on the Surface of the Respiratory Syncytial Nucleoprotein
JOURNAL OF VIROLOGY, 86:8375-8387, AUG 2012
abstract, full text

Lilkova, E., Nacheva, G., Petkov, P., Petkov, P., Markov, S., Ilieva, N., Litov, L.
Metadynamics study of mutant human interferon-gamma forms
COMPUTERS & MATHEMATICS WITH APPLICATIONS, 64:272-277, AUG 2012
abstract, full text

Friedman, A.J., Durrant, J.D., Pierce, L.C.T., McCorvie, T.J., Timson, D.J., McCammon, J.A.
The Molecular Dynamics of Trypanosoma brucei UDP-Galactose 4 '-Epimerase: A Drug Target for African Sleeping Sickness
CHEMICAL BIOLOGY & DRUG DESIGN, 80:173-181, AUG 2012
abstract, full text

Osguthorpe, D.J., Sherman, W., Hagler, A.T.
Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering
CHEMICAL BIOLOGY & DRUG DESIGN, 80:182-193, AUG 2012
abstract, full text

Daga, P.R., Zaveri, N.T.
Homology modeling and molecular dynamics simulations of the active state of the nociceptin receptor reveal new insights intoagonist binding and activation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1948-1961, AUG 2012
abstract, full text

Beveridge, A.J., Wallis, R., Samani, N.J.
A molecular dynamics study of C1r and C1s dimers: Implications for the structure of the C1 complex
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1987-1997, AUG 2012
abstract, full text

Rennebaum, S., Caflisch, A.
Inhibition of interdomain motion in g-actin by the natural product latrunculin: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1998-2008, AUG 2012
abstract, full text

Gnanasambandan, K., Magis, A.T., Sayeski, P.P.
A shift in the salt bridge interaction of residues D620 and E621 mediates the constitutive activation of Jak2-H538Q/K539L
MOLECULAR AND CELLULAR BIOCHEMISTRY, 367:125-140, AUG 2012
abstract, full text

Fang, X., Fang, Y., Liu, L., Liu, G.J., Wu, J.H.
Mapping Paratope on Antithrombotic Antibody 6B4 to Epitope on Platelet Glycoprotein Ibalpha via Molecular Dynamic Simulations
PLOS ONE, 7: Art. No. e42263, JUL 30 2012
abstract, full text

Wang, L.Y., Dumont, R.S., Dickson, J.M.
Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressure
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 044102, JUL 28 2012
abstract, full text

O'Reilly, A.O., Eberhardt, E., Weidner, C., Alzheimer, C., Wallace, B.A., Lampert, A.
Bisphenol A Binds to the Local Anesthetic Receptor Site to Block the Human Cardiac Sodium Channel
PLOS ONE, 7: Art. No. e41667, JUL 27 2012
abstract, full text

Chien, C.H., Gao, Q.Z., Cooper, A.J.L., Lyu, J.H., Sheu, S.Y.
Structural Insights into the Catalytic Active Site and Activity of Human Nit2/omega-Amidase KINETIC ASSAY AND MOLECULAR DYNAMICS SIMULATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:25715-25726, JUL 27 2012
abstract, full text

Sinitskiy, A.V., Saunders, M.G., Voth, G.A.
Optimal Number of Coarse-Grained Sites in Different Components of Large Biomolecular Complexes
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8363-8374, JUL 26 2012
abstract, full text

Shirvanyants, D., Ding, F., Tsao, D., Ramachandran, S., Dokholyan, N.V.
Discrete Molecular Dynamics: An Efficient And Versatile Simulation Method For Fine Protein Characterization
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8375-8382, JUL 26 2012
abstract, full text

Singharoy, A., Joshi, H., Miao, Y.L., Ortoleva, P.J.
Space Warping Order Parameters and Symmetry: Application to Multiscale Simulation of Macromolecular Assemblies
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8423-8434, JUL 26 2012
abstract, full text

Su, G.X., Czader, A., Homouz, D., Bernardes, G., Mateen, S., Cheung, M.S.
Multiscale Simulation on a Light-Harvesting Molecular Triad
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8460-8473, JUL 26 2012
abstract, full text

Nishima, W., Miyashita, N., Yamaguchi, Y., Sugita, Y., Re, S.
Effect of Bisecting GlcNAc and Core Fucosylation on Conformational Properties of Biantennary Complex-Type N-Glycans in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8504-8512, JUL 26 2012
abstract, full text

Sereda, Y.V., Singharoy, A.B., Jarrold, M.F., Ortoleva, P.J.
Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8534-8544, JUL 26 2012
abstract, full text

Ovchinnikov, V., Karplus, M.
Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8584-8603, JUL 26 2012
abstract, full text

Lyons, J.A., Aragao, D., Slattery, O., Pisliakov, A.V., Soulimane, T., Caffrey, M.
Structural insights into electron transfer in caa(3)-type cytochrome oxidase
NATURE, 487:514-U137, JUL 26 2012
abstract, full text

Sardroodi, J.J., Azamat, J., Rastkar, A., Yousefnia, N.R.
The preferential permeation of ions across carbon and boron nitride nanotubes
CHEMICAL PHYSICS, 403:105-112, JUL 25 2012
abstract, full text

Swett, R., Cisneros, G.A., Feig, A.L.
Conformational Analysis of Clostridium difficile Toxin B and Its Implications for Substrate Recognition
PLOS ONE, 7: Art. No. e41518, JUL 23 2012
abstract, full text

Chen, C., Li, W.Z., Song, Y.C., Weng, L.D., Zhang, N.
Hydrogen Bonding Analysis of Hydroxyl Groups in Glucose Aqueous Solutions by a Molecular Dynamics Simulation Study
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 33:2238-2246, JUL 20 2012
abstract, full text

Bellesia, G., Chundawat, S.P.S., Langan, P., Redondo, A., Dale, B.E., Gnanakaran, S.
Coarse-Grained Model for the Interconversion between Native and Liquid Ammonia-Treated Crystalline Cellulose
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8031-8037, JUL 19 2012
abstract, full text

Li, B., Li, W., Du, P., Yu, K.Q., Fu, W.
Molecular Insights into the D1R Agonist and D2R/D3R Antagonist Effects of the Natural Product (-)-Stepholidine: Molecular Modeling and Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:8121-8130, JUL 19 2012
abstract, full text

Gumbart, J., Schreiner, E., Wilson, D.N., Beckmann, R., Schulten, K.
Mechanisms of SecM-Mediated Stalling in the Ribosome
BIOPHYSICAL JOURNAL, 103:331-341, JUL 18 2012
abstract, full text, TCBG publications

Kraszewski, S., Bianco, A., Tarek, M., Ramseyer, C.
Insertion of Short Amino-Functionalized Single-Walled Carbon Nanotubes into Phospholipid Bilayer Occurs by Passive Diffusion
PLOS ONE, 7: Art. No. e40703, JUL 16 2012
abstract, full text

Verkhivker, G.M.
Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics
PLOS ONE, 7: Art. No. e40897, JUL 16 2012
abstract, full text

Alies, B., LaPenna, G., Sayen, S., Guillon, E., Hureau, C., Faller, P.
Insights into the Mechanisms of Amyloid Formation of Zn-II-Ab11-28: pH-Dependent Zinc Coordination and Overall Charge as Key Parameters for Kinetics and the Structure of Zn-II-Ab11-28 Aggregates
INORGANIC CHEMISTRY, 51:7897-7902, JUL 16 2012
abstract, full text

Berezniak, T., Jaschke, A., Smith, J.C., Imhof, P.
Stereoselection in the diels-alderase ribozyme: A molecular dynamics study
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1603-1614, JUL 15 2012
abstract, full text

Yesylevskyy, S.O.
Pteros: Fast and easy to use open-source C++ library for molecular analysis
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1632-1636, JUL 15 2012
abstract, full text

Shadrina, M.S., English, A.M., Peslherbe, G.H.
Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O-2 Pathways and Escape Routes in T-state Deoxyhemoglobin
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:11177-11184, JUL 11 2012
abstract, full text

Bhatnagar, N., Kamath, G., Chelst, I., Potoff, J.J.
Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 137: Art. No. 014502, JUL 7 2012
abstract, full text

Lahti, J.L., Tang, G.W., Capriotti, E., Liu, T.Y., Altman, R.B.
Bioinformatics and variability in drug response: a protein structural perspective
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 9:1409-1437, JUL 7 2012
abstract, full text

Liu, M., Wang, S., Sun, T.G., Su, J.G., Zhang, Y.X., Yue, J.J., Sun, Z.W.
Insight into the Structure, Dynamics and the Unfolding Property of Amylosucrases: Implications of Rational Engineering on Thermostability
PLOS ONE, 7: Art. No. e40441, JUL 6 2012
abstract, full text

Nemec, A.A., Donigan, K.A., Murphy, D.L., Jaeger, J., Sweasy, J.B.
Colon Cancer-associated DNA Polymerase beta Variant Induces Genomic Instability and Cellular Transformation
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:23840-23849, JUL 6 2012
abstract, full text

Jana, S., Dalapati, S., Ghosh, S., Guchhait, N.
Study of microheterogeneous environment of protein Human Serum Albumin by an extrinsic fluorescent reporter: A spectroscopic study in combination with Molecular Docking and Molecular Dynamics Simulation
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 112:48-58, JUL 2 2012
abstract, full text

Sawada, Y., Murase, M., Sokabe, M.
The gating mechanism of the bacterial mechanosensitive channel MscL revealed by molecular dynamics simulations From tension sensing to channel opening
CHANNELS, 6:317-331, JUL-AUG 2012
abstract, full text

Anderson, J.S., LeMaster, D.M.
Rotational velocity rescaling of molecular dynamics trajectories for direct prediction of protein NMR relaxation
BIOPHYSICAL CHEMISTRY, 168:28-39, JUL 2012
abstract, full text

Louet, M., Martinez, J., Floquet, N.
GDP Release Preferentially Occurs on the Phosphate Side in Heterotrimeric G-proteins
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002595, JUL 2012
abstract, full text

Kundu, S., Mukherjee, S., Bhattacharyya, D.
Effect of temperature on DNA double helix: An insight from molecular dynamics simulation
JOURNAL OF BIOSCIENCES, 37:445-455, JUL 2012
abstract, full text

Dalton, J., Kalid, O., Schushan, M., Ben-Tal, N., Villa-Freixa, J.
New Model of Cystic Fibrosis Transmembrane Conductance Regulator Proposes Active Channel-like Conformation
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1842-1853, JUL 2012
abstract, full text

de Brevern, A.G., Bornot, A., Craveur, P., Etchebest, C., Gelly, J.C.
PredyFlexy: flexibility and local structure prediction from sequence
NUCLEIC ACIDS RESEARCH, 40:W317-W322, JUL 2012
abstract, full text

Senne, M., Trendelkamp-Schroer, B., Mey, A.S.J.S., Schutte, C., Noe, F.
EMMA: A Software Package for Markov Model Building and Analysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2223-2238, JUL 2012
abstract, full text

Branduardi, D., Bussi, G., Parrinello, M.
Metadynamics with Adaptive Gaussians
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2247-2254, JUL 2012
abstract, full text

Flaig, D., Beer, M., Ochsenfeld, C.
Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2260-2271, JUL 2012
abstract, full text

Harrison, C.B., Schulten, K.
Quantum and Classical Dynamics Simulations of ATP Hydrolysis in Solution
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2328-2335, JUL 2012
abstract, full text, TCBG publications

Bakan, A., Nevins, N., Lakdawala, A.S., Bahar, I.
Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2435-2447, JUL 2012
abstract, full text

Tanner, D.E., Phillips, J.C., Schulten, K.
GPU/CPU Algorithm for Generalized Born/Solvent-Accessible Surface Area Implicit Solvent Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2521-2530, JUL 2012
abstract, full text, TCBG publications

De Biase, P.M., Solano, C.J.F., Markosyan, S., Czapla, L., Noskov, S.Y.
BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:2540-2551, JUL 2012
abstract, full text

Chen, B.D., Yang, C.L., Yang, J.S., Wang, M.S., Ma, X.G.
The translocation of DNA oligonucleotide with the water stream in carbon nanotubes
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 991:93-97, JUL 1 2012
abstract, full text

Lu, Z., Hou, J.L., Wang, Y., Liu, J.H.
Involvement of Ser94 in RNase HIII from Chlamydophila pneumoniae in the recognition of a single ribonucleotide misincorporated into double-stranded DNA
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1824:859-865, JUL 2012
abstract, full text

Ezzeldin, H.M., Klauda, J.B., Solares, S.D.
Modeling of the major gas vesicle protein, GvpA: From protein sequence to vesicle wall structure
JOURNAL OF STRUCTURAL BIOLOGY, 179:18-28, JUL 2012
abstract, full text

Gomez, H., Lluch, J.M., Masgrau, L.
Essential role of glutamate 317 in galactosyl transfer by alpha 3GalT: a computational study
CARBOHYDRATE RESEARCH, 356:204-208, JUL 2012
abstract, full text

Vistoli, G., Straniero, V., Pedretti, A., Fumagalli, L., Bolchi, C., Pallavicini, M., Valoti, E., Testa, B.
Predicting the physicochemical profile of diastereoisomeric histidine-containing dipeptides by property space analysis
CHIRALITY, 24:566-576, JUL 2012
abstract, full text

Tsigelny, I.F., Sharikov, Y., Greenberg, J.P., Miller, M.A., Kouznetsova, V.L., Larson, C.A., Howell, S.B.
An All-Atom Model of the Structure of Human Copper Transporter 1
CELL BIOCHEMISTRY AND BIOPHYSICS, 63:223-234, JUL 2012
abstract, full text

Schow, E.V., Freites, J.A., Nizkorodov, A., White, S.H., Tobias, D.J.
Coupling between the voltage-sensing and pore domains in a voltage-gated potassium channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1726-1736, JUL 2012
abstract, full text

Walrant, A., Vogel, A., Correia, I., Lequin, O., Olausson, B.E.S., Desbat, B., Sagan, S., Alves, I.D.
Membrane interactions of two arginine-rich peptides with different cell internalization capacities
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1755-1763, JUL 2012
abstract, full text

Sun, H.Y., Ji, F.Q.
A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 423:319-324, JUN 29 2012
abstract, full text

Wang, S.H., Orabi, E.A., Baday, S., Berneche, S., Lamoureux, G.
Ammonium Transporters Achieve Charge Transfer by Fragmenting Their Substrate
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:10419-10427, JUN 27 2012
abstract, full text

He, C.Z., Genchev, G.Z., Lu, H., Li, H.B.
Mechanically Untying a Protein Slipknot: Multiple Pathways Revealed by Force Spectroscopy and Steered Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:10428-10435, JUN 27 2012
abstract, full text

Li, M.H., Zheng, W.J.
All-Atom Structural Investigation of Kinesin-Microtubule Complex Constrained by High-Quality Cryo-Electron-Microscopy Maps
BIOCHEMISTRY, 51:5022-5032, JUN 26 2012
abstract, full text

Wise, J.G.
Catalytic Transitions in the Human MDR1 P-Glycoprotein Drug Binding Sites
BIOCHEMISTRY, 51:5125-5141, JUN 26 2012
abstract, full text

Zhang, J.L., Zheng, Q.C., Li, Z.Q., Zhang, H.X.
Molecular Dynamics Simulations Suggest Ligand's Binding to Nicotinamidase/Pyrazinamidase
PLOS ONE, 7: Art. No. e39546, JUN 26 2012
abstract, full text

Atkinson, S.C., Dogovski, C., Downton, M.T., Pearce, F.G., Reboul, C.F., Buckle, A.M., Gerrard, J.A., Dobson, R.C.J., Wagner, J., Perugini, M.A.
Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine
PLOS ONE, 7: Art. No. e38318, JUN 25 2012
abstract, full text

Craddock, T.J.A., George, M.S., Freedman, H., Barakat, K.H., Damaraju, S., Hameroff, S., Tuszynski, J.A.
Computational Predictions of Volatile Anesthetic Interactions with the Microtubule Cytoskeleton: Implications for Side Effects of General Anesthesia
PLOS ONE, 7: Art. No. e37251, JUN 25 2012
abstract, full text

Klose, D., Klare, J.P., Grohmann, D., Kay, C.W.M., Werner, F., Steinhoff, H.J.
Simulation vs. Reality: A Comparison of In Silico Distance Predictions with DEER and FRET Measurements
PLOS ONE, 7: Art. No. e39492, JUN 25 2012
abstract, full text

Negi, S., Aykut, A.O., Atilgan, A.R., Atilgan, C.
Calmodulin Readily Switches Conformation upon Protonating High pK(a) Acidic Residues
JOURNAL OF PHYSICAL CHEMISTRY B, 116:7145-7153, JUN 21 2012
abstract, full text

Li, Y.L., Gridley, C.L., Jaeger, J., Sweasy, J.B., Schlick, T.
Unfavorable Electrostatic and Steric Interactions in DNA Polymerase beta E295K Mutant Interfere with the Enzyme's Pathway
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:9999-10010, JUN 20 2012
abstract, full text

Siddiqua, A., Luo, Y., Meyer, V., Swanson, M.A., Yu, X., Wei, G.H., Zheng, J., Eaton, G.R., Ma, B.Y., Nussinov, R., Eaton, S.S., Margittai, M.
Conformational Basis for Asymmetric Seeding Barrier in Filaments of Three- and Four-Repeat Tau
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:10271-10278, JUN 20 2012
abstract, full text

Cueva, J.G., Hsin, J., Huang, K.C., Goodman, M.B.
Posttranslational Acetylation of alpha-Tubulin Constrains Protofilament Number in Native Microtubules
CURRENT BIOLOGY, 22:1066-1074, JUN 19 2012
abstract, full text

Pogoryelov, D., Klyszejko, A.L., Krasnoselska, G.O., Heller, E.M., Leone, V., Langerd, J.D., Vonck, J., Muller, D.J., Faraldo-Gomez, J.D., Meier, T.
Engineering rotor ring stoichiometries in the ATP synthase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E1599-E1608, JUN 19 2012
abstract, full text

Pettelkau, J., Schroder, T., Ihling, C.H., Olausson, B.E.S., Kolbel, K., Lange, C., Sinz, A.
Structural Insights into Retinal Guanylylcyclase-GCAP-2 Interaction Determined by Cross-Linking and Mass Spectrometry
BIOCHEMISTRY, 51:4932-4949, JUN 19 2012
abstract, full text

Popp, D., Narita, A., Lee, L.J., Ghoshdastider, U., Xue, B., Srinivasan, R., Balasubramanian, M.K., Tanaka, T., Robinson, R.C.
Novel Actin-like Filament Structure from Clostridium tetani
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:21121-21129, JUN 15 2012
abstract, full text

Jaron-Mendelson, M., Yossef, R., Appel, M.Y., Zilka, A., Hadad, U., Afergan, F., Rosental, B., Engel, S., Nedvetzki, S., Braiman, A., Porgador, A.
Dimerization of NKp46 Receptor Is Essential for NKp46-Mediated Lysis: Characterization of the Dimerization Site by Epitope Mapping
JOURNAL OF IMMUNOLOGY, 188:6165-6174, JUN 15 2012
abstract, full text

Chen, K., Eargle, J., Lai, J., Kim, H., Abeysirigunawardena, S., Mayerle, M., Woodson, S., Ha, T., Luthey-Schulten, Z.
Assembly of the Five-Way Junction in the Ribosomal Small Subunit Using Hybrid MD-Go Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6819-6831, JUN 14 2012
abstract, full text

Salsbury, F.R., Yuan, Y., Knaggs, M.H., Poole, L.B., Fetrow, J.S.
Structural and Electrostatic Asymmetry at the Active Site in Typical and Atypical Peroxiredoxin Dimers
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6832-6843, JUN 14 2012
abstract, full text

Lee, O.S., Cho, V.Y., Schatz, G.C.
A- to B-Form Transition in DNA Between Gold Surfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 116:7000-7005, JUN 14 2012
abstract, full text

Chen, W.T., Sun, S.S., Li, Z.
Two Glycosylation Sites in H5N1 Influenza Virus Hemagglutinin That Affect Binding Preference by Computer-Based Analysis
PLOS ONE, 7: Art. No. e38794, JUN 14 2012
abstract, full text

Soekmadji, C., Angkawidjaja, C., Kelly, L.E.
Ca2+ Regulates the Drosophila Stoned-A and Stoned-B Proteins Interaction with the C2B Domain of Synaptotagmin-1
PLOS ONE, 7: Art. No. e38822, JUN 12 2012
abstract, full text

Hsin, J., Gopinathan, A., Huang, K.C.
Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:9432-9437, JUN 12 2012
abstract, full text

Bussiere, C., Hashem, Y., Arora, S., Frank, J., Johnson, A.W.
Integrity of the P-site is probed during maturation of the 60S ribosomal subunit
JOURNAL OF CELL BIOLOGY, 197:747-759, JUN 11 2012
abstract, full text

Richards, L.A., Schafer, A.I., Richards, B.S., Corry, B.
The Importance of Dehydration in Determining Ion Transport in Narrow Pores
SMALL, 8:1701-1709, JUN 11 2012
abstract, full text

Kireeva, M.L., Opron, K., Seibold, S.A., Domecq, C., Cukier, R.I., Coulombe, B., Kashlev, M., Burton, Z.F.
Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase
BMC BIOPHYSICS, 5: Art. No. 11, JUN 7 2012
abstract, full text

Ozer, G., Quirk, S., Hernandez, R.
Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 215104, JUN 7 2012
abstract, full text

Anisimov, V.M., Bliznyuk, A.A.
Charge Transfer Effects in the GroEL-GroES Chaperonin Tetramer in Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6261-6268, JUN 7 2012
abstract, full text

Yu, T., Wang, X.Q., Sang, J.P., Pan, C.X., Zou, X.W., Chen, T.Y., Zou, X.Q.
Influences of Mutations on the Electrostatic Binding Free Energies of Chloride Ions in Escherichia coli CIC
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6431-6438, JUN 7 2012
abstract, full text

Priya, M.H., Merchant, S., Asthagiri, D., Paulaitis, M.E.
Quasi-Chemical Theory of Cosolvent Hydrophobic Preferential Interactions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6506-6513, JUN 7 2012
abstract, full text

Huggins, D.J.
Benchmarking the thermodynamic analysis of water molecules around a model beta sheet
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1383-1392, JUN 5 2012
abstract, full text

Xiong, W., Cui, T.X., Cheng, K.J., Yang, F., Chen, S.R., Willenbring, D., Guan, Y., Pan, H.L., Ren, K., Xu, Y., Zhang, L.
Cannabinoids suppress inflammatory and neuropathic pain by targeting alpha 3 glycine receptors
JOURNAL OF EXPERIMENTAL MEDICINE, 209:1121-1134, JUN 4 2012
abstract, full text

Ricci, A., Anthopoulos, A., Massarotti, A., Grimstead, I., Brancale, A.
Haptic-driven applications to molecular modeling: state-of-the-art and perspectives
FUTURE MEDICINAL CHEMISTRY, 4:1219-1228, JUN 2012
abstract, full text

Lee, W., Strumpfer, J., Bennett, V., Schulten, K., Marszalek, P.E.
Mutation of Conserved Histidines Alters Tertiary Structure and Nanomechanics of Consensus Ankyrin Repeats
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:19115-19121, JUN 1 2012
abstract, full text, TCBG publications

Osipiuk, J., Mulligan, R., Bargassa, M., Hamilton, J.E., Cunningham, M.A., Joachimiak, A.
Characterization of Member of DUF1888 Protein Family, Self-cleaving and Self-assembling Endopeptidase
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:19452-19461, JUN 1 2012
abstract, full text

Sim, A.Y.L., Minary, P., Levitt, M.
Modeling nucleic acids
CURRENT OPINION IN STRUCTURAL BIOLOGY, 22:273-278, JUN 2012
abstract, full text

Chakrabarty, K., Gupta, S.N., Das, G.K., Roy, S.
Theoretical studies on the pyridoxal-5 '-phosphate dependent enzyme dopa decarboxylase: Effect of Thr 246 residue on the co-factor-enzyme binding and reaction mechanism
INDIAN JOURNAL OF BIOCHEMISTRY & BIOPHYSICS, 49:155-164, JUN 2012
abstract, full text

Guo, W.W., Wan, D., Liao, L.F., Lin, Y.W.
Unusual peroxidase activity of a myoglobin mutant with two distal histidines
CHINESE CHEMICAL LETTERS, 23:741-744, JUN 2012
abstract, full text

Pina, J.E., Lee, K.H., Ytreberg, F.M.
Effects of the binding of calcium ions on the structure and dynamics of the I broken vertical bar X174 virus investigated using molecular dynamics
JOURNAL OF BIOLOGICAL PHYSICS, 38:397-404, JUN 2012
abstract, full text

Dunstan, M.S., Barkauskaite, E., Lafite, P., Knezevic, C.E., Brassington, A., Ahel, M., Hergenrother, P.J., Leys, D., Ahel, I.
Structure and mechanism of a canonical poly(ADP-ribose) glycohydrolase
NATURE COMMUNICATIONS, 3: Art. No. 878, JUN 2012
abstract, full text

Stagno, J.R., Ma, B.Y., Li, J., Altieri, A.S., Byrd, R.A., Ji, X.H.
Crystal structure of a plectonemic RNA supercoil
NATURE COMMUNICATIONS, 3: Art. No. 901, JUN 2012
abstract, full text

Martin, D.R., Ozkan, S.B., Matyushov, D.V.
Dissipative electro-elastic network model of protein electrostatics
PHYSICAL BIOLOGY, 9: Art. No. 036004, JUN 2012
abstract, full text

Reboul, C.F., Porebski, B.T., Griffin, M.D.W., Dobson, R.C.J., Perugini, M.A., Gerrard, J.A., Buckle, A.M.
Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002537, JUN 2012
abstract, full text

Sgrignani, J., Magistrato, A.
Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1595-1606, JUN 2012
abstract, full text

Akbal-Delibas, B., Hashmi, I., Shehu, A., Haspel, N.
AN EVOLUTIONARY CONSERVATION-BASED METHOD FOR REFINING AND RERANKING PROTEIN COMPLEX STRUCTURES
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 10: Art. No. 1242002, JUN 2012
abstract, full text

Librando, V., Pappalardo, M.
Engineered enzyme interactions with polycyclic aromatic hydrocarbons: A theoretical approach
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 36:30-35, JUN 2012
abstract, full text

Puhl, A.C., Bernardes, A., Silveira, R.L., Yuan, J., Campos, J.L.O., Saidemberg, D.M., Palma, M.S., Cvoro, A., Ayers, S.D., Webb, P., Reinach, P.S., Skaf, M.S., Polikarpov, I.
Mode of Peroxisome Proliferator-Activated Receptor gamma Activation by Luteolin
MOLECULAR PHARMACOLOGY, 81:788-799, JUN 2012
abstract, full text

Pietra, F.
Molecular-Dynamics Simulation of Dioxygen Egress from 12/15-Lipoxygenase?Arachidonic Acid Complex
CHEMISTRY & BIODIVERSITY, 9:1019-1032, JUN 2012
abstract, full text

Prevost, M.S., Sauguet, L., Nury, H., Van Renterghem, C., Huon, C., Poitevin, F., Baaden, M., Delarue, M., Corringer, P.J.
A locally closed conformation of a bacterial pentameric proton-gated ion channel
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 19:642-+, JUN 2012
abstract, full text

Mihajlovic, T., Kachrimanis, K., Graovac, A., Djuric, Z., Ibric, S.
Improvement of Aripiprazole Solubility by Complexation with (2-Hydroxy)propyl-beta-cyclodextrin Using Spray Drying Technique
AAPS PHARMSCITECH, 13:623-631, JUN 2012
abstract, full text

Bermudez-Lugo, J.A., Perez-Gonzalez, O., Rosales-Hernandez, M.C., Ilizaliturri-Flores, I., Trujillo-Ferrara, J., Correa-Basurto, J.
Exploration of the valproic acid binding site on histone deacetylase 8 using docking and molecular dynamic simulations
JOURNAL OF MOLECULAR MODELING, 18:2301-2310, JUN 2012
abstract, full text

Nandi, T.K., Bairagya, H.R., Mukhopadhyay, B.P., Mallik, P., Sukul, D., Bera, A.K.
Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid-base coupled mechanism in plant thiol protease
JOURNAL OF MOLECULAR MODELING, 18:2633-2644, JUN 2012
abstract, full text

Bung, N., Priyakumar, U.D.
Computational investigation of the effect of thermal perturbation on the mechanical unfolding of titin I27
JOURNAL OF MOLECULAR MODELING, 18:2823-2829, JUN 2012
abstract, full text

Colletier, J.P., Aleksandrov, A., Coquelle, N., Mraihi, S., Mendoza-Barbera, E., Field, M., Madern, D.
Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions
MOLECULAR BIOLOGY AND EVOLUTION, 29:1683-1694, JUN 2012
abstract, full text

Baker, J., Wright, S.H., Tama, F.
Simulations of substrate transport in the multidrug transporter EmrD
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1620-1632, JUN 2012
abstract, full text

Holland, B.W., Vafaei, S., Tomberli, B.
Computer data analysis of the oscillating forward-reverse method
JOURNAL OF COMPUTATIONAL PHYSICS, 231:4355-4364, JUN 1 2012
abstract, full text

Yu, R.L., Kaas, Q., Craik, D.J.
Delineation of the Unbinding Pathway of alpha-Conotoxin Iml from the alpha 7 Nicotinic Acetylcholine Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 116:6097-6105, MAY 31 2012
abstract, full text

Akcapinar, G.B., Gul, O., Sezerman, U.O.
From in silico to in vitro: Modelling and production of Trichoderma reesei endoglucanase 1 and its mutant in Pichia pastoris
JOURNAL OF BIOTECHNOLOGY, 159:61-68, MAY 31 2012
abstract, full text

Gomes, T.C.F., Skaf, M.S.
Cellulose-Builder: A toolkit for building crystalline structures of cellulose
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:1338-1346, MAY 30 2012
abstract, full text

Kuo, A.T., Chang, C.H., Shinoda, W.
Molecular Dynamics Study of Catanionic Bilayers Composed of Ion Pair Amphiphile with Double-Tailed Cationic Surfactant
LANGMUIR, 28:8156-8164, MAY 29 2012
abstract, full text

Querol-Audi, J., Yan, C.L., Xu, X.J., Tsutakawa, S.E., Tsai, M.S., Tainer, J.A., Cooper, P.K., Nogales, E., Ivanov, I.
Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:8528-8533, MAY 29 2012
abstract, full text

Rivalta, I., Sultan, M.M., Lee, N.S., Manley, G.A., Loria, J.P., Batista, V.S.
Allosteric pathways in imidazole glycerol phosphate synthase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E1428-E1436, MAY 29 2012
abstract, full text

Sura, L., Zima, V., Marsakova, L., Hynkova, A., Barvik, I., Vlachova, V.
C-terminal Acidic Cluster Is Involved in Ca2+-induced Regulation of Human Transient Receptor Potential Ankyrin 1 Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:18067-18077, MAY 25 2012
abstract, full text

Zayner, J.P., Antoniou, C., Sosnick, T.R.
The Amino-Terminal Helix Modulates Light-Activated Conformational Changes in AsLOV2
JOURNAL OF MOLECULAR BIOLOGY, 419:61-74, MAY 25 2012
abstract, full text

Apgar, J., Ross, M., Zuo, X., Dohle, S., Sturtevant, D., Shen, B.Z., de la Vega, H., Lessard, P., Lazar, G., Raab, R.M.
A Predictive Model of Intein Insertion Site for Use in the Engineering of Molecular Switches
PLOS ONE, 7: Art. No. e37355, MAY 23 2012
abstract, full text

Liberato, M.V., Nascimento, A.S., Ayers, S.D., Lin, J.Z., Cvoro, A., Silveira, R.L., Martinez, L., Souza, P.C.T., Saidemberg, D., Deng, T., Amato, A.A., Togashi, M., Hsueh, W.A., Phillips, K., Palma, M.S., Neves, F.A.R., Skaf, M.S., Webb, P., Polikarpov, I.
Medium Chain Fatty Acids Are Selective Peroxisome Proliferator Activated Receptor (PPAR) gamma Activators and Pan-PPAR Partial Agonists
PLOS ONE, 7: Art. No. e36297, MAY 23 2012
abstract, full text

Brunk, E., Arey, J.S., Rothlisberger, U.
Role of Environment for Catalysis of the DNA Repair Enzyme MutY
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:8608-8616, MAY 23 2012
abstract, full text

Maiti, A., Noon, M.S., MacKerell, A.D., Pozharski, E., Drohat, A.C.
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:8091-8096, MAY 22 2012
abstract, full text

Herrou, J., Rotskoff, G., Luo, Y., Roux, B., Crosson, S.
Structural basis of a protein partner switch that regulates the general stress response of alpha-proteobacteria
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:E1415-E1423, MAY 22 2012
abstract, full text

Kneller, G.R., Hinsen, K., Calligari, P.
Communication: A minimal model for the diffusion-relaxation backbone dynamics of proteins
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 191101, MAY 21 2012
abstract, full text

Dixit, A., Verkhivker, G.M.
Probing Molecular Mechanisms of the Hsp90 Chaperone: Biophysical Modeling Identifies Key Regulators of Functional Dynamics
PLOS ONE, 7: Art. No. e37605, MAY 18 2012
abstract, full text

Silveira, R.L., Martinez, J., Skaf, M.S., Martinez, L.
Enzyme Microheterogeneous Hydration and Stabilization in Supercritical Carbon Dioxide
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5671-5678, MAY 17 2012
abstract, full text

Legare, S., Lague, P.
The Influenza Fusion Peptide Adopts a Flexible Flat V Conformation in Membranes
BIOPHYSICAL JOURNAL, 102:2270-2278, MAY 16 2012
abstract, full text

Elder, R.M., Jayaraman, A.
Sequence-Specific Recognition of Cancer Drug-DNA Adducts by HMGB1a Repair Protein
BIOPHYSICAL JOURNAL, 102:2331-2338, MAY 16 2012
abstract, full text

Sander, W., Roy, S., Polyak, I., Ramirez-Anguita, J.M., Sanchez-Garcia, E.
The Phenoxyl Radical-Water Complex-A Matrix Isolation and Computational Study
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:8222-8230, MAY 16 2012
abstract, full text

Reboul, C.F., Mahmood, K., Whisstock, J.C., Dunstone, M.A.
Predicting giant transmembrane beta-barrel architecture
BIOINFORMATICS, 28:1299-1302, MAY 15 2012
abstract, full text

Wereszczynski, J., McCammon, J.A.
Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:7759-7764, MAY 15 2012
abstract, full text

Yakubovich, A.V., Surdutovich, E., Soloy'yov, A.V.
Thermomechanical damage of nucleosome by the shock wave initiated by ion passing through liquid water
NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION B-BEAM INTERACTIONS WITH MATERIALS AND ATOMS, 279:135-139, MAY 15 2012
abstract, full text

da Silva, L.P., da Silva, J.C.G.E.
Theoretical analysis of the color tuning mechanism of oxyluciferin and 5-hydroxyoxyluciferin
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 988:56-62, MAY 15 2012
abstract, full text

Sinha, S.K., Bandyopadhyay, S.
Polar solvation dynamics of lysozyme from molecular dynamics studies
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 185102, MAY 14 2012
abstract, full text

Stolzenberg, S., Khelashvili, G., Weinstein, H.
Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5372-5383, MAY 10 2012
abstract, full text

Li, X.Y., Shi, Y.C., Miao, B., Zhao, Y.L.
Effects of Embedded Carbon Nanotube on Properties of Biomembrane
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5391-5397, MAY 10 2012
abstract, full text

Zhang, M., Abrams, C., Wang, L.P., Gizzi, A., He, L.P., Lin, R.H., Chen, Y., Loll, P.J., Pascal, J.M., Zhang, J.F.
Structural Basis for Calmodulin as a Dynamic Calcium Sensor
STRUCTURE, 20:911-923, MAY 9 2012
abstract, full text

Li, X.Y., Shi, Y.C., Yang, Y.L., Du, H.L., Zhou, R.H., Zhao, Y.L.
How does water-nanotube interaction influence water flow through the nanochannel?
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 175101, MAY 7 2012
abstract, full text

Weber, A.C.J., Pizzirusso, A., Muccioli, L., Zannoni, C., Meerts, W.L., de Lange, C.A., Burnell, E.E.
Efficient analysis of highly complex nuclear magnetic resonance spectra of flexible solutes in ordered liquids by using molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 174506, MAY 7 2012
abstract, full text

Kim, T., Ravilious, G.E., Sept, D., Cooper, J.A.
Mechanism for CARMIL Protein Inhibition of Heterodimeric Actin-capping Protein
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:15251-15262, MAY 4 2012
abstract, full text

Mori, K., Mahmood, M.I., Neya, S., Matsuzaki, K., Hoshino, T.
Formation of GM1 Ganglioside Clusters on the Lipid Membrane Containing Sphingomyeline and Cholesterol
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5111-5121, MAY 3 2012
abstract, full text

Liu, Y.X., Strumpfer, J., Freddolino, P.L., Gruebele, M., Schulten, K.
Structural Characterization of lambda-Repressor Folding from All-Atom Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:1117-1123, MAY 3 2012
abstract, full text, TCBG publications

Ohkubo, Y.Z., Pogorelov, T.V., Arcario, M.J., Christensen, G.A., Tajkhorshid, E.
Accelerating Membrane Insertion of Peripheral Proteins with a Novel Membrane Mimetic Model
BIOPHYSICAL JOURNAL, 102:2130-2139, MAY 2 2012
abstract, full text

Palmer, S.G., Porotto, M., Palermo, L.M., Cunha, L.F., Greengard, O., Moscona, A.
Adaptation of Human Parainfluenza Virus to Airway Epithelium Reveals Fusion Properties Required for Growth in Host Tissue
MBIO, 3: Art. No. e00137-12, MAY-JUN 2012
abstract, full text

LeBard, D.N., Henin, J., Eckenhoff, R.G., Klein, M.L., Brannigan, G.
General Anesthetics Predicted to Block the GLIC Pore with Micromolar Affinity
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002532, MAY 2012
abstract, full text

Lawrenz, M., Wereszczynski, J., Ortiz-Sanchez, J.M., Nichols, S.E., McCammon, J.A.
Thermodynamic integration to predict host-guest binding affinities
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 26:569-576, MAY 2012
abstract, full text

Demchuk, O.M., Karpov, P.A., Blume, Y.B.
Docking small ligands to molecule of the plant FtsZ protein: Application of the CUDA technology for faster computations
CYTOLOGY AND GENETICS, 46:172-179, MAY 2012
abstract, full text

Sahu, B.S., Obbineni, J.M., Sahu, G., Singh, P.K., Sonawane, P.J., Sasi, B.K., Allu, P.K.R., Maji, S.K., Bera, A.K., Senapati, S., Mahapatra, N.R.
Molecular interactions of the physiological anti-hypertensive peptide catestatin with the neuronal nicotinic acetylcholine receptor
JOURNAL OF CELL SCIENCE, 125:2323-2337, MAY 1 2012
abstract, full text

Zapata-Torres, G., Fierro, A., Miranda-Rojas, S., Guajardo, C., Saez-Briones, P., Salgado, J.C., Celis-Barros, C.
Influence of Protonation on Substrate and Inhibitor Interactions at the Active Site of Human Monoamine Oxidase-A
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1213-1221, MAY 2012
abstract, full text

Demir, O., Amaro, R.E.
Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1308-1318, MAY 2012
abstract, full text

Miyake, Y., Nagata, T., Tanaka, H., Yamazaki, M., Ohta, M., Kokawa, R., Ogawa, T.
Entropy-Controlled 2D Supramolecular Structures of N,N '-Bis(n-alkyl)-naphthalenediimides on a HOPG Surface
ACS NANO, 6:3876-3887, MAY 2012
abstract, full text

Whitby, R.L.D., Gun'ko, V.M., Korobeinyk, A., Busquets, R., Cundy, A.B., Laszlo, K., Skubiszewska-Zieba, J., Leboda, R., Tombacz, E., Toth, I.Y., Kovacs, K., Mikhalovsky, S.V.
Driving Forces of Conformational Changes in Single-Layer Graphene Oxide
ACS NANO, 6:3967-3973, MAY 2012
abstract, full text

Chan, H., Demortiere, A., Vukovic, L., Kral, P., Petit, C.
Colloidal Nanocube Supercrystals Stabilized by Multipolar Coulombic Coupling
ACS NANO, 6:4203-4213, MAY 2012
abstract, full text

Masciocchi, D., Villa, S., Meneghetti, F., Pedretti, A., Barlocco, D., Legnani, L., Toma, L., Kwon, B.M., Nakano, S., Asai, A., Gelain, A.
Biological and computational evaluation of an oxadiazole derivative (MD77) as a new lead for direct STAT3 inhibitors
MEDCHEMCOMM, 3:592-599, MAY 2012
abstract, full text

Sciacca, M.F.M., Chillemi, R., Sciuto, S., Pappalardo, M., La Rosa, C., Grasso, D., Milardi, D.
Interactions of two O-phosphorylresveratrol derivatives with model membranes
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 521:111-116, MAY 2012
abstract, full text

Rogacheva, O.N., Shchegolev, B.F., Stefanov, V.E., Zakharov, G.A., Savvateeva-Popova, E.V.
Initiation of the 3 ':5 '-AMP-Induced Protein Kinase A I alpha Regulatory Subunit Conformational Transition. Part I. A202 and A326 are Critical Residues
BIOCHEMISTRY-MOSCOW, 77:456-464, MAY 2012
abstract, full text

Chao, Y., Makale, M., Karmali, P.P., Sharikov, Y., Tsigelny, I., Merkulov, S., Kesari, S., Wrasidlo, W., Ruoslahti, E., Simberg, D.
Recognition of Dextran-Superparamagnetic Iron Oxide Nanoparticle Conjugates (Feridex) via Macrophage Scavenger Receptor Charged Domains
BIOCONJUGATE CHEMISTRY, 23:1003-1009, MAY 2012
abstract, full text

Palermo, E.F., Vemparala, S., Kuroda, K.
Cationic Spacer Arm Design Strategy for Control of Antimicrobial Activity and Conformation of Amphiphilic Methacrylate Random Copolymers
BIOMACROMOLECULES, 13:1632-1641, MAY 2012
abstract, full text

Maffeo, C., Luan, B.Q., Aksimentiev, A.
End-to-end attraction of duplex DNA
NUCLEIC ACIDS RESEARCH, 40:3812-3821, MAY 2012
abstract, full text

Kraft, J.F., Vestergaard, M., Schiott, B., Thogersen, L.
Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1556-1569, MAY 2012
abstract, full text

Aguayo, D., Gonzalez-Nilo, F.D., Chipot, C.
Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1765-1773, MAY 2012
abstract, full text

He, R., Zhao, L.Y., Petrone, N., Kim, K.S., Roth, M., Hone, J., Kim, P., Pasupathy, A., Pinczuk, A.
Large Physisorption Strain in Chemical Vapor Deposition of Graphene on Copper Substrates
NANO LETTERS, 12:2408-2413, MAY 2012
abstract, full text

Sokkar, P., Sathis, V., Ramachandran, M.
Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies
JOURNAL OF MOLECULAR MODELING, 18:1691-1700, MAY 2012
abstract, full text

Prasad, N.K., Vindal, V., Narayana, S.L., Ramakrishna, V., Kunal, S.P., Srinivas, M.
In silico analysis of Pycnoporus cinnabarinus laccase active site with toxic industrial dyes
JOURNAL OF MOLECULAR MODELING, 18:2013-2019, MAY 2012
abstract, full text

Lagos, C.F., Araya-Secchi, R., Thomas, P., Perez-Acle, T., Tapia, R.A., Salas, C.O.
Molecular modeling of Trypanosoma cruzi glutamate cysteine ligase and investigation of its interactions with glutathione
JOURNAL OF MOLECULAR MODELING, 18:2055-2064, MAY 2012
abstract, full text

Anbar, M., Gul, O., Lamed, R., Sezerman, U.O., Bayer, E.A.
Improved Thermostability of Clostridium thermocellum Endoglucanase Cel8A by Using Consensus-Guided Mutagenesis
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 78:3458-3464, MAY 2012
abstract, full text

Sharma, V., Wikstrom, M., Kaila, V.R.I.
Dynamic water networks in cytochrome cbb(3) oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1817:726-734, MAY 2012
abstract, full text

Hospital, A., Andrio, P., Fenollosa, C., Cicin-Sain, D., Orozco, M., Gelpi, J.L.
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
BIOINFORMATICS, 28:1278-1279, MAY 1 2012
abstract, full text

Cui, Y.B., Bastien, D.A.
Molecular dynamics simulations of PfAQP from the malarial parasite Plasmodium falciparum
MOLECULAR MEDICINE REPORTS, 5:1197-1201, MAY 2012
abstract, full text

Pandit, K.R., Klauda, J.B.
Membrane models of E-coli containing cyclic moieties in the aliphatic lipid chain
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1205-1210, MAY 2012
abstract, full text

Bondarenko, V., Mowrey, D., Tillman, T., Cui, T.X., Liu, L.T., Xu, Y., Tang, P.
NMR structures of the transmembrane domains of the alpha 4 beta 2 nAChR
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1261-1268, MAY 2012
abstract, full text

Mihajlovic, M., Lazaridis, T.
Charge distribution and imperfect amphipathicity affect pore formation by antimicrobial peptides
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1274-1283, MAY 2012
abstract, full text

Wang, Y., Schlamadinger, D.E., Kim, J.E., McCammon, J.A.
Comparative molecular dynamics simulations of the antimicrobial peptide CM15 in model lipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1402-1409, MAY 2012
abstract, full text

Chatterjee, P., Sengupta, N.
Effect of the A30P mutation on the structural dynamics of micelle-bound alpha Synuclein released in water: a molecular dynamics study
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 41:483-489, MAY 2012
abstract, full text

Friesen, D.E., Barakat, K.H., Semenchenko, V., Perez-Pineiro, R., Fenske, B.W., Mane, J., Wishart, D.S., Tuszynski, J.A.
Discovery of Small Molecule Inhibitors that Interact with gamma-Tubulin
CHEMICAL BIOLOGY & DRUG DESIGN, 79:639-652, MAY 2012
abstract, full text

Chen, C., Li, W.Z., Song, Y.C., Weng, L.D., Zhang, N.
Effects of Glycerol Concentrations on Self-diffusion Coefficients of Glycerol in Glycerol-Water-Sodium Chloride Ternary Solutions
ACTA CHIMICA SINICA, 70:1043-1046, APR 28 2012
abstract, full text

Perilla, J.R., Woolf, T.B.
Towards the prediction of order parameters from molecular dynamics simulations in proteins
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 164101, APR 28 2012
abstract, full text

Yu, X., Luo, Y., Dinkel, P., Zheng, J., Wei, G.H., Margittai, M., Nussinov, R., Ma, B.Y.
Cross-seeding and Conformational Selection between Three- and Four-repeat Human Tau Proteins
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:14950-14959, APR 27 2012
abstract, full text

Chen, R., Chung, S.H.
Conserved Functional Surface of Antimammalian Scorpion beta-Toxins
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4796-4800, APR 26 2012
abstract, full text

Xu, Y., Ma, B.Y., Nussinov, R.
Structural and Functional Consequences of Phosphate-Arsenate Substitutions in Selected Nucleotides: DNA, RNA, and ATP
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4801-4811, APR 26 2012
abstract, full text

Rashid, M.H., Kuyucak, S.
Affinity and Selectivity of ShK Toxin for the Kv1 Potassium Channels from Free Energy Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4812-4822, APR 26 2012
abstract, full text

Yi, Z., Miao, Y.L., Baudry, J., Jain, N., Smith, J.C.
Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering
JOURNAL OF PHYSICAL CHEMISTRY B, 116:5028-5036, APR 26 2012
abstract, full text

Yu, X., Wang, Q.M., Lin, Y.A., Zhao, J., Zhao, C., Zheng, J.
Structure, Orientation, and Surface Interaction of Alzheimer Amyloid-beta Peptides on the Graphite
LANGMUIR, 28:6595-6605, APR 24 2012
abstract, full text

Han, C., Wang, J.P.
Influence of an Unnatural Amino Acid Side Chain on the Conformational Dynamics of Peptides
CHEMPHYSCHEM, 13:1522-1534, APR 23 2012
abstract, full text

Matsushita, S., Inoue, Y., Adachi, T.
Quantitative analysis of extension-torsion coupling of actin filaments
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 420:710-713, APR 20 2012
abstract, full text

Zanuy, D., Preat, J., Perpete, E.A., Aleman, C.
Response of Crown Ether Functionalized Polythiophenes to Alkaline Ions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4575-4583, APR 19 2012
abstract, full text

Long, F., Su, C.C., Lei, H.T., Bolla, J.R., Do, S.V., Yu, E.W.
Structure and mechanism of the tripartite CusCBA heavy-metal efflux complex
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 367:1047-1058, APR 19 2012
abstract, full text

Jana, A.K., Sengupta, N.
Adsorption Mechanism and Collapse Propensities of the Full-Length, Monomeric A beta(1-42) on the Surface of a Single-Walled Carbon Nanotube: A Molecular Dynamics Simulation Study
BIOPHYSICAL JOURNAL, 102:1889-1896, APR 18 2012
abstract, full text

Papamokos, G.V., Tziatzos, G., Papageorgiou, D.G., Georgatos, S.D., Politou, A.S., Kaxiras, E.
Structural Role of RKS Motifs in Chromatin Interactions: A Molecular Dynamics Study of HP1 Bound to a Variably Modified Histone Tail
BIOPHYSICAL JOURNAL, 102:1926-1933, APR 18 2012
abstract, full text

Lv, C.M., Tan, C., Qin, M., Zou, D.W., Cao, Y., Wang, W.
Low Folding Cooperativity of Hp35 Revealed by Single-Molecule Force Spectroscopy and Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 102:1944-1951, APR 18 2012
abstract, full text

Vashisth, H., Maragliano, L., Abrams, C.F.
"DFG-Flip" in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop
BIOPHYSICAL JOURNAL, 102:1979-1987, APR 18 2012
abstract, full text

Moss, C.L., Turecek, F.
Protonation sites in peptide dications and cation-radicalls containing beta-amino acid residues
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 316:57-67, APR 15 2012
abstract, full text

Liu, F.F., Liu, Z., Bai, S., Dong, X.Y., Sun, Y.
Exploring the inter-molecular interactions in amyloid-beta protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 145101, APR 14 2012
abstract, full text

Krishnan, M., Smith, J.C.
Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4124-4133, APR 12 2012
abstract, full text

Feng, J., Slocik, J.M., Sarikaya, M., Naik, R.R., Farmer, B.L., Heinz, H.
Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution
SMALL, 8:1049-1059, APR 10 2012
abstract, full text

Connelly, L., Jang, H., Arce, F.T., Ramachandran, S., Kagan, B.L., Nussinov, R., Lal, R.
Effects of Point Substitutions on the Structure of Toxic Alzheimer's beta-Amyloid Channels: Atomic Force Microscopy and Molecular Dynamics Simulations
BIOCHEMISTRY, 51:3031-3038, APR 10 2012
abstract, full text

Sen, K., Hackett, J.C.
Coupled Electron Transfer and Proton Hopping in the Final Step of CYP19-Catalyzed Androgen Aromatization
BIOCHEMISTRY, 51:3039-3049, APR 10 2012
abstract, full text

Sarver, J.L., Townsend, J.E., Rajapakse, G., Jen-Jacobson, L., Saxena, S.
Simulating the Dynamics and Orientations of Spin-Labeled Side Chains in a Protein-DNA Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 116:4024-4033, APR 5 2012
abstract, full text

Lakkaraju, A.K.K., Abrami, L., Lemmin, T., Blaskovic, S., Kunz, B., Kihara, A., Dal Peraro, M., van der Goot, F.G.
Palmitoylated calnexin is a key component of the ribosome-translocon complex
EMBO JOURNAL, 31:1823-1835, APR 4 2012
abstract, full text

Saunders, M.G., Voth, G.A.
Comparison between Actin Filament Models: Coarse-Graining Reveals Essential Differences
STRUCTURE, 20:641-653, APR 4 2012
abstract, full text

Utesch, T., Sezer, M., Weidinger, I.M., Mroginski, M.A.
Adsorption of Sulfite Oxidase on Self-Assembled Mono layers from Molecular Dynamics Simulations
LANGMUIR, 28:5761-5769, APR 3 2012
abstract, full text

Lee, K.H., Ytreberg, F.M.
Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure
ENTROPY, 14:630-641, APR 2012
abstract, full text

Feng, Z.W., Hou, T.J., Li, Y.Y.
Studies on the Interactions between beta(2) Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:1005-1014, APR 2012
abstract, full text

Selvin, J.F.A., Priyadarzini, T.R.K., Veluraja, K.
Sialyldisaccharide conformations: a molecular dynamics perspective
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 26:375-385, APR 2012
abstract, full text

Thompson, D., Hermes, J.P., Quinn, A.J., Mayor, M.
Scanning the Potential Energy Surface for Synthesis of Dendrimer-Wrapped Gold Clusters: Design Rules for True Single-Molecule Nanostructures
ACS NANO, 6:3007-3017, APR 2012
abstract, full text

Lu, S.J., Chong, F.C.
Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 13:4496-4507, APR 2012
abstract, full text

Lin, Y.W., Wu, Y.M., Liao, L.F., Nie, C.M.
Molecular modeling of cytochrome b(5) with a single cytochrome c-like thioether linkage
JOURNAL OF MOLECULAR MODELING, 18:1553-1560, APR 2012
abstract, full text

Lin, Y.W., Wu, Y.M., Liao, L.F.
Dynamics comparison of two myoglobins with a distinct heme active site
JOURNAL OF MOLECULAR MODELING, 18:1591-1596, APR 2012
abstract, full text

Furini, S., Domene, C.
On Conduction in a Bacterial Sodium Channel
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002476, APR 2012
abstract, full text

Shan, J.F., Khelashvili, G., Mondal, S., Mehler, E.L., Weinstein, H.
Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002473, APR 2012
abstract, full text

Hernandez, G., Anderson, J.S., LeMaster, D.M.
Experimentally assessing molecular dynamics sampling of the protein native state conformational distribution
BIOPHYSICAL CHEMISTRY, 163:21-34, APR 2012
abstract, full text

Aktulga, H.M., Fogarty, J.C., Pandit, S.A., Grama, A.Y.
Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques
PARALLEL COMPUTING, 38:245-259, APR-MAY 2012
abstract, full text

Saladino, G., Gauthier, L., Bianciotto, M., Gervasio, F.L.
Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1165-1170, APR 2012
abstract, full text

Sieradzan, A.K., Scheraga, H.A., Liwo, A.
Determination of Effective Potentials for the Stretching of C-alpha center dot center dot center dot C-alpha Virtual Bonds in Polypeptide Chains for Coarse-Grained Simulations of Proteins from ab Initio Energy Surfaces of N-Methylacetamide and N-Acetylpyrrolidine
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1334-1343, APR 2012
abstract, full text

Singharoy, A., Sereda, Y., Ortoleva, P.J.
Hierarchical Order Parameters for Macromolecular Assembly Simulations. 1. Construction and Dynamical Properties of Order Parameters
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1379-1392, APR 2012
abstract, full text

Espinoza-Moraga, M., Caballero, J., Gaube, F., Winckler, T., Santos, L.S.
1-Benzyl-1,2,3,4-Tetrahydro-ss-Carboline as Channel Blocker of N-Methyl-d-Aspartate Receptors
CHEMICAL BIOLOGY & DRUG DESIGN, 79:594-599, APR 2012
abstract, full text

Bukovnik, U., Gao, J., Cook, G.A., Shank, L.P., Seabra, M.B., Schultz, B.D., Iwamoto, T., Chen, J., Tomich, J.M.
Structural and biophysical properties of a synthetic channel-forming peptide: Designing a clinically relevant anion selective pore
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:1039-1048, APR 2012
abstract, full text

Li, Y., Hao, M., Ren, H., Zhang, S.W., Wang, X., Ma, M., Li, G.H., Yang, L.
Exploring the structure requirement for KC theta inhibitory activity of pyridinecarbonitrile derivatives: an in silico analysis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 34:76-88, APR 2012
abstract, full text

Zhang, L., Yan, F., Zhang, S.L., Lei, D.S., Charles, M.A., Cavigiolio, G., Oda, M., Krauss, R.M., Weisgraber, K.H., Rye, K.A., Pownall, H.J., Qiu, X.Y., Ren, G.
Structural basis of transfer between lipoproteins by cholesteryl ester transfer protein
NATURE CHEMICAL BIOLOGY, 8:342-349, APR 2012
abstract, full text

Gonnet, P.
A short note on the fast evaluation of dihedral angle potentials and their derivatives
JOURNAL OF COMPUTATIONAL PHYSICS, 231:2691-2694, APR 1 2012
full text

Wereszczynski, J., McCammon, J.A.
Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates
PROTEIN SCIENCE, 21:475-486, APR 2012
abstract, full text

Calligari, P.A., Salgado, G.F., Pelupessy, P., Lopes, P., Ouazzani, J., Bodenhausen, G., Abergel, D.
Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1196-1210, APR 2012
abstract, full text

Asses, Y., Venkatraman, V., Leroux, V., Ritchie, D.W., Maigret, B.
Exploring c-Met kinase flexibility by sampling and clustering its conformational space
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1227-1238, APR 2012
abstract, full text

Priyadarzini, T.R.K., Subashini, B., Selvin, J.F.A., Veluraja, K.
Molecular dynamics simulation and quantum mechanical calculations on alpha-D-N-acetylneuraminic acid
CARBOHYDRATE RESEARCH, 351:93-97, APR 1 2012
abstract, full text

Oakley, A.J., Bhatia, S., Ecroyd, H., Garner, B.
Molecular Dynamics Analysis of Apolipoprotein-D - Lipid Hydroperoxide Interactions: Mechanism for Selective Oxidation of Met-93
PLOS ONE, 7: Art. No. e34057, MAR 30 2012
abstract, full text

Werner, T., Morris, M.B., Dastmalchi, S., Church, W.B.
Structural modelling and dynamics of proteins for insights into drug interactions
ADVANCED DRUG DELIVERY REVIEWS, 64:323-343, MAR 30 2012
abstract, full text

Clare, D.K., Vasishtan, D., Stagg, S., Quispe, J., Farr, G.W., Topf, M., Horwich, A.L., Saibil, H.R.
ATP-Triggered Conformational Changes Delineate Substrate-Binding and -Folding Mechanics of the GroEL Chaperonin
CELL, 149:113-123, MAR 30 2012
abstract, full text

Zhao, Y., De Nicola, A., Kawakatsu, T., Milano, G.
Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:868-880, MAR 30 2012
abstract, full text

Pizzirusso, A., Di Cicco, M.B., Tiberio, G., Muccioli, L., Berardi, R., Zannoni, C.
Alignment of Small Organic Solutes in a Nematic Solvent: The Effect of Electrostatic Interactions
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3760-3771, MAR 29 2012
abstract, full text

Giussani, L., Tabacchi, G., Gianotti, E., Coluccia, S., Fois, E.
Disentangling protein-silica interactions
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 370:1463-1477, MAR 28 2012
abstract, full text

Huang, Y.L., Rizzo, R.C.
A Water-Based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases
BIOCHEMISTRY, 51:2390-2406, MAR 27 2012
abstract, full text

Jeong, W.J., Ha, M.Y., Yoon, H.S., Ambrosia, M.
Dynamic Behavior of Water Droplets on Solid Surfaces with Pillar-Type Nanostructures
LANGMUIR, 28:5360-5371, MAR 27 2012
abstract, full text

Craddock, T.J.A., Tuszynski, J.A., Chopra, D., Casey, N., Goldstein, L.E., Hameroff, S.R., Tanzi, R.E.
The Zinc Dyshomeostasis Hypothesis of Alzheimer's Disease
PLOS ONE, 7: Art. No. e33552, MAR 23 2012
abstract, full text

Helbing, J., Devereux, M., Nienhaus, K., Nienhaus, G.U., Hamm, P., Meuwly, M.
Temperature Dependence of the Heat Diffusivity of Proteins
JOURNAL OF PHYSICAL CHEMISTRY A, 116:2620-2628, MAR 22 2012
abstract, full text

Jones, P.M., George, A.M.
Role of the D-Loops in Allosteric Control of ATP Hydrolysis in an ABC Transporter
JOURNAL OF PHYSICAL CHEMISTRY A, 116:3004-3013, MAR 22 2012
abstract, full text

Kwon, T., Roux, B., Jo, S., Klauda, J.B., Harris, A.L., Bargiello, T.A.
Molecular Dynamics Simulations of the Cx26 Hemichannel: Insights into Voltage-Dependent Loop-Gating
BIOPHYSICAL JOURNAL, 102:1341-1351, MAR 21 2012
abstract, full text

Cheng, M.H., Coalson, R.D.
Molecular Dynamics Investigation of Cl- and Water Transport through a Eukaryotic CLC Transporter
BIOPHYSICAL JOURNAL, 102:1363-1371, MAR 21 2012
abstract, full text

Choi, K.M., Kwon, C.H., Kim, H.L., Hwang, H.
Potential of Mean Force Calculations for Ion Selectivity in a Cyclic Peptide Nanotube
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 33:911-916, MAR 20 2012
abstract, full text

Wilkins, S.E., Karttunen, S., Hampton-Smith, R.J., Murchland, I., Chapman-Smith, A., Peet, D.J.
Factor Inhibiting HIF (FIH) Recognizes Distinct Molecular Features within Hypoxia-inducible Factor-alpha (HIF-alpha) versus Ankyrin Repeat Substrates
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:8769-8781, MAR 16 2012
abstract, full text

Chen, C., Li, W.Z., Song, Y.C., Weng, L.D., Zhang, N.
Formation of water and glucose clusters by hydrogen bonds in glucose aqueous solutions
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 984:85-92, MAR 15 2012
abstract, full text

Falvo, C., Zhuang, W., Kim, Y.S., Axelsen, P.H., Hochstrasser, R.M., Mukamel, S.
Frequency Distribution of the Amide-I Vibration Sorted by Residues in Amyloid Fibrils Revealed by 2D-IR Measurements and Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3322-3330, MAR 15 2012
abstract, full text

Yeh, I.C., Ripoll, D.R., Wallqvist, A.
Free Energy Difference in Indolicidin Attraction to Eukaryotic and Prokaryotic Model Cell Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3387-3396, MAR 15 2012
abstract, full text

Wang, B.B., Weng, J.W., Fan, K.N., Wang, W.N.
Interdomain Flexibility and pH-Induced Conformational Changes of AcrA Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3411-3420, MAR 15 2012
abstract, full text

Moss, C.L., Chamot-Rooke, J., Nicol, E., Brown, J., Campuzano, I., Richardson, K., Williams, J.P., Bush, M.F., Bythell, B., Paizs, B., Turecek, F.
Assigning Structures to Gas-Phase Peptide Cations and Cation-Radicals. An Infrared Multiphoton Dissociation, Ion Mobility, Electron Transfer, and Computational Study of a Histidine Peptide Ion
JOURNAL OF PHYSICAL CHEMISTRY B, 116:3445-3456, MAR 15 2012
abstract, full text

McCullagh, M., Franco, I., Ratner, M.A., Schatz, G.C.
Defects in DNA: Lessons from Molecular Motor Design
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:689-693, MAR 15 2012
abstract, full text

Zobnina, V.G., Kosevich, M.V., Chagovets, V.V., Boryak, O.A., Vekey, K., Gomory, A., Kulyk, A.N.
Interactions of oligomers of organic polyethers with histidine amino acid
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 26:532-540, MAR 15 2012
abstract, full text

Harada, R., Sugita, Y., Feig, M.
Protein Crowding Affects Hydration Structure and Dynamics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:4842-4849, MAR 14 2012
abstract, full text

Bastug, T., Heinzelmann, G., Kuyucak, S., Salim, M., Vandenberg, R.J., Ryan, R.M.
Position of the Third Na+ Site in the Aspartate Transporter Glt(Ph) and the Human Glutamate Transporter, EAAT1
PLOS ONE, 7: Art. No. e33058, MAR 13 2012
abstract, full text

Ngo, V.A.
Parallel-pulling protocol for free-energy evaluation
PHYSICAL REVIEW E, 85: Art. No. 036702, MAR 13 2012
abstract, full text

Sanford, B., Cao, B., Johnson, J.M., Zimmerman, K., Strom, A.M., Mueller, R.M., Bhattacharyya, S., Musier-Forsyth, K., Hati, S.
Role of Coupled Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases
BIOCHEMISTRY, 51:2146-2156, MAR 13 2012
abstract, full text

Du, J., Dong, H., Zhou, H.X.
Gating mechanism of a P2X4 receptor developed from normal mode analysis and molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:4140-4145, MAR 13 2012
abstract, full text

Diaz, N., Suarez, D.
Alternative Interdomain Configurations of the Full-Length MMP-2 Enzyme Explored by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2677-2686, MAR 8 2012
abstract, full text

Rodriguez, J., Elola, M.D., Laria, D.
Ionic Liquid Aqueous Solutions under Nanoconfinement
JOURNAL OF PHYSICAL CHEMISTRY C, 116:5394-5400, MAR 8 2012
abstract, full text

Chen, R., Chung, S.H.
Engineering a Potent and Specific Blocker of Voltage-Gated Potassium Channel Kv1.3, a Target for Autoimmune Diseases
BIOCHEMISTRY, 51:1976-1982, MAR 6 2012
abstract, full text

Ranganathan, S., Singh, P.K., Singh, U., Singru, P.S., Padinhateeri, R., Maji, S.K.
Molecular Interpretation of ACTH-beta-Endorphin Coaggregation: Relevance to Secretory Granule Biogenesis
PLOS ONE, 7: Art. No. e31924, MAR 5 2012
abstract, full text

Huang, Q., Herrmann, A.
Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues
PROTEIN & CELL, 3:230-238, MAR 2012
abstract, full text

Ghodsi, H., Kazemi, M.T.
Elastic Properties of Actin Assemblies in Different States of Nucleotide Binding
CELLULAR AND MOLECULAR BIOENGINEERING, 5:1-13, MAR 2012
abstract, full text

Gorham, R.D., Kieslich, C.A., Morikis, D.
Complement Inhibition by Staphylococcus aureus: Electrostatics of C3d-EfbC and C3d-Ehp Association
CELLULAR AND MOLECULAR BIOENGINEERING, 5:32-43, MAR 2012
abstract, full text

Wan, D., Liao, L.F., Zhao, M.M., Wu, M.L., Wu, Y.M., Lin, Y.W.
Interactions of uranyl ion with cytochrome b(5) and its His39Ser variant as revealed by molecular simulation in combination with experimental methods
JOURNAL OF MOLECULAR MODELING, 18:1009-1013, MAR 2012
abstract, full text

Gabrielsen, M., Ravna, A.W., Kristiansen, K., Sylte, I.
Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 18:1073-1085, MAR 2012
abstract, full text

Moreno-Vargas, L., Correa-Basurto, J., Maroun, R.C., Fernandez, F.J.
Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking
JOURNAL OF MOLECULAR MODELING, 18:1189-1205, MAR 2012
abstract, full text

Xia, D.H., Ren, X.D., Jiao, L., Li, H.
Inclusion Modes of Berberine with beta-Cyclodextrin in Aqueous Solution
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 28:282-286, MAR 2012
abstract, full text

Moss, C.L., Liang, W., Li, X.S., Turecek, F.
The Early Life of a Peptide Cation-Radical. Ground and Excited-State Trajectories of Electron-Based Peptide Dissociations During the First 330 Femtoseconds
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 23:446-459, MAR 2012
abstract, full text

Pan, J.J., Chen, Q., Willenbring, D., Yoshida, K., Tillman, T., Kashlan, O.B., Cohen, A., Kong, X.P., Xu, Y., Tang, P.
Structure of the pentameric ligand-gated ion channel ELIC cocrystallized with its competitive antagonist acetylcholine
NATURE COMMUNICATIONS, 3: Art. No. 714, MAR 2012
abstract, full text

Satpati, P., Simonson, T.
Conformational selection through electrostatics: Free energy simulations of gtp and gdp binding to archaeal initiation factor 2
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1264-1282, MAR 2012
abstract, full text

Lu, W.Z., Negi, S.S., Oberhauser, A.F., Braun, W.
Engineering proteins with enhanced mechanical stability by force-specific sequence motifs
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1308-1315, MAR 2012
abstract, full text

Jamroz, M., Kolinski, A., Kihara, D.
Structural features that predict real-value fluctuations of globular proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1425-1435, MAR 2012
abstract, full text

Bernini, C., Pogni, R., Basosi, R., Sinicropi, A.
The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: Insights from quantum mechanical/molecular mechanics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:1476-1483, MAR 2012
abstract, full text

Saiz-Poseu, J., Faraudo, J., Figueras, A., Alibes, R., Busque, F., Ruiz-Molina, D.
Switchable Self-Assembly of a Bioinspired Alkyl Catechol at a Solid/Liquid Interface: Competitive Interfacial, Noncovalent, and Solvent Interactions
CHEMISTRY-A EUROPEAN JOURNAL, 18:3056-3063, MAR 2012
abstract, full text

Pietra, F.
Understanding How H-NOX (Heme Nitric Oxide/Oxygen) Domain Works Needs First Clarifying How Diatomic Gases Are Relocated Inside This Sensing Protein. A Molecular-Mechanics Approach
CHEMISTRY & BIODIVERSITY, 9:606-614, MAR 2012
abstract, full text

Tsigelny, I.F., Sharikov, Y., Wrasidlo, W., Gonzalez, T., Desplats, P.A., Crews, L., Spencer, B., Masliah, E.
Role of alpha-synuclein penetration into the membrane in the mechanisms of oligomer pore formation
FEBS JOURNAL, 279:1000-1013, MAR 2012
abstract, full text

Denisov, I.G., Shih, A.Y., Sligar, S.G.
Structural differences between soluble and membrane bound cytochrome P450s
JOURNAL OF INORGANIC BIOCHEMISTRY, 108:150-158, MAR 2012
abstract, full text

Zou, X.Q., Ma, W., Solov'yov, I.A., Chipot, C., Schulten, K.
Recognition of methylated DNA through methyl-CpG binding domain proteins
NUCLEIC ACIDS RESEARCH, 40:2747-2758, MAR 2012
abstract, full text, TCBG publications

Craddock, T.J.A., Tuszynski, J.A., Hameroff, S.
Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002421, MAR 2012
abstract, full text

Reboul, C.F., Meyer, G.R., Porebski, B.T., Borg, N.A., Buckle, A.M.
Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002404, MAR 2012
abstract, full text

Ballenegger, V., Cerda, J.J., Holm, C.
How to Convert SPME to P3M: Influence Functions and Error Estimates
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:936-947, MAR 2012
abstract, full text

Capone, R., Jang, H., Kotler, S.A., Connelly, L., Arce, F.T., Ramachandran, S., Kagan, B.L., Nussinov, R., Lal, R.
All-D-Enantiomer of beta-Amyloid Peptide Forms Ion Channels in Lipid Bilayers
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:1143-1152, MAR 2012
abstract, full text

Li, L., Li, S.L., Jones, M.K., Segrest, J.P.
Rotational and hinge dynamics of discoidal high density lipoproteins probed by interchain disulfide bond formation
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 1821:481-489, MAR 2012
abstract, full text

Gautieri, A., Vesentini, S., Redaelli, A., Buehler, M.J.
Viscoelastic properties of model segments of collagen molecules
MATRIX BIOLOGY, 31:141-149, MAR 2012
abstract, full text

Yanagita, H., Yamamoto, N., Fuji, H., Liu, X.L., Ogata, M., Yokota, M., Takaku, H., Hasegawa, H., Odagiri, T., Tashiro, M., Hoshino, T.
Mechanism of Drug Resistance of Hemagglutinin of Influenza Virus and Potent Scaffolds Inhibiting Its Function
ACS CHEMICAL BIOLOGY, 7:552-562, MAR 2012
abstract, full text

Morozov, D., Khrenova, M., Andrijchenko, N., Grigorenko, B., Nemukhin, A.
Minimum energy reaction profiles for the hydrolysis reaction of the cyclic guanosine monophosphate in water: Comparison of the results of two QM/MM approaches
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 983:88-94, MAR 1 2012
abstract, full text

Jana, S., Dalapati, S., Ghosh, S., Guchhait, N.
Binding interaction between plasma protein bovine serum albumin and flexible charge transfer fluorophore: A spectroscopic study in combination with molecular docking and molecular dynamics simulation
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY, 231:19-27, MAR 1 2012
abstract, full text

Willis, C.D., Oashi, T., Busby, B., Mackerell, A.D., Bloch, R.J.
Hydrophobic residues in small ankyrin 1 participate in binding to obscurin
MOLECULAR MEMBRANE BIOLOGY, 29:36-51, MAR 2012
abstract, full text

Stober, S.T., Abrams, C.F.
Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors
PROTEIN SCIENCE, 21:307-317, MAR 2012
abstract, full text

Perez-Siles, G., Nunez, E., Morreale, A., Jimenez, E., Leo-Macias, A., Pita, G., Cherubino, F., Sangaletti, R., Bossi, E., Ortiz, A.R., Aragon, C., Lopez-Corcuera, B.
An aspartate residue in the external vestibule of GLYT2 (glycine transporter 2) controls cation access and transport coupling
BIOCHEMICAL JOURNAL, 442:323-334, MAR 1 2012
abstract, full text

Sergelius, C., Niinivehmas, S., Maula, T., Kurita, M., Yamaguchi, S., Yamamoto, T., Katsumura, S., Pentikainen, O.T., Slotte, J.P.
Structure-activity relationship of sphingomyelin analogs with sphingomyelinase from Bacillus cereus
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:474-480, MAR 2012
abstract, full text

Cui, T.X., Mowrey, D., Bondarenko, V., Tillman, T., Ma, D.J., Landrum, E., Perez-Aguilar, J.M., He, J., Wang, W., Saven, J.G., Eckenhoff, R.G., Tang, P., Xu, Y.
NMR structure and dynamics of a designed water-soluble transmembrane domain of nicotinic acetylcholine receptor
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:617-626, MAR 2012
abstract, full text

Kuttel, M., Ravenscroft, N., Foschiatti, M., Cescutti, P., Rizzo, R.
Conformational properties of two exopolysaccharides produced by Inquilinus limosus, a cystic fibrosis lung pathogen
CARBOHYDRATE RESEARCH, 350:40-48, MAR 1 2012
abstract, full text

Sun, C.B., Tang, T., Uludag, H.
Molecular Dynamics Simulations for Complexation of DNA with 2 kDa PEI Reveal Profound Effect of PEI Architecture on Complexation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2405-2413, MAR 1 2012
abstract, full text

Wedberg, R., Abildskov, J., Peters, G.H.
Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2575-2585, MAR 1 2012
abstract, full text

Vanni, S., Rothlisberger, U.
A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations
CURRENT MEDICINAL CHEMISTRY, 19:1135-1145, MAR 2012
abstract, full text

Noinaj, N., Easley, N.C., Oke, M., Mizuno, N., Gumbart, J., Boura, E., Steere, A.N., Zak, O., Aisen, P., Tajkhorshid, E., Evans, R.W., Gorringe, A.R., Mason, A.B., Steven, A.C., Buchanan, S.K.
Structural basis for iron piracy by pathogenic Neisseria
NATURE, 483:53-U92, MAR 1 2012
abstract, full text

Domene, C., Illingworth, C.J.R.
Effects of point mutations in pVHL on the binding of HIF-1 alpha
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:733-746, MAR 2012
abstract, full text

Girolami, A., Scarparo, P., Bonamigo, E., Santarossa, L., Cristiani, A., Moro, S., Lombardi, A.M.
A cluster of factor XI-deficient patients due to a new mutation (Ile 436 Lys) in northeastern Italy
EUROPEAN JOURNAL OF HAEMATOLOGY, 88:229-236, MAR 2012
abstract, full text

Enlow, M.A.
Binding of TNT to amplifying fluorescent polymers: An ab initio and molecular dynamics study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 33:12-18, MAR 2012
abstract, full text

Norris, S.E., Landstrom, J., Weintraub, A., Bull, T.E., Widmalm, G., Freedberg, D.I.
Transient hydrogen bonding in uniformly 13C,15N-Labeled Carbohydrates in Water
BIOPOLYMERS, 97:145-154, MAR 2012
abstract, full text

Ramya, L., Gautham, N.
Conformational space exploration of met- and Leu-enkephalin using the mols method, molecular dynamics, and Monte Carlo simulation-a comparative study
BIOPOLYMERS, 97:165-176, MAR 2012
abstract, full text

Domene, C., Furini, S.
Molecular Dynamics Simulations of the TrkH Membrane Protein
BIOCHEMISTRY, 51:1559-1565, FEB 28 2012
abstract, full text

Ishikawa, T., Krzysko, K.A., Kowalska-Loth, B., Skrajna, A.M., Czubaty, A., Girstun, A., Cieplak, M.K., Lesyng, B., Staron, K.
Activities of Topoisomerase I in Its Complex with SRSF1
BIOCHEMISTRY, 51:1803-1816, FEB 28 2012
abstract, full text

Wang, H.L., Cheng, X.L., Sine, S.M.
Intramembrane Proton Binding Site Linked to Activation of Bacterial Pentameric Ion Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:6482-6489, FEB 24 2012
abstract, full text

Zhou, K., Gao, Y., Hoy, J.A., Mann, F.M., Honzatko, R.B., Peters, R.J.
Insights into Diterpene Cyclization from Structure of Bifunctional Abietadiene Synthase from Abies grandis
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:6840-6850, FEB 24 2012
abstract, full text

Avila-Salas, F., Sandoval, C., Caballero, J., Guinez-Molinos, S., Santos, L.S., Cachau, R.E., Gonzalez-Nilo, F.D.
Study of Interaction Energies between the PAMAM Dendrimer and Nonsteroidal Anti-Inflammatory Drug Using a Distributed Computational Strategy and Experimental Analysis by ESI-MS/MS
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2031-2039, FEB 23 2012
abstract, full text

Sgrignani, J., Magistrato, A.
The Structural Role of Mg2+ Ions in a Class I RNA Polymerase Ribozyme: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2259-2268, FEB 23 2012
abstract, full text

Hilder, T.A., Yang, R., Gordon, D., Rendell, A.P., Chung, S.H.
Silicon Carbide Nanotube as a Chloride-Selective Channel
JOURNAL OF PHYSICAL CHEMISTRY C, 116:4465-4470, FEB 23 2012
abstract, full text

Liu, P., Chipot, C., Shao, X.G., Cai, W.S.
Solvent-Controlled Shuttling in a Molecular Switch
JOURNAL OF PHYSICAL CHEMISTRY C, 116:4471-4476, FEB 23 2012
abstract, full text

Becker, T., Franckenberg, S., Wickles, S., Shoemaker, C.J., Anger, A.M., Armache, J.P., Sieber, H., Ungewickell, C., Berninghausen, O., Daberkow, I., Karcher, A., Thomm, M., Hopfner, K.P., Green, R., Beckmann, R.
Structural basis of highly conserved ribosome recycling in eukaryotes and archaea
NATURE, 482:501-U221, FEB 23 2012
abstract, full text

Gumbart, J., Roux, B.
Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 102:795-801, FEB 22 2012
abstract, full text

Nong, E.X., DeVience, S.J., Herschbach, D.
Minimalist Model for Force-Dependent DNA Replication
BIOPHYSICAL JOURNAL, 102:810-818, FEB 22 2012
abstract, full text

Smith, N.E., Vrielink, A., Attwood, P.V., Corry, B.
Biological Channeling of a Reactive Intermediate in the Bifunctional Enzyme DmpFG
BIOPHYSICAL JOURNAL, 102:868-877, FEB 22 2012
abstract, full text

Ma, C.W., Xiu, Z.L., Zeng, A.P.
Discovery of Intramolecular Signal Transduction Network Based on a New Protein Dynamics Model of Energy Dissipation
PLOS ONE, 7: Art. No. e31529, FEB 20 2012
abstract, full text

Qiu, H., Guo, W.L.
Detecting ssDNA at single-nucleotide resolution by sub-2-nanometer pore in monoatomic graphene: A molecular dynamics study
APPLIED PHYSICS LETTERS, 100: Art. No. 083106, FEB 20 2012
abstract, full text

Das, R.K., Crick, S.L., Pappu, R.V.
N-Terminal Segments Modulate the alpha-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins
JOURNAL OF MOLECULAR BIOLOGY, 416:287-299, FEB 17 2012
abstract, full text

Tipmanee, V., Blumberger, J.
Kinetics of the Terminal Electron Transfer Step in Cytochrome c Oxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1876-1883, FEB 16 2012
abstract, full text

Ravi, H.K., Simona, F., Hulliger, J., Cascella, M.
Molecular Origin of Piezo- and Pyroelectric Properties in Collagen Investigated by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1901-1907, FEB 16 2012
abstract, full text

Gordon, D., Chen, R., Ho, J.M., Coote, M.L., Chung, S.H.
Rigid Body Brownian Dynamics as a Tool for Studying Ion Channel Blockers
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1933-1941, FEB 16 2012
abstract, full text

da Silva, L.P., da Silva, J.C.G.E.
TD-DFT/Molecular Mechanics Study of the Photinus pyralis Bioluminescence System
JOURNAL OF PHYSICAL CHEMISTRY B, 116:2008-2013, FEB 16 2012
abstract, full text

Cakir, B., Dagliyan, O., Dagyildiz, E., Baris, I., Kavakli, I.H., Kizilel, S., Turkay, M.
Structure Based Discovery of Small Molecules to Regulate the Activity of Human Insulin Degrading Enzyme
PLOS ONE, 7: Art. No. e31787, FEB 15 2012
abstract, full text

Gao, C., Pan, M.M., Lei, Y.J., Tian, L.Q., Jiang, H.Y., Li, X.L., Shi, Q., Tian, C., Yuan, Y.K., Fan, G.X., Dong, X.P.
A point mutation in the DNA-binding domain of HPV-2 E2 protein increases its DNA-binding capacity and reverses its transcriptional regulatory activity on the viral early promoter
BMC MOLECULAR BIOLOGY, 13: Art. No. 5, FEB 15 2012
abstract, full text

Gonzalez, W., Riedelsberger, J., Morales-Navarro, S.E., Caballero, J., Alzate-Morales, J.H., Gonzalez-Nilo, F.D., Dreyer, I.
The pH sensor of the plant K+-uptake channel KAT1 is built from a sensory cloud rather than from single key amino acids
BIOCHEMICAL JOURNAL, 442:57-63, FEB 15 2012
abstract, full text

Rao, F., Spichty, M.
Thermodynamics and kinetics of large-time-step molecular dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:475-483, FEB 15 2012
abstract, full text

Huggins, D.J.
Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 064518, FEB 14 2012
abstract, full text

Pfaendtner, J., Volkmann, N., Hanein, D., Dalhaimer, P., Pollard, T.D., Voth, G.A.
Key Structural Features of the Actin Filament Arp2/3 Complex Branch Junction Revealed by Molecular Simulation
JOURNAL OF MOLECULAR BIOLOGY, 416:148-161, FEB 10 2012
abstract, full text

Potoyan, D.A., Zhuravlev, P.I., Papoian, G.A.
Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase Using All Atom Explicit Solvent Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1709-1715, FEB 9 2012
abstract, full text

Connelly, L., Jang, H., Arce, F.T., Capone, R., Kotler, S.A., Ramachandran, S., Kagan, B.L., Nussinov, R., Lal, R.
Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer's beta-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1728-1735, FEB 9 2012
abstract, full text

Comer, J., Aksimentiev, A.
Predicting the DNA Sequence Dependence of Nanopore Ion Current Using Atomic-Resolution Brownian Dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 116:3376-3393, FEB 9 2012
abstract, full text

Cheung, L.S.L., Kanwar, M., Ostermeier, M., Konstantopoulos, K.
A Hot-Spot Motif Characterizes the Interface between a Designed Ankyrin-Repeat Protein and Its Target Ligand
BIOPHYSICAL JOURNAL, 102:407-416, FEB 8 2012
abstract, full text

Chen, R., Chung, S.H.
Binding Modes of mu-Conotoxin to the Bacterial Sodium Channel (Na(v)Ab)
BIOPHYSICAL JOURNAL, 102:483-488, FEB 8 2012
abstract, full text

Ndlovu, H., Ashcroft, A.E., Radford, S.E., Harris, S.A.
Effect of Sequence Variation on the Mechanical Response of Amyloid Fibrils Probed by Steered Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 102:587-596, FEB 8 2012
abstract, full text

Selvaratnam, R., VanSchouwen, B., Fogolari, F., Mazhab-Jafari, M.T., Das, R., Melacini, G.
The Projection Analysis of NMR Chemical Shifts Reveals Extended EPAC Autoinhibition Determinants
BIOPHYSICAL JOURNAL, 102:630-639, FEB 8 2012
abstract, full text

Basilio, N., Garcia-Rio, L., Martin-Pastor, M.
Calixarene-Based Surfactants: Evidence of Structural Reorganization upon Micellization
LANGMUIR, 28:2404-2414, FEB 7 2012
abstract, full text

Russell, J.T., Wang, B.Y., Kral, P.
Nanodroplet Transport on Vibrated Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 3:353-357, FEB 2 2012
abstract, full text

Chen, P.C., Kuyucak, S.
Developing a Comparative Docking Protocol for the Prediction of Peptide Selectivity Profiles: Investigation of Potassium Channel Toxins
TOXINS, 4:110-138, FEB 2012
abstract, full text

Pietra, F.
Putative Binding Sites, and Pathways to Them, for Amidine and Guanidine Current Inhibitors on Acid-Sensing Ion Channels (ASIC). A Theoretical Approach with hASIC1a Homology Model
CHEMISTRY & BIODIVERSITY, 9:331-351, FEB 2012
abstract, full text

Raghunathan, D., Gayen, S., Kumar, A., Hunke, C., Gruber, G., Verma, C.S.
Subunit F modulates ATP binding and migration in the nucleotide-binding subunit B of the A(1)A(O) ATP synthase of Methanosarcina mazei Go1
JOURNAL OF BIOENERGETICS AND BIOMEMBRANES, 44:213-224, FEB 2012
abstract, full text

Stewart, A.G., Lee, L.K., Donohoe, M., Chaston, J.J., Stock, D.
The dynamic stator stalk of rotary ATPases
NATURE COMMUNICATIONS, 3: Art. No. 687, FEB 2012
abstract, full text

Best, R.B.
Atomistic molecular simulations of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 22:52-61, FEB 2012
abstract, full text

Kalyaanamoorthy, S., Chen, Y.P.P.
Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:589-603, FEB 2012
abstract, full text

Merino, F., Rivas-Pardo, J.A., Caniuguir, A., Garcia, I., Guixe, V.
Catalytic and regulatory roles of divalent metal cations on the phosphoryl-transfer mechanism of ADP-dependent sugar kinases from hyperthermophilic archaea
BIOCHIMIE, 94:516-524, FEB 2012
abstract, full text

Prakash, P., Sayyed-Ahmad, A., Gorfe, A.A.
The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
PLOS COMPUTATIONAL BIOLOGY, 8: Art. No. e1002394, FEB 2012
abstract, full text

Kowalczyk, S.W., Wells, D.B., Aksimentiev, A., Dekker, C.
Slowing down DNA Translocation through a Nanopore in Lithium Chloride
NANO LETTERS, 12:1038-1044, FEB 2012
abstract, full text

Fleming, P.J., Freites, J.A., Moon, C.P., Tobias, D.J., Fleming, K.G.
Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:126-134, FEB 2012
abstract, full text

Li, J., Tajkhorshid, E.
A gate-free pathway for substrate release from the inward-facing state of the Na+-galactose transporter
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:263-271, FEB 2012
abstract, full text

Wood, M.L., Schow, E.V., Freites, J.A., White, S.H., Tombola, F., Tobias, D.J.
Water wires in atomistic models of the Hvl proton channel
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:286-293, FEB 2012
abstract, full text

Gumbart, J., Khalili-Araghi, F., Sotomayor, M., Roux, B.
Constant electric field simulations of the membrane potential illustrated with simple systems
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:294-302, FEB 2012
abstract, full text

Receveur-Brechot, V., Durand, D.
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective
CURRENT PROTEIN & PEPTIDE SCIENCE, 13:55-75, FEB 2012
abstract, full text

Do, T.N., Ippoliti, E., Carloni, P., Varani, G., Parrinello, M.
Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:688-694, FEB 2012
abstract, full text

Mallajosyula, S.S., Guvench, O., Hatcher, E., MacKerell, A.D.
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:759-776, FEB 2012
abstract, full text

Ihle, N.T., Byers, L.A., Kim, E.S., Saintigny, P., Lee, J.J., Blumenschein, G.R., Tsao, A., Liu, S.Y., Larsen, J.E., Wang, J., Diao, L.X., Coombes, K.R., Chen, L., Zhang, S.X., Abdelmelek, M.F., Tang, X.M., Papadimitrakopoulou, V., Minna, J.D., Lippman, S.M., Hong, W.K., Herbst, R.S., Wistuba, I.I., Heymach, J.V., Powis, G.
Effect of KRAS Oncogene Substitutions on Protein Behavior: Implications for Signaling and Clinical Outcome
JOURNAL OF THE NATIONAL CANCER INSTITUTE, 104:228-239, FEB 2012
abstract, full text

Drakulic, B.J., Marinkovic, A.D., Juranic, I.O.
On the choice of optimal conformation in linear free-energy relationships. Reactivity of 2-[(carboxymethyl)sulfanyl]-4-oxo-4-arylbutanoic acids with diphenyldiazomethane
TETRAHEDRON LETTERS, 53:553-556, FEB 1 2012
abstract, full text

Liu, L., Gronenborn, A.M., Bahar, I.
Longer simulations sample larger subspaces of conformations while maintaining robust mechanisms of motion
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 80:616-625, FEB 2012
abstract, full text

Negureanu, L., Salsbury, F.R.
Insights into Protein - DNA Interactions, Stability and Allosteric Communications: A Computational Study of Muts alpha-DNA Recognition Complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:757-776, FEB 2012
abstract, full text

Uchida, M., Morris, D.S., Kang, S., Jolley, C.C., Lucon, J., Liepold, L.O., LaFrance, B., Prevelige, P.E., Douglas, T.
Site-Directed Coordination Chemistry with P22 Virus-like Particles
LANGMUIR, 28:1998-2006, JAN 31 2012
abstract, full text

Limongelli, V., Marinelli, L., Cosconati, S., La Motta, C., Sartini, S., Mugnaini, L., Da Settimo, F., Novellino, E., Parrinello, M.
Sampling protein motion and solvent effect during ligand binding
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:1467-1472, JAN 31 2012
abstract, full text

Lettieri, S., Zuckerman, D.M.
Accelerating molecular monte carlo simulations using distance and orientation-dependent energy tables: Tuning from atomistic accuracy to smoothed "coarse-grained" models
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:268-275, JAN 30 2012
abstract, full text

Mori, T., Ogushi, F., Sugita, Y.
Analysis of lipid surface area in protein-membrane systems combining voronoi tessellation and monte carlo integration methods
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:286-293, JAN 30 2012
abstract, full text

Kamath, G., Ketko, M., Baker, G.A., Potoff, J.J.
Monte Carlo predictions of phase equilibria and structure for dimethyl ether plus sulfur dioxide and dimethyl ether plus carbon dioxide
JOURNAL OF CHEMICAL PHYSICS, 136: Art. No. 044514, JAN 28 2012
abstract, full text

Jiao, W.T., Hutton, R.D., Cross, P.J., Jameson, G.B., Parker, E.J.
Dynamic Cross-Talk among Remote Binding Sites: The Molecular Basis for Unusual Synergistic Allostery
JOURNAL OF MOLECULAR BIOLOGY, 415:716-726, JAN 27 2012
abstract, full text

Taylor, C.B., Talib, M.F., McCabe, C., Bu, L.T., Adney, W.S., Himmel, M.E., Crowley, M.F., Beckham, G.T.
Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-binding Module
JOURNAL OF BIOLOGICAL CHEMISTRY, 287:3147-3155, JAN 27 2012
abstract, full text

Hernandez-Rodriguez, E.W., Sanchez-Garcia, E., Crespo-Otero, R., Montero-Alejo, A.L., Montero, L.A., Thiel, W.
Understanding Rhodopsin Mutations Linked to the Retinitis pigmentosa Disease: a QM/MM and DFT/MRCI Study
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1060-1076, JAN 26 2012
abstract, full text

Jing, Y.Y., Zheng, R.H., Li, H.X., Shi, Q.
Theoretical Study of the Electronic-Vibrational Coupling in the Q(y) States of the Photosynthetic Reaction Center in Purple Bacteria
JOURNAL OF PHYSICAL CHEMISTRY B, 116:1164-1171, JAN 26 2012
abstract, full text

Naveed, H., Xu, Y., Jackups, R., Liang, J.
Predicting Three-Dimensional Structures of Transmembrane Domains of beta-Barrel Membrane Proteins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:1775-1781, JAN 25 2012
abstract, full text

Corry, B., Thomas, M.
Mechanism of Ion Permeation and Selectivity in a Voltage Gated Sodium Channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134:1840-1846, JAN 25 2012
abstract, full text

Volkov, S.N., Paramonova, E.V., Yakubovich, A.V., Solov'yov, A.V.
Micromechanics of base pair unzipping in the DNA duplex
JOURNAL OF PHYSICS-CONDENSED MATTER, 24: Art. No. 035104, JAN 25 2012
abstract, full text

Capone, R., Jang, H., Kotler, S.A., Kagan, B.L., Nussinov, R., Lal, R.
Probing Structural Features of Alzheimer's Amyloid-beta Pores in Bilayers Using Site-Specific Amino Acid Substitutions
BIOCHEMISTRY, 51:776-785, JAN 24 2012
abstract, full text

Qi, Y., Nam, K., Spong, M.C., Banerjee, A., Sung, R.J., Zhang, M., Karplus, M., Verdine, G.L.
Strandwise translocation of a DNA glycosylase on undamaged DNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109:1086-1091, JAN 24 2012
abstract, full text

Spudich, E.N., Ozorowski, G., Schow, E.V., Tobias, D.J., Spudich, J.L., Luecke, H.
A Transporter Converted into a Sensor, a Phototaxis Signaling Mutant of Bacteriorhodopsin at 3.0 angstrom
JOURNAL OF MOLECULAR BIOLOGY, 415:455-463, JAN 20 2012
abstract, full text

Musgaard, M., Thogersen, L., Schiott, B., Tajkhorshid, E.
Tracing Cytoplasmic Ca2+ Ion and Water Access Points in the Ca2+-ATPase
BIOPHYSICAL JOURNAL, 102:268-277, JAN 18 2012
abstract, full text

Stadler, A.M., Pellegrini, E., Johnson, M., Fitter, J., Zaccai, G.
Dynamics-Stability Relationships in Apo- and Holomyoglobin: A Combined Neutron Scattering and Molecular Dynamics Simulations Study
BIOPHYSICAL JOURNAL, 102:351-359, JAN 18 2012
abstract, full text

Razavian, N.S., Kamisetty, H., Langmead, C.J.
Learning generative models of molecular dynamics
BMC GENOMICS, 13: Art. No. S5, JAN 17 2012
abstract, full text

Tarus, B., Chevalier, C., Richard, C.A., Delmas, B., Di Primo, C., Slama-Schwok, A.
Molecular Dynamics Studies of the Nucleoprotein of Influenza A Virus: Role of the Protein Flexibility in RNA Binding
PLOS ONE, 7: Art. No. e30038, JAN 17 2012
abstract, full text

Weng, J.W., Fan, K.N., Wang, W.N.
The Conformational Transition Pathways of ATP-Binding Cassette Transporter BtuCD Revealed by Targeted Molecular Dynamics Simulation
PLOS ONE, 7: Art. No. e30465, JAN 17 2012
abstract, full text

Kuttner, Y.Y., Engel, S.
Protein Hot Spots: The Islands of Stability
JOURNAL OF MOLECULAR BIOLOGY, 415:419-428, JAN 13 2012
abstract, full text

Zheng, B., Sant, M., Demontis, P., Suffritti, G.B.
Force Field for Molecular Dynamics Computations in Flexible ZIF-8 Framework
JOURNAL OF PHYSICAL CHEMISTRY C, 116:933-938, JAN 12 2012
abstract, full text

Lim, J.B., Rogaski, B., Klauda, J.B.
Update of the Cholesterol Force Field Parameters in CHARMM
JOURNAL OF PHYSICAL CHEMISTRY B, 116:203-210, JAN 12 2012
abstract, full text

Kucerka, N., Holland, B.W., Gray, C.G., Tomberli, B., Katsaras, J.
Scattering Density Profile Model of POPG Bilayers As Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-ray Scattering Experiments
JOURNAL OF PHYSICAL CHEMISTRY B, 116:232-239, JAN 12 2012
abstract, full text

Huang, B., Liu, F.F., Dong, X.Y., Sun, Y.
Molecular Mechanism of the Effects of Salt and pH on the Affinity between Protein A and Human lmmunoglobulin G1 Revealed by Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 116:424-433, JAN 12 2012
abstract, full text

Lee, H.J., Hota, P.K., Chugha, P., Guo, H., Miao, H., Zhang, L.Q., Kim, S.J., Stetzik, L., Wang, B.C., Buck, M.
NMR Structure of a Heterodimeric SAM:SAM Complex: Characterization and Manipulation of EphA2 Binding Reveal New Cellular Functions of SHIP2
STRUCTURE, 20:41-55, JAN 11 2012
abstract, full text

Satpati, P., Simonson, T.
Conformational Selection by the aIF2 GTPase: A Molecular Dynamics Study of Functional Pathways
BIOCHEMISTRY, 51:353-361, JAN 10 2012
abstract, full text

Arkun, Y., Gur, M.
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding
PLOS ONE, 7: Art. No. e29628, JAN 6 2012
abstract, full text

Mastrangelo, E., Bolognesi, M., Milani, M.
Flaviviral helicase: Insights into the mechanism of action of a motor protein
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 417:84-87, JAN 6 2012
abstract, full text

Makiya, M., Dolan, M., Agulto, L., Purcell, R., Chen, Z.C.
Structural basis of anthrax edema factor neutralization by a neutralizing antibody
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 417:324-329, JAN 6 2012
abstract, full text

Barnard, T.J., Gumbart, J., Peterson, J.H., Noinaj, N., Easley, N.C., Dautin, N., Kuszak, A.J., Tajkhorshid, E., Bernstein, H.D., Buchanan, S.K.
Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter
JOURNAL OF MOLECULAR BIOLOGY, 415:128-142, JAN 6 2012
abstract, full text

Gonnet, P.
Pairwise Verlet Lists: Combining Cell Lists and Verlet Lists to Improve Memory Locality and Parallelism
JOURNAL OF COMPUTATIONAL CHEMISTRY, 33:76-81, JAN 5 2012
abstract, full text

Kang, Y.Y., Lu, S.Q., Ren, P., Huo, B., Long, M.
Molecular Dynamics Simulation of Shear- and Stretch-Induced Dissociation of P-Selectin/PSGL-1 Complex
BIOPHYSICAL JOURNAL, 102:112-120, JAN 4 2012
abstract, full text

Edelkamp, S., Schrodl, S.
Heuristic Search: Theory and Applications
HEURISTIC SEARCH: THEORY AND APPLICATIONS, , 2012
full text

Nemukhin, A.V., Grigorenko, B.L., Lushchekina, S.V., Varfolomeev, S.D.
Quantum chemical modelling in the research of molecular mechanisms of enzymatic catalysis
RUSSIAN CHEMICAL REVIEWS, 81:1011-1025, 2012
abstract, full text

Dimitrijevic, B.P., Borozan, S.Z., Stojanovic, S.D.
pi-pi and cation-pi interactions in protein-porphyrin complex crystal structures
RSC ADVANCES, 2:12963-12972, 2012
abstract, full text

van Gunsteren, W.F., Dolenc, J.
Thirty-five years of biomolecular simulation: development of methodology, force fields and software
MOLECULAR SIMULATION, 38:1271-1281, 2012
abstract, full text

Shi, W., Damodaran, K., Nulwala, H.B., Luebke, D.R.
Theoretical and experimental studies of water interaction in acetate based ionic liquids
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:15897-15908, 2012
abstract, full text

Wang, K.F., Leng, Y., Lu, X., Ren, F.Z., Ge, X., Ding, Y.H.
Theoretical analysis of protein effects on calcium phosphate precipitation in simulated body fluid
CRYSTENGCOMM, 14:5870-5878, 2012
abstract, full text

Zhang, M.M., Wang, B.B., Jiang, T., Jiang, M.J., Yi, T.
From nano ribbon to fibre by concentration control
CRYSTENGCOMM, 14:8057-8062, 2012
abstract, full text

Feng, Z.W., Hou, T.J., Li, Y.Y.
Unidirectional peristaltic movement in multisite drug binding pockets of AcrB from molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 8:2699-2709, 2012
abstract, full text

Huggins, D.J.
Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:15106-15117, 2012
abstract, full text

Correa-Basurto, J., Ramos-Morales, F.R., Matus, M.H., Rosales-Hernandez, M.C., Mancilla-Percino, T., Trujillo-Ferrara, J., Ilizaliturri-Flores, I.
Docking and DFT Studies to explore the Topoisomerase II ATP Pocket employing 3-Substituted 2,6-Piperazindiones for drug design
MOLECULAR SIMULATION, 38:1072-1084, 2012
abstract, full text

Shintani, M., Matsuo, Y., Sakuraba, S., Matubayasi, N.
Interaction of naphthalene derivatives with lipids in membranes studied by the H-1-nuclear Overhauser effect and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:14049-14060, 2012
abstract, full text

Singh, S., Chopra, M., de Pablo, J.J.
Density of States-Based Molecular Simulations
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 3, 3:369-394, 2012
abstract, full text

Dror, R.O., Dirks, R.M., Grossman, J.P., Xu, H.F., Shaw, D.E.
Biomolecular Simulation: A Computational Microscope for Molecular Biology
ANNUAL REVIEW OF BIOPHYSICS, VOL 41, 41:429-452, 2012
abstract, full text

Wang, D.Q., van Gunsteren, W.F., Chai, Z.F.
Recent advances in computational actinoid chemistry
CHEMICAL SOCIETY REVIEWS, 41:5836-5865, 2012
abstract, full text

Morales-Quintana, L., Moya-Leon, M.A., Herrera, R.
Molecular docking simulation analysis of alcohol acyltransferases from two related fruit species explains their different substrate selectivities
MOLECULAR SIMULATION, 38:912-921, 2012
abstract, full text

Saiz-Poseu, J., Martinez-Otero, A., Roussel, T., Hui, J.K.H., Montero, M.L., Urcuyo, R., MacLachlan, M.J., Faraudo, J., Ruiz-Molina, D.
Self-assembly of a catechol-based macrocycle at the liquid-solid interface: experiments and molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:11937-11943, 2012
abstract, full text

Cui, Y.B., Bastien, D.A.
Molecular Dynamics Simulation and Bioinformatics Study on Yeast Aquaporin Aqy1 from Pichia pastoris
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES, 8:1026-1035, 2012
abstract, full text

Alijanianzadeh, M., Saboury, A.A., Ganjali, M.R., Hadi-Alijanvand, H., Moosavi-Movahedi, A.A.
Inhibition of mushroom tyrosinase by a newly synthesized ligand: inhibition kinetics and computational simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30:448-459, 2012
abstract, full text

Pietropaolo, A.
Exploring metal-driven stereoselectivity of glycopeptides by free-energy calculations
PURE AND APPLIED CHEMISTRY, 84:1919-1930, 2012
abstract, full text

Pandey, R.B., Kuang, Z.F., Farmer, B.L., Kim, S.S., Naik, R.R.
Stability of peptide (P1 and P2) binding to a graphene sheet via an all-atom to all-residue coarse-grained approach
SOFT MATTER, 8:9101-9109, 2012
abstract, full text

Elder, R.M., Jayaraman, A.
Role of structure and dynamics of DNA with cisplatin and oxaliplatin adducts in various sequence contexts on binding of HMGB1a
MOLECULAR SIMULATION, 38:793-808, 2012
abstract, full text

Coveney, P.V., Swadling, J.B., Wattis, J.A.D., Greenwell, H.C.
Theory, modelling and simulation in origins of life studies
CHEMICAL SOCIETY REVIEWS, 41:5430-5446, 2012
abstract, full text

Richards, L.A., Schafer, A.I., Richards, B.S., Corry, B.
Quantifying barriers to monovalent anion transport in narrow non-polar pores
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:11633-11638, 2012
abstract, full text

Jia, Y.F., Gao, C.Y., He, J., Feng, D.F., Xing, K.L., Wu, M., Liu, Y., Cai, W.S., Feng, X.Z.
Unlabeled multi tumor marker detection system based on bioinitiated light addressable potentiometric sensor
ANALYST, 137:3806-3813, 2012
abstract, full text

Venkateshwari, S., Veluraja, K.
Conformational analysis of GT1B ganglioside and its interaction with botulinum neurotoxin type B: a study by molecular modeling and molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30:255-268, 2012
abstract, full text

Negureanu, L., Salsbury, F.R.
The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutS alpha-DNA complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30:347-361, 2012
abstract, full text

Katti, D.R., Katti, K.S., Raviprasad, M., Gu, C.J.
Role of Polymer Interactions with Clays and Modifiers on Nanomechanical Properties and Crystallinity in Polymer Clay Nanocomposites
JOURNAL OF NANOMATERIALS, Art. No. 341056, 2012
abstract, full text

Lopez-Perez, D.E., Revilla-Lopez, G., Jacquemin, D., Zanuy, D., Palys, B., Sek, S., Aleman, C.
Intermolecular interactions in electron transfer through stretched helical peptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:10332-10344, 2012
abstract, full text

Cuong, P.V., Kvamme, B., Kuznetsova, T., Jensen, B.
Molecular dynamics study of calcite, hydrate and the temperature effect on CO2 transport and adsorption stability in geological formations
MOLECULAR PHYSICS, 110:1097-1106, 2012
abstract, full text

Androulaki, E., Vergadou, N., Ramos, J., Economou, I.G.
Structure, thermodynamic and transport properties of imidazolium-based bis(trifluoromethylsulfonyl)imide ionic liquids from molecular dynamics simulations
MOLECULAR PHYSICS, 110:1139-1152, 2012
abstract, full text

Peskin, U.
Quantum mechanical averaging over fluctuating rates
MOLECULAR PHYSICS, 110:729-734, 2012
abstract, full text

Saito, H., Mizukami, T., Kawamoto, S., Miyakawa, T., Iwayama, M., Takasu, M., Nagao, H.
Molecular Dynamics Studies of Lipid Bilayer With Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 112:161-170, JAN 2012
abstract, full text

Gao, C.Y., Guo, Y.Y., He, J., Wu, M., Liu, Y., Chen, Z.L., Cai, W.S., Yang, Y.L., Wang, C., Feng, X.Z.
L-3,4-dihydroxyphenylalanine-collagen modified PDMS surface for controlled cell culture
JOURNAL OF MATERIALS CHEMISTRY, 22:10763-10770, 2012
abstract, full text

Zarudnev, E.S., Plokhotnichenko, A.M., Leontiev, V.S., Levitsky, I.A., Karachevtsev, V.A.
Unusual aggregation of poly(rC)-wrapped carbon nanotubes in aqueous suspension induced by cationic porphyrin
JOURNAL OF MATERIALS CHEMISTRY, 22:10795-10804, 2012
abstract, full text

Gross, A.S., Bell, A.T., Chu, J.W.
Entropy of cellulose dissolution in water and in the ionic liquid 1-butyl-3-methylimidazolim chloride
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:8425-8430, 2012
abstract, full text

Keil, F.J.
Multiscale Modelling in Computational Heterogeneous Catalysis
MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY, 307:69-107, 2012
abstract, full text

Guevara-Carrion, G., Hasse, H., Vrabec, J.
Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields
MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY, 307:201-249, 2012
abstract, full text

Kamath, G., Baker, G.A.
In silico free energy predictions for ionic liquid-assisted exfoliation of a graphene bilayer into individual graphene nanosheets
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:7929-7933, 2012
abstract, full text

Hughes, M., Frederix, P.W.J.M., Raeburn, J., Birchall, L.S., Sadownik, J., Coomer, F.C., Lin, I.H., Cussen, E.J., Hunt, N.T., Tuttle, T., Webb, S.J., Adams, D.J., Ulijn, R.V.
Sequence/structure relationships in aromatic dipeptide hydrogels formed under thermodynamic control by enzyme-assisted self-assembly
SOFT MATTER, 8:5595-5602, 2012
abstract, full text

Savitsky, A.P., Rusanov, A.L., Zherdeva, V.V., Gorodnicheva, T.V., Khrenova, M.G., Nemukhin, A.V.
FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins
THERANOSTICS, 2:215-226, 2012
abstract, full text

Espinoza-Fonseca, L.M., Ilizaliturri-Flores, I., Correa-Basurto, J.
Backbone conformational preferences of an intrinsically disordered protein in solution
MOLECULAR BIOSYSTEMS, 8:1798-1805, 2012
abstract, full text

Desai, S., Kaware, R.
Computational modeling of nanodroplet evaporation for scalable micro-/nano-manufacturing
IIE TRANSACTIONS, 44:568-579, 2012
abstract, full text

Gruber, C.C., Pleiss, J.
Molecular Modeling of Lipase Binding to a Substrate-Water Interface
LIPASES AND PHOSPHOLIPASES: METHODS AND PROTOCOLS, 861:313-327, 2012
abstract, full text

Jana, M., Bandyopadhyay, S.
Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:6628-6638, 2012
abstract, full text

Liu, Y.Z., Chipot, C., Shao, X.G., Cai, W.S.
Edge effects control helical wrapping of carbon nanotubes by polysaccharides
NANOSCALE, 4:2584-2589, 2012
abstract, full text

Xie, L., Xie, L., Kinnings, S.L., Bourne, P.E.
Novel Computational Approaches to Polypharmacology as a Means to Define Responses to Individual Drugs
ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 52, 52:361-+, 2012
abstract, full text

Gautieri, A., Vesentini, S., Redaelli, A., Buehler, M.J.
Osteogenesis imperfecta mutations lead to local tropocollagen unfolding and disruption of H-bond network
RSC ADVANCES, 2:3890-3896, 2012
abstract, full text

Heinke, F., Labudde, D.
Membrane Protein Stability Analyses by Means of Protein Energy Profiles in Case of Nephrogenic Diabetes Insipidus
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, Art. No. 790281, 2012
abstract, full text

Akhshi, P., Mosey, N.J., Wu, G.
Free-Energy Landscapes of Ion Movement through a G-Quadruplex DNA Channel
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 51:2850-2854, 2012
full text

Landstrom, J., Bergstrom, M., Hamark, C., Ohlson, S., Widmalm, G.
Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies
ORGANIC & BIOMOLECULAR CHEMISTRY, 10:3019-3032, 2012
abstract, full text

Li, Y., Zhang, R.Q., Lin, Z.J., Van Hove, M.A.
Energetics and dynamics of a new type of extended line defects in graphene
NANOSCALE, 4:2580-2583, 2012
abstract, full text

Zhang, J.F., He, Z.Q., Wang, Q.G., Barz, B., Kosztin, I., Shang, Y., Xu, D.
Prediction of Protein Tertiary Structures Using MUFOLD
FUNCTIONAL GENOMICS: METHODS AND PROTOCOLS, SECOND EDITION, 815:3-13, 2012
abstract, full text

Chen, C., Li, W.Z., Song, Y.C., Weng, L.D., Zhang, N.
Concentration dependence of water self-diffusion coefficients in dilute glycerol-water binary and glycerol-water-sodium chloride ternary solutions and the insights from hydrogen bonds
MOLECULAR PHYSICS, 110:283-291, 2012
abstract, full text

Cheng, C.L., Zhao, G.J.
Steered molecular dynamics simulation study on dynamic self-assembly of single-stranded DNA with double-walled carbon nanotube and graphene
NANOSCALE, 4:2301-2305, 2012
abstract, full text

Kamath, G., Bhatnagar, N., Baker, G.A., Baker, S.N., Potoff, J.J.
Computational prediction of ionic liquid 1-octanol/water partition coefficients
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:4339-4342, 2012
abstract, full text

Fogolari, F., Corazza, A., Toppo, S., Tosatto, S.C.E., Viglino, P., Ursini, F., Esposito, G.
Studying Interactions by Molecular Dynamics Simulations at High Concentration
JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY, Art. No. 303190, 2012
abstract, full text

Anandarajah, A., Amarasinghe, P.M.
Microstructural Investigation of Soil Suction and Hysteresis of Fine-Grained Soils
JOURNAL OF GEOTECHNICAL AND GEOENVIRONMENTAL ENGINEERING, 138:38-46, JAN 2012
abstract, full text

Anand, R., Ottani, S., Manoli, F., Manet, I., Monti, S.
A close-up on doxorubicin binding to gamma-cyclodextrin: an elucidating spectroscopic, photophysical and conformational study
RSC ADVANCES, 2:2346-2357, 2012
abstract, full text

Chen, X., Chen, X.L., Wu, T., Wang, Q.
Simulation of steered molecular dynamics on the exploration of the dynamic structure of HIV-1 protease
MOLECULAR SIMULATION, 38:293-299, 2012
abstract, full text

Lawrenz, M., Baron, R., Wang, Y., McCammon, J.A.
Independent-Trajectory Thermodynamic Integration: A Practical Guide to Protein-Drug Binding Free Energy Calculations Using Distributed Computing
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:469-486, 2012
abstract, full text

Besker, N., Gervasio, F.L.
Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:501-513, 2012
abstract, full text

Amaro, R.E., Li, W.W.
Molecular-Level Simulation of Pandemic Influenza Glycoproteins
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:575-594, 2012
abstract, full text

Chang, C.E.A., Ai, R.Z., Gutierrez, M., Marsella, M.J.
Homology Modeling of Cannabinoid Receptors: Discovery of Cannabinoid Analogues for Therapeutic Use
COMPUTATIONAL DRUG DISCOVERY AND DESIGN, 819:595-613, 2012
abstract, full text

Liu, J., Fan, J.F.
Relationship between the Permeation-Diffusion Parameters of a Single-File Channel
CHINESE PHYSICS LETTERS, 29: Art. No. 010502, JAN 2012
abstract, full text

Saiz-Poseu, J., Alcon, I., Alibes, R., Busque, F., Faraudo, J., Ruiz-Molina, D.
Self-assembly of alkylcatechols on HOPG investigated by scanning tunneling microscopy and molecular dynamics simulations
CRYSTENGCOMM, 14:264-271, 2012
abstract, full text

Xu, X., Li, R.B., Ma, M., Wang, X., Wang, Y.H., Zou, H.F.
Multidrug resistance protein P-glycoprotein does not recognize nanoparticle C-60: experiment and modeling
SOFT MATTER, 8:2915-2923, 2012
abstract, full text

Czajkowsky, D.M., Li, L., Sun, J.L., Hu, J., Shao, Z.F.
Heteroepitaxial Streptavidin Nanocrystals Reveal Critical Role of Proton "Fingers" and Subsurface Atoms in Determining Adsorbed Protein Orientation
ACS NANO, 6:190-198, JAN 2012
abstract, full text

Feng, R., Xenos, M., Girdhar, G., Kang, W., Davenport, J.W., Deng, Y.F., Bluestein, D.
Viscous flow simulation in a stenosis model using discrete particle dynamics: a comparison between DPD and CFD
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 11:119-129, JAN 2012
abstract, full text

Schmid, M., Nogueira, E.S., Monnard, F.W., Ward, T.R., Meuwly, M.
Arylsulfonamides as inhibitors for carbonic anhydrase: prediction & validation
CHEMICAL SCIENCE, 3:690-700, 2012
abstract, full text

Orts, J., Bartoschek, S., Griesinger, C., Monecke, P., Carlomagno, T.
An NMR-based scoring function improves the accuracy of binding pose predictions by docking by two orders of magnitude
JOURNAL OF BIOMOLECULAR NMR, 52:23-30, JAN 2012
abstract, full text

Luan, B.Q., Stolovitzky, G., Martyna, G.
Slowing and controlling the translocation of DNA in a solid-state nanopore
NANOSCALE, 4:1068-1077, 2012
abstract, full text

Jana, S., Ghosh, S., Dalapati, S., Guchhait, N.
Exploring structural change of protein bovine serum albumin by external perturbation using extrinsic fluorescence probe: spectroscopic measurement, molecular docking and molecular dynamics simulation
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 11:323-332, 2012
abstract, full text

Munz, M., Biggin, P.C.
JGromacs: A Java Package for Analyzing Protein Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 52:255-259, JAN 2012
abstract, full text

Lauer, T.M., Agrawal, N.J., Chennamsetty, N., Egodage, K., Helk, B., Trout, B.L.
Developability index: A rapid in silico tool for the screening of antibody aggregation propensity
JOURNAL OF PHARMACEUTICAL SCIENCES, 101:102-115, JAN 2012
abstract, full text

Giannozzi, P., Jansen, K., La Penna, G., Minicozzi, V., Morante, S., Rossi, G., Stellato, F.
Zn induced structural aggregation patterns of beta-amyloid peptides by first-principle simulations and XAS measurements
METALLOMICS, 4:156-165, 2012
abstract, full text

Barr, D., van der Vaart, A.
The natural DNA bending angle in the lac repressor headpiece-O1 operator complex is determined by protein-DNA contacts and water release
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:2070-2077, 2012
abstract, full text

Fjell, C.D., Hiss, J.A., Hancock, R.E.W., Schneider, G.
Designing antimicrobial peptides: form follows function
NATURE REVIEWS DRUG DISCOVERY, 11:37-51, JAN 2012
abstract, full text

Sinha, S.K., Bandyopadhyay, S.
Local heterogeneous dynamics of water around lysozyme: a computer simulation study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:899-913, 2012
abstract, full text

Sanderson, J.P., Waldburger-Hauri, K., Garzon, D., Matulis, G., Mansour, S., Pumphrey, N.J., Lissin, N., Villiger, P.M., Jakobsen, B., Faraldo-Gomez, J.D., Gadola, S.D.
Natural variations at position 93 of the invariant Va24-Ja18 a chain of human iNKT-cell TCRs strongly impact on CD1d binding
EUROPEAN JOURNAL OF IMMUNOLOGY, 42:248-255, JAN 2012
abstract, full text

Fedoseyenko, D., Raghuraman, A., Ko, E., Burgess, K.
Omegatides: constrained analogs of peptide primary sequence
ORGANIC & BIOMOLECULAR CHEMISTRY, 10:921-924, 2012
full text

Agnew, C.R.J., Warrilow, A.G.S., Burton, N.M., Lamb, D.C., Kelly, S.L., Brady, R.L.
An Enlarged, Adaptable Active Site in CYP164 Family P450 Enzymes, the Sole P450 in Mycobacterium leprae
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 56:391-402, JAN 2012
abstract, full text

Pizzirusso, A., Berardi, R., Muccioli, L., Ricci, M., Zannoni, C.
Predicting surface anchoring: molecular organization across a thin film of 5CB liquid crystal on silicon
CHEMICAL SCIENCE, 3:573-579, 2012
abstract, full text

Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L., MacKerell, A.D.
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:348-362, JAN 2012
abstract, full text

Figueras, L., Faraudo, J.
Competition between hydrogen bonding and electric field in single-file transport of water in carbon nanotubes
MOLECULAR SIMULATION, 38:23-25, 2012
abstract, full text

Fu, J., Bottegoni, G., Sasso, O., Bertorelli, R., Rocchia, W., Masetti, M., Guijarro, A., Lodola, A., Armirotti, A., Garau, G., Bandiera, T., Reggiani, A., Mor, M., Cavalli, A., Piomelli, D.
A catalytically silent FAAH-1 variant drives anandamide transport in neurons
NATURE NEUROSCIENCE, 15:64-U82, JAN 2012
abstract, full text

Gorny, K., Dendzik, Z., Raczynski, P., Gburski, Z.
Dynamic properties of propylene glycol confined in ZSM-5 zeolite matrix-A computer simulation study
SOLID STATE COMMUNICATIONS, 152:8-12, JAN 2012
abstract, full text

Zhu, X., Lopes, P.E.M., MacKerell, A.D.
Recent developments and applications of the CHARMM force fields
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 2:167-185, JAN-FEB 2012
abstract, full text

Zhang, Y.B., Cui, Y.B., Chen, L.Y.
Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel
BIOPHYSICAL CHEMISTRY, 160:69-74, JAN 2012
abstract, full text

Espinoza-Fonseca, L.M.
Aromatic residues link binding and function of intrinsically disordered proteins
MOLECULAR BIOSYSTEMS, 8:237-246, 2012
abstract, full text

Muszala, S.P., Alaghband, G., Hack, J., Connors, D.
Natural Load Indices (NLI) for scientific simulation
JOURNAL OF SUPERCOMPUTING, 59:392-413, JAN 2012
abstract, full text

Sapay, N., Cabannes, E., Petitou, M., Imberty, A.
Molecular Model of Human Heparanase with Proposed Binding Mode of a Heparan Sulfate Oligosaccharide and Catalytic Amino Acids
BIOPOLYMERS, 97:21-34, JAN 2012
abstract, full text

Golebiowska, M., Roth, M., Firlej, L., Kuchta, B., Wexler, C.
The reversibility of the adsorption of methane-methyl mercaptan mixtures in nanoporous carbon
CARBON, 50:225-234, JAN 2012
abstract, full text

Georgoulia, P.S., Glykos, N.M.
Using J-Coupling Constants for Force Field Validation: Application to Hepta-alanine
JOURNAL OF PHYSICAL CHEMISTRY B, 115:15221-15227, DEC 29 2011
abstract, full text

Faro, T.M.C., Skaf, M.S., Coluci, V.R.
Mechanisms of the rotational dynamics of C-70 in C-70-cubane heteromolecular crystals
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 244510, DEC 28 2011
abstract, full text

Sinha, S.K., Bandyopadhyay, S.
Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 245104, DEC 28 2011
abstract, full text

Musgaard, M., Thogersen, L., Schiott, B.
Protonation States of Important Acidic Residues in the Central Ca2+ Ion Binding Sites of the Ca2+-ATPase: A Molecular Modeling Study
BIOCHEMISTRY, 50:11109-11120, DEC 27 2011
abstract, full text

Araya-Secchi, R., Garate, J.A., Holmes, D.S., Perez-Acle, T.
Molecular dynamics study of the archaeal aquaporin AqpM
BMC GENOMICS, 12: Art. No. S8, DEC 22 2011
abstract, full text

Jones, P.M., Robinson, M.W., Dalton, J.P., George, A.M.
The Plasmodium falciparum Malaria M1 Alanyl Aminopeptidase (PfA-M1): Insights of Catalytic Mechanism and Function from MD Simulations
PLOS ONE, 6: Art. No. e28589, DEC 21 2011
abstract, full text

Krueger, S., Shin, J.H., Raghunandan, S., Curtis, J.E., Kelman, Z.
Atomistic Ensemble Modeling and Small-Angle Neutron Scattering of Intrinsically Disordered Protein Complexes: Applied to Minichromosome Maintenance Protein
BIOPHYSICAL JOURNAL, 101:2999-3007, DEC 21 2011
abstract, full text

Zhao, J., Wang, Q., Liang, G., Zheng, J.
Molecular Dynamics Simulations of Low-Ordered Alzheimer beta-Amyloid Oligomers from Dimer to Hexamer on Self-Assembled Monolayers
LANGMUIR, 27:14876-14887, DEC 20 2011
abstract, full text

Puri, A., Jang, H., Yavlovich, A., Masood, M.A., Veenstra, T.D., Luna, C., Aranda-Espinoza, H., Nussinov, R., Blumenthal, R.
Material Properties of Matrix Lipids Determine the Conformation and Intermolecular Reactivity of Diacetylenic Phosphatidylcholine in the Lipid Bilayer
LANGMUIR, 27:15120-15128, DEC 20 2011
abstract, full text

Gannon, G., O'Dwyer, C., Larsson, J.A., Thompson, D.
Interdigitating Organic Bilayers Direct the Short Inter layer Spacing in Hybrid Organic-Inorganic Layered Vanadium Oxide Nanostructures
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14518-14525, DEC 15 2011
abstract, full text

Vivcharuk, V., Kaznessis, Y.N.
Thermodynamic Analysis of Protegrin-1 Insertion and Permeation through a Lipid Bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14704-14712, DEC 15 2011
abstract, full text

Matysiak, S., Debenedetti, P.G., Rossky, P.J.
Dissecting the Energetics of Hydrophobic Hydration of Polypeptides
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14859-14865, DEC 15 2011
abstract, full text

Christelle, B., Eduardo, B.D.O., Latifa, C., Elaine-Rose, M., Bernard, M., Evelyne, R.H., Mohamed, G., Jean-Marc, E., Catherine, H.
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation
JOURNAL OF BIOTECHNOLOGY, 156:203-210, DEC 10 2011
abstract, full text

Vargas, E., Bezanilla, F., Roux, B.
In Search of a Consensus Model of the Resting State of a Voltage-Sensing Domain
NEURON, 72:713-720, DEC 8 2011
abstract, full text

Rudzinski, J.F., Noid, W.G.
Coarse-graining entropy, forces, and structures
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 214101, DEC 7 2011
abstract, full text

Chen, R., Robinson, A., Gordon, D., Chung, S.H.
Modeling the Binding of Three Toxins to the Voltage-Gated Potassium Channel (Kv1.3)
BIOPHYSICAL JOURNAL, 101:2652-2660, DEC 7 2011
abstract, full text

Gordon, D., Chung, S.H.
Permeation and Block of the Kv1.2 Channel Examined Using Brownian and Molecular Dynamics
BIOPHYSICAL JOURNAL, 101:2671-2678, DEC 7 2011
abstract, full text

Bucher, D., Grant, B.J., McCammon, J.A.
Induced Fit or Conformational Selection? The Role of the Semi-closed State in the Maltose Binding Protein
BIOCHEMISTRY, 50:10530-10539, DEC 6 2011
abstract, full text

Marinelli, F., Kuhlmann, S.I., Grell, E., Kunte, H.J., Ziegler, C., Faraldo-Gomez, J.D.
Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:E1285-E1292, DEC 6 2011
abstract, full text

Lin, Y.W., Nie, C.M., Liao, L.F.
Insights into Uranyl Ion Binding to Ubiquitin from Molecular Modeling and Dynamics Simulations
CHEMISTRY LETTERS, 40:1330-1331, DEC 5 2011
abstract, full text

Castro-Nallar, E., Martin, M.C.S., Mascayano, C., Molina, C., Crandall, K.A.
Molecular Phylodynamics and Protein Modeling of Infectious Salmon Anemia Virus (ISAV)
BMC EVOLUTIONARY BIOLOGY, 11: Art. No. 349, DEC 2 2011
abstract, full text

Krammer, E.M., Homble, F., Prevost, M.
Concentration Dependent Ion Selectivity in VDAC: A Molecular Dynamics Simulation Study
PLOS ONE, 6: Art. No. e27994, DEC 2 2011
abstract, full text

Ruiz, L., Keten, S.
ATOMISTIC MODELING AND MECHANICS OF SELF-ASSEMBLED ORGANIC NANOTUBES
INTERNATIONAL JOURNAL OF APPLIED MECHANICS, 3:667-684, DEC 2011
abstract, full text

Biswas, M., Voltz, K., Smith, J.C., Langowski, J.
Role of Histone Tails in Structural Stability of the Nucleosome
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002279, DEC 2011
abstract, full text

Wanunu, M., Bhattacharya, S., Xie, Y., Tor, Y., Aksimentiev, A., Drndic, M.
Nanopore Analysis of Individual RNA/Antibiotic Complexes
ACS NANO, 5:9345-9353, DEC 2011
abstract, full text

Tordesillas, L., Gamboa, P., Sanz, M.L., Palacin, A., Gomez-Casado, C., Cuesta-Herranz, J., Pacios, L.F., Salcedo, G., Diaz-Perales, A.
A mutant of the major melon allergen, Cuc m 2, with reduced IgE binding capacity is a good candidate for specific immunotherapy
MOLECULAR IMMUNOLOGY, 49:504-511, DEC 2011
abstract, full text

Mrinal, N., Tomar, A., Nagaraju, J.
Role of sequence encoded kappa B DNA geometry in gene regulation by Dorsal
NUCLEIC ACIDS RESEARCH, 39:9574-9591, DEC 2011
abstract, full text

Kurkcuoglu, Z., Ural, G., Akten, E.D., Doruker, P.
Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human
MOLECULAR INFORMATICS, 30:986-995, DEC 2011
abstract, full text

Zobnina, V.G., Kosevich, M.V., Chagovets, V.V., Boryak, O.A., Kulik, A.N., Gomory, A.
Stable associates of polyether oligomers with chlorine anion as revealed by the data of electrospray mass spectrometry and molecular dynamics
JOURNAL OF ANALYTICAL CHEMISTRY, 66:1341-1347, DEC 2011
abstract, full text

Melillo, M., Zhu, F.Q., Snyder, M.A., Mittal, J.
Water Transport through Nanotubes with Varying Interaction Strength between Tube Wall and Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2978-2983, DEC 1 2011
abstract, full text

Colpitts, C.C., Kim, S.S., Posehn, S.E., Jepson, C., Kim, S.Y., Wiedemann, G., Reski, R., Wee, A.G.H., Douglas, C.J., Suh, D.Y.
PpASCL, a moss ortholog of anther-specific chalcone synthase-like enzymes, is a hydroxyalkylpyrone synthase involved in an evolutionarily conserved sporopollenin biosynthesis pathway
NEW PHYTOLOGIST, 192:855-868, DEC 2011
abstract, full text

Wang, X.L., Kumar, S., Singh, S.K.
Disulfide Scrambling in IgG2 Monoclonal Antibodies: Insights from Molecular Dynamics Simulations
PHARMACEUTICAL RESEARCH, 28:3128-3144, DEC 2011
abstract, full text

Sanli, D., Keskin, O., Gursoy, A., Erman, B.
Structural cooperativity in histone H3 tail modifications
PROTEIN SCIENCE, 20:1982-1990, DEC 2011
abstract, full text

Matthai, C.C., March, N.H.
The application of condensed matter methods to the study of the conformation and elastic properties of biopolymers and the transport of DNA through cell membranes
THEORETICAL CHEMISTRY ACCOUNTS, 130:1155-1167, DEC 2011
abstract, full text

Schmidtke, P., Bidon-Chanal, A., Luque, F.J., Barril, X.
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
BIOINFORMATICS, 27:3276-3285, DEC 1 2011
abstract, full text

Ren, H., Jiang, J., Mukamel, S.
Deep UV Resonance Raman Spectroscopy of beta-Sheet Amyloid Fibrils: A QM/MM Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13955-13962, DEC 1 2011
abstract, full text

Du, H.L., Li, J.Y., Zhang, J., Su, G., Li, X.Y., Zhao, Y.L.
Separation of Hydrogen and Nitrogen Gases with Porous Graphene Membrane
JOURNAL OF PHYSICAL CHEMISTRY C, 115:23261-23266, DEC 1 2011
abstract, full text

Lin, Y.W., Liao, L.F.
Probing interactions between uranyl ions and lipid membrane by molecular dynamics simulation
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 976:130-134, DEC 1 2011
abstract, full text

Skjaerven, L., Reuter, N., Martinez, A.
Dynamics, flexibility and ligand-induced conformational changes in biological macromolecules: a computational approach
FUTURE MEDICINAL CHEMISTRY, 3:2079-2100, DEC 2011
abstract, full text

Bairagya, H.R., Mukhopadhyay, B.P., Bera, A.K.
Role of Salt Bridge Dynamics in Inter Domain Recognition of Human IMPDH Isoforms: An Insight to Inhibitor Topology for Isoform-II
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:441-462, DEC 2011
abstract, full text

Izanloo, C., Parsafar, G.A., Abroshan, H., Akbarzadeh, H.
Denaturation of Drew-Dickerson DNA in a High Salt Concentration Medium: Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3354-3361, DEC 2011
abstract, full text

Renthal, R., Brancaleon, L., Pena, I., Silva, F., Chen, L.Y.
Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles
BIOPHYSICAL CHEMISTRY, 159:321-327, DEC 2011
abstract, full text

Dawid, A., Gorny, K., Gburski, Z.
The structural studies of fullerenol C-60(OH)(24) and nitric oxide mixture in water solvent - MD simulation
NITRIC OXIDE-BIOLOGY AND CHEMISTRY, 25:373-380, NOV 30 2011
abstract, full text

Abdel-Azeim, S., Li, X., Chung, L.W., Morokuma, K.
Zinc-Homocysteine Binding in Cobalamin-Dependent Methionine Synthase and its Role in the Substrate Activation: DFT, ONIOM, and QM/MM Molecular Dynamics Studies
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3154-3167, NOV 30 2011
abstract, full text

Bannerman, M.N., Sargant, R., Lue, L.
DynamO: A Free O(N) General Event-Driven Molecular Dynamics Simulator
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3329-3338, NOV 30 2011
abstract, full text

Xiang, X., Lee, C.Y., Li, T., Chen, W., Lou, J.Z., Zhu, C.
Structural Basis and Kinetics of Force-Induced Conformational Changes of an alpha A Domain-Containing Integrin
PLOS ONE, 6: Art. No. e27946, NOV 28 2011
abstract, full text

Joshi, H., Cheluvaraja, S., Somogyi, E., Brown, D.R., Ortoleva, P.
A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity
VACCINE, 29:9423-9430, NOV 28 2011
abstract, full text

Fu, C.W., Lin, T.H.
Theoretical Study on the Alkaline Hydrolysis of Methyl Thioacetate in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY A, 115:13523-13533, NOV 24 2011
abstract, full text

Gross, A.S., Bell, A.T., Chu, J.W.
Thermodynamics of Cellulose Solvation in Water and the Ionic Liquid 1-Butyl-3-Methylimidazolim Chloride
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13433-13440, NOV 24 2011
abstract, full text

Priya, M.H., Ashbaugh, H.S., Paulaitis, M.E.
Cosolvent Preferential Molecular Interactions in Aqueous Solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13633-13642, NOV 24 2011
abstract, full text

Yuzlenko, O., Lazandis, T.
Interactions between Ionizable Amino Acid Side Chains at a Lipid Bilayer-Water Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13674-13684, NOV 24 2011
abstract, full text

Shukla, D., Schneider, C.P., Trout, B.L.
Complex Interactions between Molecular Ions in Solution and Their Effect on Protein Stability
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:18713-18718, NOV 23 2011
abstract, full text

Nemkevich, A., Spackman, M.A., Corry, B.
Mechanism of Concerted Hydrogen Bond Reorientation in Clathrates of Dianin's Compound and Hydroquinone
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:18880-18888, NOV 23 2011
abstract, full text

Yamaguchi, S., Watanabe, H., Mondal, S.K., Kundu, A., Tahara, T.
"Up" versus "down" alignment and hydration structures of solutes at the air/water interface revealed by heterodyne-detected electronic sum frequency generation with classical molecular dynamics simulation
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 194705, NOV 21 2011
abstract, full text

Schneider, C.P., Shukla, D., Trout, B.L.
Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers
PLOS ONE, 6: Art. No. e27665, NOV 18 2011
abstract, full text

da Silva, L.P., da Silva, J.C.G.E.
Study on the Effects of Intermolecular Interactions on Firefly Multicolor Bioluminescence
CHEMPHYSCHEM, 12:3002-3008, NOV 18 2011
abstract, full text

Dai, Z.W., Wan, L.S., Huang, X.J., Ling, J., Xu, Z.K.
Selective Adsorption of Isopropyl Alcohol Aqueous Solution on Polypropylene Surfaces: A Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY C, 115:22415-22421, NOV 17 2011
abstract, full text

Sun, S., Wong, J.T.Y., Zhang, T.Y.
Atomistic Simulations of Electroporation in Water Preembedded Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13355-13359, NOV 17 2011
abstract, full text

Cho, S.S., Reddy, G., Straub, J.E., Thirumalai, D.
Entropic Stabilization of Proteins by TMAO
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13401-13407, NOV 17 2011
abstract, full text

Heinzelmann, G., Bastug, T., Kuyucak, S.
Free Energy Simulations of Ligand Binding to the Aspartate Transporter Glt(Ph)
BIOPHYSICAL JOURNAL, 101:2380-2388, NOV 16 2011
abstract, full text

Re, S., Miyashita, N., Yamaguchi, Y., Sugita, Y.
Structural Diversity and Changes in Conformational Equilibria of Biantennary Complex-Type N-Glycans in Water Revealed by Replica-Exchange Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 101:L44-L46, NOV 16 2011
abstract, full text

Shekhar, P., Nanda, H., Losche, M., Heinrich, F.
Continuous distribution model for the investigation of complex molecular architectures near interfaces with scattering techniques
JOURNAL OF APPLIED PHYSICS, 110: Art. No. 102216, NOV 15 2011
abstract, full text

Luo, Y., Harder, E., Faibish, R.S., Roux, B.
Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane
JOURNAL OF MEMBRANE SCIENCE, 384:1-9, NOV 15 2011
abstract, full text

Lam, A.R., Jiang, J., Mukamel, S.
Distinguishing Amyloid Fibril Structures in Alzheimer's Disease (AD) by Two-Dimensional Ultraviolet (2DUV) Spectroscopy
BIOCHEMISTRY, 50:9809-9816, NOV 15 2011
abstract, full text

Garate, J.A., English, N.J., Singh, A., Ryan, K.M., Mooney, D.A., MacElroy, J.M.D.
Electrophoretic Deposition of Poly(3-decylthiophene) onto Gold-Mounted Cadmium Selenide Nanorods
LANGMUIR, 27:13506-13513, NOV 15 2011
abstract, full text

Ganesan, N., Bauer, B.A., Lucas, T.R., Patel, S., Taufer, M.
Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers From Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs)
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2958-2973, NOV 15 2011
abstract, full text

Borstnik, U., Miller, B.T., Brooks, B.R., Janezic, D.
The Distributed Diagonal Force Decomposition Method for Parallelizing Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3005-3013, NOV 15 2011
abstract, full text

Garcia-Risueno, P., Echenique, P., Alonso, J.L.
Exact and Efficient Calculation of Lagrange Multipliers in Biological Polymers with Constrained Bond Lengths and Bond Angles: Proteins and Nucleic Acids as Example Cases
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3039-3046, NOV 15 2011
abstract, full text

Jo, S., Song, K.C., Desaire, H., MacKerell, A.D., Im, W.
Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:3135-3141, NOV 15 2011
abstract, full text

Weber, V., Merchant, S., Asthagiri, D.
Communication: Regularizing binding energy distributions and thermodynamics of hydration: Theory and application to water modeled with classical and ab initio simulations
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 181101, NOV 14 2011
abstract, full text

Ferrer, T., Cordero-Morales, J.F., Arias, M., Ficker, E., Medovoy, D., Perozo, E., Tristani-Firouzi, M.
Molecular Coupling in the Human ether-a-go-go-related gene-1 (hERG1) K+ Channel Inactivation Pathway
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:39091-39099, NOV 11 2011
abstract, full text

Li, M.H., Zheng, W.J.
Probing the Structural and Energetic Basis of Kinesin-Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
BIOCHEMISTRY, 50:8645-8655, NOV 11 2011
abstract, full text

Lim, K.H., Huang, H., Pralle, A., Park, S.
Engineered Streptavidin Monomer and Dimer with Improved Stability and Function
BIOCHEMISTRY, 50:8682-8691, NOV 11 2011
abstract, full text

Elola, M.D., Rodriguez, J., Laria, D.
Liquid Methanol Confined within Functionalized Silica Nanopores. 2. Solvation Dynamics of Coumarin 153
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12859-12867, NOV 10 2011
abstract, full text

D'Antonio, E.L., D'Antonio, J., de Serrano, V., Gracz, H., Thompson, M.K., Ghiladi, R.A., Bowden, E.F., Franzen, S.
Functional Consequences of the Creation of an Asp-His-Fe Triad in a 3/3 Globin
BIOCHEMISTRY, 50:9664-9680, NOV 8 2011
abstract, full text

Calligari, P., Calandrini, V., Kneller, G.R., Abergel, D.
From NMR Relaxation to Fractional Brownian Dynamics in Proteins: Results from a Virtual Experiment
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12370-12379, NOV 3 2011
abstract, full text

Karachevtsev, V.A., Stepanian, S.G., Glamazda, A.Y., Karachevtsev, M.V., Eremenko, V.V., Lytvyn, O.S., Adamowicz, L.
Noncovalent Interaction of Single-Walled Carbon Nanotubes with 1-Pyrenebutanoic Acid Succinimide Ester and Glucoseoxidase
JOURNAL OF PHYSICAL CHEMISTRY C, 115:21072-21082, NOV 3 2011
abstract, full text

Mondal, S., Khelashvili, G., Shan, J.F., Andersen, O.S., Weinstein, H.
Quantitative Modeling of Membrane Deformations by Multihelical Membrane Proteins: Application to G-Protein Coupled Receptors
BIOPHYSICAL JOURNAL, 101:2092-2101, NOV 2 2011
abstract, full text

Luan, B.Q., Martyna, G., Stolovitzky, G.
Characterizing and Controlling the Motion of ssDNA in a Solid-State Nanopore
BIOPHYSICAL JOURNAL, 101:2214-2222, NOV 2 2011
abstract, full text

Anisimov, V.M., Ziemys, A., Kizhake, S., Yuan, Z.Y., Natarajan, A., Cavasotto, C.N.
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:1071-1084, NOV 2011
abstract, full text

Elder, R.M., Emrick, T., Jayaraman, A.
Understanding the Effect of Polylysine Architecture on DNA Binding Using Molecular Dynamics Simulations
BIOMACROMOLECULES, 12:3870-3879, NOV 2011
abstract, full text

Gao, X., Zhang, N., Wei, T.D., Su, H.N., Xie, B.B., Dong, C.C., Zhang, X.Y., Chen, X.L., Zhou, B.C., Wang, Z.X., Wu, J.W., Zhang, Y.Z.
Crystal structure of the N-terminal domain of linker L-R and the assembly of cyanobacterial phycobilisome rods
MOLECULAR MICROBIOLOGY, 82:698-705, NOV 2011
abstract, full text

Kraszewski, S., Tarek, M., Ramseyer, C.
Uptake and Translocation Mechanisms of Cationic Amino Derivatives Functionalized on Pristine C-60 by Lipid Membranes: A Molecular Dynamics Simulation Study
ACS NANO, 5:8571-8578, NOV 2011
abstract, full text

Sathe, C., Zou, X.Q., Leburton, J.P., Schulten, K.
Computational Investigation of DNA Detection Using Graphene Nanopores
ACS NANO, 5:8842-8851, NOV 2011
abstract, full text, TCBG publications

Huggins, D.J., Marsh, M., Payne, M.C.
Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3514-3522, NOV 2011
abstract, full text

Tanner, D.E., Chan, K.Y., Phillips, J.C., Schulten, K.
Parallel Generalized Born Implicit Solvent Calculations with NAMD
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3635-3642, NOV 2011
abstract, full text, TCBG publications

Gilman-Politi, R., Harries, D.
Unraveling the Molecular Mechanism of Enthalpy Driven Peptide Folding by Polyol Osmolytes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3816-3828, NOV 2011
abstract, full text

Durrant, J.D., McCammon, J.A.
HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 31:5-9, NOV 2011
abstract, full text

Du, X.N., Zhang, X., Qi, J.L., An, H.L., Li, J.W., Wan, Y.M., Fu, Y., Gao, H.X., Gao, Z.B., Zhan, Y., Zhang, H.L.
Characteristics and molecular basis of celecoxib modulation on K(v)7 potassium channels
BRITISH JOURNAL OF PHARMACOLOGY, 164:1722-1737, NOV 2011
abstract, full text

Kwon, T., Harris, A.L., Rossi, A., Bargiello, T.A.
Molecular dynamics simulations of the Cx26 hemichannel: Evaluation of structural models with Brownian dynamics
JOURNAL OF GENERAL PHYSIOLOGY, 138:475-493, NOV 2011
abstract, full text

Feldmann, E.A., Ni, S., Sahu, I.D., Mishler, C.H., Risser, D.D., Murakami, J.L., Tom, S.K., McCarrick, R.M., Lorigan, G.A., Tolbert, B.S., Callahan, S.M., Kennedy, M.A.
Evidence for Direct Binding between HetR from Anabaena sp PCC 7120 and PatS-5
BIOCHEMISTRY, 50:9212-9224, NOV 1 2011
abstract, full text

Mishra, S., Caflisch, A.
Dynamics in the Active Site of beta-Secretase: A Network Analysis of Atomistic Simulations
BIOCHEMISTRY, 50:9328-9339, NOV 1 2011
abstract, full text

Valley, C.C., Perlmutter, J.D., Braun, A.R., Sachs, J.N.
NaCl Interactions with Phosphatidylcholine Bilayers Do Not Alter Membrane Structure but Induce Long-Range Ordering of Ions and Water
JOURNAL OF MEMBRANE BIOLOGY, 244:35-42, NOV 2011
abstract, full text

Utesch, T., Daminelli, G., Mroginski, M.A.
Molecular Dynamics Simulations of the Adsorption of Bone Morphogenetic Protein-2 on Surfaces with Medical Relevance
LANGMUIR, 27:13144-13153, NOV 1 2011
abstract, full text

Barata, T.S., Brocchini, S., Teo, I., Shaunak, S., Zloh, M.
From sequence to 3D structure of hyperbranched molecules: application to surface modified PAMAM dendrimers
JOURNAL OF MOLECULAR MODELING, 17:2741-2749, NOV 2011
abstract, full text

Mazzucco, N., Zanconato, S., De Lucrezia, D., Argese, E., Poli, I., Minervini, G.
Design and dynamic simulation of minimal metallo-proteins
JOURNAL OF MOLECULAR MODELING, 17:2919-2925, NOV 2011
abstract, full text

Sadasivan, V.D., Narpala, S.R., Budil, D.E., Sacco, A., Carrier, R.L.
Modeling the human intestinal Mucin (MUC2) C-terminal cystine knot dimer
JOURNAL OF MOLECULAR MODELING, 17:2953-2963, NOV 2011
abstract, full text

Severin, P.M.D., Zou, X.Q., Gaub, H.E., Schulten, K.
Cytosine methylation alters DNA mechanical properties
NUCLEIC ACIDS RESEARCH, 39:8740-8751, NOV 2011
abstract, full text, TCBG publications

Contreras-Torres, F.F., Martinez-Loran, E.
DNA insertion in and wrapping around carbon nanotubes
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:902-919, NOV-DEC 2011
abstract, full text

Caulfield, T., Medina-Franco, J.L.
Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A
JOURNAL OF STRUCTURAL BIOLOGY, 176:185-191, NOV 2011
abstract, full text

Sammond, D.W., Joce, C., Takeshita, R., McQuate, S.E., Ghosh, N., Martin, J.M., Yin, H.
Transmembrane Peptides Used to Investigate the Homo-Oligomeric Interface and Binding Hotspot of Latent Membrane Protein 1
BIOPOLYMERS, 95:772-784, NOV 2011
abstract, full text

Durrant, J.D., McCammon, J.A.
Molecular dynamics simulations and drug discovery
BMC BIOLOGY, 9: Art. No. 71, OCT 28 2011
abstract, full text

Espinoza-Fonseca, L.M., Thomas, D.D.
Atomic-Level Characterization of the Activation Mechanism of SERCA by Calcium
PLOS ONE, 6: Art. No. e26936, OCT 27 2011
abstract, full text

Tsutakawa, S.E., Van Wynsberghe, A.W., Freudenthal, B.D., Weinacht, C.P., Gakhar, L., Washington, M.T., Zhuang, Z.H., Tainer, J.A., Ivanov, I.
Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:17672-17677, OCT 25 2011
abstract, full text

Nam, K.Y., Chang, B.H., No, K.T.
Conformational Study of N-terminal Prion Peptides by Molecular Dynamics Simulations
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 32:3553-3554, OCT 20 2011
full text

Teh, A.H., Saito, J.A., Baharuddin, A., Tuckerman, J.R., Newhouse, J.S., Kanbe, M., Newhouse, E.I., Rahim, R.A., Favier, F., Didierjean, C., Sousa, E.H.S., Stott, M.B., Dunfield, P.F., Gonzalez, G., Gilles-Gonzalez, M.A., Najimudin, N., Alam, M.
Hell's Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin
FEBS LETTERS, 585:3250-3258, OCT 20 2011
abstract, full text

Lee, T.S., Giambasu, G.M., Harris, M.E., York, D.M.
Characterization of the Structure and Dynamics of the HDV Ribozyme in Different Stages Along the Reaction Path
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2538-2543, OCT 20 2011
abstract, full text

Shukla, D., Trout, B.L.
Understanding the Synergistic Effect of Arginine and Glutamic Acid Mixtures on Protein Solubility
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11831-11839, OCT 20 2011
abstract, full text

Willenbring, D., Liu, L.T., Mowrey, D., Xu, Y., Tang, P.
Isoflurane Alters the Structure and Dynamics of GLIC
BIOPHYSICAL JOURNAL, 101:1905-1912, OCT 19 2011
abstract, full text

Ettig, R., Kepper, N., Stehr, R., Wedemann, G., Rippe, K.
Dissecting DNA-Histone Interactions in the Nucleosome by Molecular Dynamics Simulations of DNA Unwrapping
BIOPHYSICAL JOURNAL, 101:1999-2008, OCT 19 2011
abstract, full text

Virtanen, J.J., Makowski, L., Sosnick, T.R., Freed, K.F.
Modeling the Hydration Layer around Proteins: Applications to Small- and Wide-Angle X-Ray Scattering
BIOPHYSICAL JOURNAL, 101:2061-2069, OCT 19 2011
abstract, full text

Lin, Y.C., Silvestre-Ryan, J., Himmel, M.E., Crowley, M.F., Beckham, G.T., Chu, J.W.
Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:16617-16624, OCT 19 2011
abstract, full text

Mekhaiel, D.N.A., Czajkowsky, D.M., Andersen, J.T., Shi, J.G., El-Faham, M., Doenhoff, M., McIntosh, R.S., Sandlie, I., He, J.F., Hu, J., Shao, Z.F., Pleass, R.J.
Polymeric human Fc-fusion proteins with modified effector functions
SCIENTIFIC REPORTS, 1: Art. No. 124, OCT 19 2011
abstract, full text

Ma, C.W., Xiu, Z.L., Zeng, A.P.
A New Concept to Reveal Protein Dynamics Based on Energy Dissipation
PLOS ONE, 6: Art. No. e26453, OCT 17 2011
abstract, full text

Jackson, P.L., Noerager, B.D., Jablonsky, M.J., Hardison, M.T., Cox, B.D., Patterson, J.C., Dhanapal, B., Blalock, J.E., Muccio, D.D.
A CXCL8 receptor antagonist based on the structure of N-acetyl-proline-glycine-proline
EUROPEAN JOURNAL OF PHARMACOLOGY, 668:435-442, OCT 15 2011
abstract, full text

Saunders, M.G., Voth, G.A.
Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis
JOURNAL OF MOLECULAR BIOLOGY, 413:279-291, OCT 14 2011
abstract, full text

Pedretti, A., Labozzetta, A., Lo Monte, M., Beccari, A.R., Moriconi, A., Vistoli, G.
Exploring the activation mechanism of TRPM8 channel by targeted MD simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 414:14-19, OCT 14 2011
abstract, full text

Palermo, G., Branduardi, D., Masetti, M., Lodoa, A., Mor, M., Piomelli, D., Cavalli, A., De Vivo, M.
Covalent Inhibitors of Fatty Acid Amide Hydrolase: A Rationale for the Activity of Piperidine and Piperazine Aryl Ureas
JOURNAL OF MEDICINAL CHEMISTRY, 54:6612-6623, OCT 13 2011
abstract, full text

Dlugosz, M., Trylska, J.
Secondary Structures of Native and Pathogenic Huntingtin N-Terminal Fragments
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11597-11608, OCT 13 2011
abstract, full text

Souza, P.C.T., Barra, G.B., Velasco, L.F.R., Ribeiro, I.C.J., Simeoni, L.A., Togashi, M., Webb, P., Neves, F.A.R., Skaf, M.S., Martinez, L., Polikarpov, I.
Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants
JOURNAL OF MOLECULAR BIOLOGY, 412:882-893, OCT 7 2011
abstract, full text

Duff, N., Peters, B.
Polymorph specific RMSD local order parameters for molecular crystals and nuclei: alpha-, beta-, and gamma-glycine
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 134101, OCT 7 2011
abstract, full text

Sinha, S.K., Bandyopadhyay, S.
Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 135101, OCT 7 2011
abstract, full text

Sorensen, J., Periole, X., Skeby, K.K., Marrink, S.J., Schiott, B.
Protofibrillar Assembly Toward the Formation of Amyloid Fibrils
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2385-2390, OCT 6 2011
abstract, full text

Carnevale, V., Treptow, W., Klein, M.L.
Sodium Ion Binding Sites and Hydration in the Lumen of a Bacterial Ion Channel from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2504-2508, OCT 6 2011
abstract, full text

Dixit, A., Verkhivker, G.M.
The Energy Landscape Analysis of Cancer Mutations in Protein Kinases
PLOS ONE, 6: Art. No. e26071, OCT 6 2011
abstract, full text

Goldsmith, J., Hinds, B.J.
Simulation of Steady-State Methanol Flux through a Model Carbon Nanotube Catalyst Support
JOURNAL OF PHYSICAL CHEMISTRY C, 115:19158-19164, OCT 6 2011
abstract, full text

Giangreco, I., Lattanzi, G., Nicolotti, O., Catto, M., Laghezza, A., Leonetti, F., Stefanachi, A., Carotti, A.
Insights into the Complex Formed by Matrix Metalloproteinase-2 and Alloxan Inhibitors: Molecular Dynamics Simulations and Free Energy Calculations
PLOS ONE, 6: Art. No. e25597, OCT 5 2011
abstract, full text

Furini, S., Domene, C.
Gating at the Selectivity Filter of Ion Channels that Conduct Na+ and K+ Ions
BIOPHYSICAL JOURNAL, 101:1623-1631, OCT 5 2011
abstract, full text

Sarkar, A., Zhou, C., Meklemburg, R., Wintrode, P.L.
Local Conformational Flexibility Provides a Basis for Facile Polymer Formation in Human Neuroserpin
BIOPHYSICAL JOURNAL, 101:1758-1765, OCT 5 2011
abstract, full text

Patapati, K.K., Glykos, N.M.
Three Force Fields' Views of the 3(10) Helix
BIOPHYSICAL JOURNAL, 101:1766-1771, OCT 5 2011
abstract, full text

Bisson, M., Bernaschi, M., Melchionna, S.
Parallel Molecular Dynamics with Irregular Domain Decomposition
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 10:1071-1088, OCT 2011
abstract, full text

Demir, O., Baronio, R., Salehi, F., Wassman, C.D., Hall, L., Hatfield, G.W., Chamberlin, R., Kaiser, P., Lathrop, R.H., Amaro, R.E.
Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002238, OCT 2011
abstract, full text

Dixit, A., Verkhivker, G.M.
Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002179, OCT 2011
abstract, full text

Koldso, H., Noer, P., Grouleff, J., Autzen, H.E., Sinning, S., Schiott, B.
Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002246, OCT 2011
abstract, full text

Sethi, A., Goldstein, B., Gnanakaran, S.
Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002192, OCT 2011
abstract, full text

Atkinson, J., Kapralov, A.A., Yanamala, N., Tyurina, Y.Y., Amoscato, A.A., Pearce, L., Peterson, J., Huang, Z.T., Jiang, J.F., Samhan-Arias, A.K., Maeda, A., Feng, W.H., Wasserloos, K., Belikova, N.A., Tyurin, V.A., Wang, H., Fletcher, J., Wang, Y.S., Vlasova, I.I., Klein-Seetharaman, J., Stoyanovsky, D.A., Bayir, H., Pitt, B.R., Epperly, M.W., Greenberger, J.S., Kagan, V.E.
A mitochondria-targeted inhibitor of cytochrome c peroxidase mitigates radiation-induced death
NATURE COMMUNICATIONS, 2: Art. No. 497, OCT 2011
abstract, full text

Ahmed, A.A., Goldsmith, J., Fokt, I., Le, X.F., Krzysko, K.A., Lesyng, B., Bast, R.C., Priebe, W.
A genistein derivative, ITB-301, induces microtubule depolymerization and mitotic arrest in multidrug-resistant ovarian cancer
CANCER CHEMOTHERAPY AND PHARMACOLOGY, 68:1033-1044, OCT 2011
abstract, full text

Han, C., Wang, J.P.
Temperature-Dependence of the Amide-I Frequency Map for Peptides Proteins
CHINESE JOURNAL OF CHEMICAL PHYSICS, 24:529-537, OCT 2011
abstract, full text

Lindbo, D., Tornberg, A.K.
Spectral accuracy in fast Ewald-based methods for particle simulations
JOURNAL OF COMPUTATIONAL PHYSICS, 230:8744-8761, OCT 1 2011
abstract, full text

Vaitheeswaran, S., Chen, J., Thirumalai, D.
Hydrophobic and Ionic-Interactions in Bulk and Confined Water with Implications for Collapse and Folding of Proteins
JOURNAL OF STATISTICAL PHYSICS, 145:276-292, OCT 2011
abstract, full text

Skillman, K.M., Diraviyam, K., Khan, A., Tang, K.L., Sept, D., Sibley, L.D.
Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites
PLOS PATHOGENS, 7: Art. No. e1002280, OCT 2011
abstract, full text

Joshi, H., Singharoy, A., Sereda, Y.V., Cheluvaraja, S.C., Ortoleva, P.J.
Multiscale simulation of microbe structure and dynamics
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 107:200-217, OCT 2011
abstract, full text

Vassiliev, S., Mahboob, A., Bruce, D.
Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes
PHOTOSYNTHESIS RESEARCH, 110:25-38, OCT 2011
abstract, full text

Volzing, K., Biliouris, K., Kaznessis, Y.N.
proTeOn and proTeOff, New Protein Devices That Inducibly Activate Bacterial Gene Expression
ACS CHEMICAL BIOLOGY, 6:1107-1116, OCT 2011
abstract, full text

Muixi, L., Gay, M., Munoz-Torres, P.M., Guitart, C., Cedano, J., Abian, J., Alvarez, I., Jaraquemada, D.
The peptide-binding motif of HLA-DR8 shares important structural features with other type 1 diabetes-associated alleles
GENES AND IMMUNITY, 12:504-512, OCT 2011
abstract, full text

Durrant, J.D., Friedman, A.J., McCammon, J.A.
CrystalDock: A Novel Approach to Fragment-Based Drug Design
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2573-2580, OCT 2011
abstract, full text

Wright, D.W., Coveney, P.V.
Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2636-2649, OCT 2011
abstract, full text

Guvench, O., Mallajosyula, S.S., Raman, E.P., Hatcher, E., Vanommeslaeghe, K., Foster, T.J., Jamison, F.W., MacKerell, A.D.
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate-Protein Modeling
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3162-3180, OCT 2011
abstract, full text

Wang, Y., Markwick, P.R.L., de Oliveira, C.A.F., McCammon, J.A.
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3199-3207, OCT 2011
abstract, full text

Nayar, D., Agarwal, M., Chakravarty, C.
Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3354-3367, OCT 2011
abstract, full text

Patel, J.S., Branduardi, D., Masetti, M., Rocchia, W., Cavalli, A.
Insights into Ligand-Protein Binding from Local Mechanical Response
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3368-3378, OCT 2011
abstract, full text

Eichenberger, A.P., Allison, J.R., Dolenc, J., Geerke, D.P., Horta, B.A.C., Meier, K., Oostenbrink, C., Schmid, N., Steiner, D., Wang, D.Q., van Gunsteren, W.F.
GROMOS plus plus Software for the Analysis of Biomolecular Simulation Trajectories
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3379-3390, OCT 2011
abstract, full text

Sun, C.B., T'ang, T., Uludag, H.
Molecular Dynamics Simulations of PEI Mediated DNA Aggregation
BIOMACROMOLECULES, 12:3698-3707, OCT 2011
abstract, full text

Soriano-Ursua, M.A., Correa-Basurto, J., Trujillo-Ferrara, J.G., Kaumann, A.J.
Homology model and docking studies on porcine beta(2) adrenoceptor: description of two binding sites
JOURNAL OF MOLECULAR MODELING, 17:2525-2538, OCT 2011
abstract, full text

Spangberg, D., Larsson, D.S.D., van der Spoel, D.
Trajectory NG: portable, compressed, general molecular dynamics trajectories
JOURNAL OF MOLECULAR MODELING, 17:2669-2685, OCT 2011
abstract, full text

Blasco, B., Stenta, M., Alonso-Sarduy, L., Dietler, G., Dal Peraro, M., Cole, S.T., Pojer, F.
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
MOLECULAR MICROBIOLOGY, 82:251-264, OCT 2011
abstract, full text

Korchowiec, B., Korchowiec, J., Hato, M., Rogalska, E.
Glycolipid-cholesterol monolayers: Towards a better understanding of the interaction between the membrane components
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2466-2476, OCT 2011
abstract, full text

Warshaviak, D.T., Muellner, M.J., Chachisvilis, M.
Effect of membrane tension on the electric field and dipole potential of lipid bilayer membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2608-2617, OCT 2011
abstract, full text

Li, P., Liu, M., Tan, J.J., Zhang, X.Y., Chen, W.Z., Wang, C.X.
Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:311-323, OCT 2011
abstract, full text

Liu, Y.Z., Chipot, C., Shao, X.G., Cai, W.S.
The effects of 7-dehydrocholesterol on the structural properties of membranes
PHYSICAL BIOLOGY, 8: Art. No. 056005, OCT 2011
abstract, full text

Lucas, M.F., Rousseau, D.L., Guallar, V.
Electron transfer pathways in cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:1305-1313, OCT 2011
abstract, full text

Wan, S.Z., Coveney, P.V.
Molecular Dynamics Simulation Reveals Structural and Thermodynamic Features of Kinase Activation by Cancer Mutations Within the Epidermal Growth Factor Receptor
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2843-2852, OCT 2011
abstract, full text

Ma, B.Y., Nussinov, R.
Polymorphic Triple beta-Sheet Structures Contribute to Amide Hydrogen/Deuterium (H/D) Exchange Protection in the Alzheimer Amyloid beta 42 Peptide
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:34244-34253, SEP 30 2011
abstract, full text

Lee, K.H., Miller, C.R., Nagel, A.C., Wichman, H.A., Joyce, P., Ytreberg, F.M.
First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus
PLOS ONE, 6: Art. No. e25640, SEP 29 2011
abstract, full text

Slade, D., Dunstan, M.S., Barkauskaite, E., Weston, R., Lafite, P., Dixon, N., Ahel, M., Leys, D., Ahel, I.
The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase
NATURE, 477:616-U150, SEP 29 2011
abstract, full text

Mallajosyula, S.S., MacKerell, A.D.
Influence of Solvent and Intramolecular Hydrogen Bonding on the Conformational Properties of O-Linked Glycopeptides
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11215-11229, SEP 29 2011
abstract, full text

Bardhan, J.P., Knepley, M.G.
Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: Exact results for spherical inclusions
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 124107, SEP 28 2011
abstract, full text

Calero, C., Faraudo, J., Bastos-Gonzalez, D.
Interaction of Monovalent Ions with Hydrophobic and Hydrophilic Colloids: Charge Inversion and Ionic Specificity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:15025-15035, SEP 28 2011
abstract, full text

Torres, R., Swift, R.V., Chim, N., Wheatley, N., Lan, B.S., Atwood, B.R., Pujol, C., Sankaran, B., Bliska, J.B., Amaro, R.E., Goulding, C.W.
Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis
PLOS ONE, 6: Art. No. e25084, SEP 26 2011
abstract, full text

Monajjemi, M., Sabaghzadeh, R., Ilkhani, A.R., Mollaamin, F.
Nano-modeling of insulin-like growth factor 1 (IGF-1) by computational methods
AFRICAN JOURNAL OF MICROBIOLOGY RESEARCH, 5:2895-2905, SEP 23 2011
abstract, full text

Favia, A.D., Masetti, M., Recanatini, M., Cavalli, A.
Substrate Binding Process and Mechanistic Functioning of Type 1 11 beta-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods
PLOS ONE, 6: Art. No. e25375, SEP 23 2011
abstract, full text

Shim, J.Y., Bertalovitz, A.C., Kendall, D.A.
Identification of Essential Cannabinoid-binding Domains STRUCTURAL INSIGHTS INTO EARLY DYNAMIC EVENTS IN RECEPTOR ACTIVATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:33422-33435, SEP 23 2011
abstract, full text

Kim, S.N., Kuang, Z.F., Slocik, J.M., Jones, S.E., Cui, Y., Farmer, B.L., McAlpine, M.C., Naik, R.R.
Preferential Binding of Peptides to Graphene Edges and Planes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14480-14483, SEP 21 2011
abstract, full text

Miao, Y.L., Baudry, J.
Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process
BIOPHYSICAL JOURNAL, 101:1493-1503, SEP 21 2011
abstract, full text

King, D.T., Warren, D.B., Pouton, C.W., Chalmers, D.K.
Using Molecular Dynamics to Study Liquid Phase Behavior: Simulations of the Ternary Sodium Laurate/Sodium Oleate/Water System
LANGMUIR, 27:11381-11393, SEP 20 2011
abstract, full text

Barr, D., Oashi, T., Burkhard, K., Lucius, S., Samadani, R., Zhang, J., Shapiro, P., MacKerell, A.D., van der Vaart, A.
Importance of Domain Closure for the Autoactivation of ERK2
BIOCHEMISTRY, 50:8038-8048, SEP 20 2011
abstract, full text

Modi, N., Singh, P.R., Mahendran, K.R., Schulz, R., Winterhalter, M., Kleinekathofer, U.
Probing the Transport of Ionic Liquids in Aqueous Solution through Nanopores
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2331-2336, SEP 15 2011
abstract, full text

Naidu, M.D., Agarwal, R., Pena, L.A., Cunha, L., Mezei, M., Shen, M., Wilson, D.M., Liu, Y., Sanchez, Z., Chaudhary, P., Wilson, S.H., Waring, M.J.
Lucanthone and Its Derivative Hycanthone Inhibit Apurinic Endonuclease-1 (APE1) by Direct Protein Binding
PLOS ONE, 6: Art. No. e23679, SEP 15 2011
abstract, full text

Singleton, B.K., Lau, W., Fairweather, V.S.S., Burton, N.M., Wilson, M.C., Parsons, S.F., Richardson, B.M., Trakarnsanga, K., Brady, R.L., Anstee, D.J., Frayne, J.
Mutations in the second zinc finger of human EKLF reduce promoter affinity but give rise to benign and disease phenotypes
BLOOD, 118:3137-3145, SEP 15 2011
abstract, full text

Matyushov, D.V.
Nanosecond Stokes Shift Dynamics, Dynamical Transition, and Gigantic Reorganization Energy of Hydrated Heme Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10715-10724, SEP 15 2011
abstract, full text

Videla, P.E., Sala, J., Marti, J., Guardia, E., Laria, D.
Aqueous electrolytes confined within functionalized silica nanopores
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 104503, SEP 14 2011
abstract, full text

Ulucan, O., Keskin, O., Erman, B., Gursoy, A.
A Comparative Molecular Dynamics Study of Methylation State Specificity of JMJD2A
PLOS ONE, 6: Art. No. e24664, SEP 13 2011
abstract, full text

Cui, Y.B., Bastien, D.A.
Water transport in human aquaporin-4: Molecular dynamics (MD) simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 412:654-659, SEP 9 2011
abstract, full text

Lawrence, S.A., Hackett, J.C., Moran, R.G.
Tetrahydrofolate Recognition by the Mitochondrial Folate Transporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:31480-31489, SEP 9 2011
abstract, full text

Shah, M., Santiso, E.E., Trout, B.L.
Computer Simulations of Homogeneous Nucleation of Benzene from the Melt
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10400-10412, SEP 8 2011
abstract, full text

Cho, H.M., Gross, A.S., Chu, J.W.
Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14033-14041, SEP 7 2011
abstract, full text

Hsin, J., LaPointe, L.M., Kazy, A., Chipot, C., Senes, A., Schulten, K.
Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14071-14081, SEP 7 2011
abstract, full text, TCBG publications

Gonzalez, A., Perez-Acle, T., Pardo, L., Deupi, X.
Molecular Basis of Ligand Dissociation in beta-Adrenergic Receptors
PLOS ONE, 6: Art. No. e23815, SEP 7 2011
abstract, full text

Chan, K.Y., Gumbart, J., McGreevy, R., Watermeyer, J.M., Sewell, B.T., Schulten, K.
Symmetry-Restrained Flexible Fitting for Symmetric EM Maps
STRUCTURE, 19:1211-1218, SEP 7 2011
abstract, full text, TCBG publications

McParland, V., Varsano, G., Li, X., Thornton, J., Baby, J., Aravind, A., Meyer, C., Pavic, K., Rios, P., Kohn, M.
The Metastasis-Promoting Phosphatase PRL-3 Shows Activity toward Phosphoinositides
BIOCHEMISTRY, 50:7579-7590, SEP 6 2011
abstract, full text

Perlmutter, J.D., Drasler, W.J., Xie, W.S., Gao, J.L., Popot, J.L., Sachs, J.N.
All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer
LANGMUIR, 27:10523-10537, SEP 6 2011
abstract, full text

Gentilucci, L., Tolomelli, A., De Marco, R., Spampinato, S., Bedini, A., Artali, R.
The Inverse Type II beta-Turn on D-Trp-Phe, a Pharmacophoric Motif for MOR Agonists
CHEMMEDCHEM, 6:1640-1653, SEP 5 2011
abstract, full text

Henry, L.K., Iwamoto, H., Field, J.R., Kaufmann, K., Dawson, E.S., Jacobs, M.T., Adams, C., Felts, B., Zdravkovic, I., Armstrong, V., Combs, S., Solis, E., Rudnick, G., Noskov, S.Y., DeFelice, L.J., Meiler, J., Blakely, R.D.
A Conserved Asparagine Residue in Transmembrane Segment 1 (TM1) of Serotonin Transporter Dictates Chloride-coupled Neurotransmitter Transport
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:30823-30836, SEP 2 2011
abstract, full text

Long, M., Sato, M., Lim, C.T., Wu, J.H., Adachi, T., Inoue, Y.
Advances in Experiments and Modeling in Micro- and Nano-Biomechanics: A Mini Review
CELLULAR AND MOLECULAR BIOENGINEERING, 4:327-339, SEP 2011
abstract, full text

Huang, Q.S., Lou, J.Z., Wu, J.H., Zhu, C.
Conformational Transition of Glycoprotein Ib alpha Mutants in Flow Molecular Dynamics Simulation
CELLULAR AND MOLECULAR BIOENGINEERING, 4:495-504, SEP 2011
abstract, full text

Barducci, A., Bonomi, M., Parrinello, M.
Metadynamics
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:826-843, SEP-OCT 2011
abstract, full text

Heinrich, J.C., Tuukkanen, A., Schroeder, M., Fahrig, T., Fahrig, R.
RP101 (brivudine) binds to heat shock protein HSP27 (HSPB1) and enhances survival in animals and pancreatic cancer patients
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY, 137:1349-1361, SEP 2011
abstract, full text

Meredith, J.S., Roth, P.C., Spafford, K.L., Vetter, J.S.
PERFORMANCE IMPLICATIONS OF NONUNIFORM DEVICE TOPOLOGIES IN SCALABLE HETEROGENEOUS ARCHITECTURES
IEEE MICRO, 31:66-75, SEP-OCT 2011
full text

Wang, Y.T., Lee, W.J., Su, Z.Y., Chen, C.L.
Carbon-nanotube-based artificial peptide channel: Transportation of small peptide under external electric field force
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS, 42:724-726, SEP 2011
abstract, full text

Phatak, M., Adamczak, R., Cao, B.Q., Wagner, M., Meller, J.
Solvent and Lipid Accessibility Prediction as a Basis for Model Quality Assessment in Soluble and Membrane Proteins
CURRENT PROTEIN & PEPTIDE SCIENCE, 12:563-573, SEP 2011
abstract, full text

Necula, G., Mihai, M.E., Sbarcea, C.E., Dinu, S., Lupulescu, E., Ceausu, E., Streinu-Cercel, A., Mihailescu, D.F., Alexandrescu, V.I.
Overview of influenza virus antiviral resistance in Romania in the last four epidemic seasons - phenotyping, genotyping and molecular analysis study
REVISTA ROMANA DE MEDICINA DE LABORATOR, 19:227-240, SEP 2011
abstract, full text

Styrcz, A., Mrozek, J., Mazur, G.
A NEURAL-NETWORK CONTROLLED DYNAMIC EVOLUTIONARY SCHEME FOR GLOBAL MOLECULAR GEOMETRY OPTIMIZATION
INTERNATIONAL JOURNAL OF APPLIED MATHEMATICS AND COMPUTER SCIENCE, 21:559-566, SEP 2011
abstract, full text

Moldovan, C., Thompson, D.
Molecular dynamics of the "hydrophobic patch" that immobilizes hydrophobin protein HFBII on silicon
JOURNAL OF MOLECULAR MODELING, 17:2227-2235, SEP 2011
abstract, full text

Mikulska, K., Peplowski, L., Nowak, W.
Nanomechanics of Ig-like domains of human contactin (BIG-2)
JOURNAL OF MOLECULAR MODELING, 17:2313-2323, SEP 2011
abstract, full text

Izanloo, C., Parsafar, G.A., Abroshan, H., Akbarzade, H.
Calculation of Melting Temperature and Transition Curve for Dickerson DNA Dodecamer on the Basis of Configurational Entropy, Hydrogen Bonding Energy, and Heat Capacity: A Molecular Dynamics Simulation Study
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 8:708-716, SEP 2011
abstract, full text

Vazquez, N., Schmeisser, H., Dolan, M.A., Bekisz, J., Zoon, K.C., Wahl, S.M.
Structural variants of IFN alpha preferentially promote antiviral functions
BLOOD, 118:2567-2577, SEP 1 2011
abstract, full text

Robinson, D., Besley, N.A., O'Shea, P., Hirst, J.D.
Water Order Profiles on Phospholipid/Cholesterol Membrane Bilayer Surfaces
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2613-2618, SEP 2011
abstract, full text

Pietropaolo, A., Branduardi, D., Bonomi, M., Parrinello, M.
A Chirality-Based Metrics for Free-Energy Calculations in Biomolecular Systems
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2627-2637, SEP 2011
abstract, full text

Da Silva, L.P., Da Silva, J.C.G.E.
Theoretical Modulation of the Color of Light Emitted by Firefly Oxyluciferin
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2654-2663, SEP 2011
abstract, full text

Vetter, J.S., Glassbrook, R., Dongarra, J., Schwan, K., Loftis, B., McNally, S., Meredith, J., Rogers, J., Roth, P., Spafford, K., Yalamanchili, S.
KEENELAND: BRINGING HETEROGENEOUS GPU COMPUTING TO THE COMPUTATIONAL SCIENCE COMMUNITY
COMPUTING IN SCIENCE & ENGINEERING, 13:90-95, SEP-OCT 2011
full text

Balaeff, A., Craig, S.L., Beratan, D.N.
B-DNA to Zip-DNA: Simulating a DNA Transition to a Novel Structure with Enhanced Charge-Transport Characteristics
JOURNAL OF PHYSICAL CHEMISTRY A, 115:9377-9391, SEP 1 2011
abstract, full text

Oteri, F., Falconi, M., Chillemi, G., Andersen, F.F., Oliveira, C.L.P., Pedersen, J.S., Knudsen, B.R., Desideri, A.
Simulative Analysis of a Truncated Octahedral DNA Nanocage Family Indicates the Single-Stranded Thymidine Linkers as the Major Player for the Conformational Variability
JOURNAL OF PHYSICAL CHEMISTRY C, 115:16819-16827, SEP 1 2011
abstract, full text

Montanez, M.I., Najera, F., Perez-Inestrosa, E.
NMR Studies and Molecular Dynamic Simulation of Synthetic Dendritic Antigens
POLYMERS, 3:1533-1553, SEP 2011
abstract, full text

Pittala, V., Siracusa, M.A., Modica, M.N., Salerno, L., Pedretti, A., Vistoli, G., Cagnotto, A., Mennini, T., Romeo, G.
Synthesis and molecular modeling of 1H-pyrrolopyrimidine-2,4-dione derivatives as ligands for the alpha(1)-adrenoceptors
BIOORGANIC & MEDICINAL CHEMISTRY, 19:5260-5276, SEP 1 2011
abstract, full text

Kostyuchenko, V.A., Jakana, J., Liu, X.A., Haddow, A.D., Aung, M., Weaver, S.C., Chiu, W., Lok, S.M.
The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions
JOURNAL OF VIROLOGY, 85:9327-9333, SEP 2011
abstract, full text

Sapay, N., Cabannes, E., Petitou, M., Imberty, A.
Molecular modeling of the interaction between heparan sulfate and cellular growth factors: Bringing pieces together
GLYCOBIOLOGY, 21:1181-1193, SEP 2011
abstract, full text

Morozov, I.V., Valuev, I.A.
Automatic distributed workflow generation with GridMD library
COMPUTER PHYSICS COMMUNICATIONS, 182:2052-2058, SEP 2011
abstract, full text

Rezende, M.C., Mascayano, C., Briones, L., Aliaga, C.
Sensing different micellar microenvironments with solvatochromic dyes of variable lipophilicity
DYES AND PIGMENTS, 90:219-224, SEP 2011
abstract, full text

Vukovic, L., Khatib, F.A., Drake, S.P., Madriaga, A., Brandenburg, K.S., Kral, P., Onyuksel, H.
Structure and Dynamics of Highly PEG-ylated Sterically Stabilized Micelles in Aqueous Media
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13481-13488, AUG 31 2011
abstract, full text

Nishima, W., Kanamaru, S., Arisaka, F., Kitao, A.
Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13571-13576, AUG 31 2011
abstract, full text

Mao, D.B., Lu, S.Q., Li, N., Zhang, Y., Long, M.
Conformational Stability Analyses of Alpha Subunit I Domain of LFA-1 and Mac-1
PLOS ONE, 6: Art. No. e24188, AUG 31 2011
abstract, full text

Wedberg, R., O'Connell, J.P., Peters, G.H., Abildskov, J.
Pair correlation function integrals: Computation and use
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 084113, AUG 28 2011
abstract, full text

Thota, A., Luckow, A., Jha, S.
Efficient large-scale replica-exchange simulations on production infrastructure
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369:3318-3335, AUG 28 2011
abstract, full text

Zasada, S.J., Haidar, A.N., Coveney, P.V.
On the usability of grid middleware and security mechanisms
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 369:3413-3428, AUG 28 2011
abstract, full text

Morishita, M., di Luccio, E.
Structural insights into the regulation and the recognition of histone marks by the SET domain of NSD1
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 412:214-219, AUG 26 2011
abstract, full text

Legrand, B., Giudice, E., Nicolas, A., Delalande, O., Le Rumeur, E.
Computational Study of the Human Dystrophin Repeats: Interaction Properties and Molecular Dynamics
PLOS ONE, 6: Art. No. e23819, AUG 25 2011
abstract, full text

van Hoof, B., Markvoort, A.J., van Santen, R.A., Hilbers, P.A.J.
The CUMULUS Coarse Graining Method: Transferable Potentials for Water and Solutes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10001-10012, AUG 25 2011
abstract, full text

Anzini, M., Valenti, S., Braile, C., Cappelli, A., Vomero, S., Acaro, S., Ortuso, F., Marinelli, L., Limongelli, V., Novellino, E., Betti, L., Giannaccini, G., Lucacchini, A., Daniele, S., Martini, C., Ghelardini, C., Mannelli, L.D., Giorgi, G., Mascia, M.P., Biggio, G.
New Insight into the Central Benzodiazepine Receptor-Ligand Interactions: Design, Synthesis, Biological Evaluation, and Molecular Modeling of 3-Substituted 6-Phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and Related Compounds
JOURNAL OF MEDICINAL CHEMISTRY, 54:5694-5711, AUG 25 2011
abstract, full text

Centrone, A., Santiso, E.E., Hatton, T.A.
Separation of Chemical Reaction Intermediates by Metal-Organic Frameworks
SMALL, 7:2356-2364, AUG 22 2011
abstract, full text

Bellesia, G., Chundawat, S.P.S., Langan, P., Dale, B.E., Gnanakaran, S.
Probing the Early Events Associated with Liquid Ammonia Pretreatment of Native Crystalline Cellulose
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9782-9788, AUG 18 2011
abstract, full text

Raghuraman, A., Ko, E., Perez, L.M., Ioerger, T.R., Burgess, K.
Pyrrolinone-Pyrrolidine Oligomers as Universal Peptidomimetics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12350-12353, AUG 17 2011
abstract, full text

Wang, J., Ma, C.L., Fiorin, G., Carnevale, V., Wang, T., Hu, F.H., Lamb, R.A., Pinto, L.H., Hong, M., Kein, M.L., DeGrado, W.F.
Molecular Dynamics Simulation Directed Rational Design of Inhibitors Targeting Drug-Resistant Mutants of Influenza A Virus M2
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12834-12841, AUG 17 2011
abstract, full text

ElSawy, K.M., Caves, L.S.D., Twarock, R.
On the Origin of Order in the Genome Organization of ssRNA Viruses
BIOPHYSICAL JOURNAL, 101:774-780, AUG 17 2011
abstract, full text

Lee, T.S., Kantarjian, H., Ma, W.L., Yeh, C.H., Giles, F., Albitar, M.
Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling
PLOS ONE, 6: Art. No. e23396, AUG 17 2011
abstract, full text

Grasso, G.I., Arena, G., Bellia, F., Maccarrone, G., Parrinello, M., Pietropaolo, A., Vecchio, G., Rizzarelli, E.
Intramolecular Weak Interactions in the Thermodynamic Stereoselectivity of Copper(II) Complexes with Carnosine-Trehalose Conjugates
CHEMISTRY-A EUROPEAN JOURNAL, 17:9448-9455, AUG 16 2011
abstract, full text

Liu, L.P., Ghosh, N., Slivka, P.F., Fiorini, Z., Hutchinson, M.R., Watkins, L.R., Yin, H.
An MD2 Hot-Spot-Mimicking Peptide that Suppresses TLR4-Mediated Inflammatory Response in vitro and in vivo
CHEMBIOCHEM, 12:1827-1831, AUG 16 2011
full text

Chen, M.H., Sandberg, D.J., Babu, K.R., Bubis, J., Surya, A., Ramos, L.S., Zapata, H.J., Galan, J.F., Sandberg, M.N., Birge, R.R., Knox, B.E.
Conserved Residues in the Extracellular Loops of Short-Wavelength Cone Visual Pigments
BIOCHEMISTRY, 50:6763-6773, AUG 16 2011
abstract, full text

Wan, S.Z., Coveney, P.V.
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 8:1114-1127, AUG 7 2011
abstract, full text

Louet, M., Perahia, D., Martinez, J., Floquet, N.
A Concerted Mechanism for Opening the GDP Binding Pocket and Release of the Nucleotide in Hetero-Trimeric G-Proteins
JOURNAL OF MOLECULAR BIOLOGY, 411:298-312, AUG 5 2011
abstract, full text

Manji, S.S.M., Miller, K.A., Williams, L.H., Andreasen, L., Siboe, M., Rose, E., Bahlo, M., Kuiper, M., Dahl, H.H.M.
An ENU-Induced Mutation of Cdh23 Causes Congenital Hearing Loss, but No Vestibular Dysfunction, in Mice
AMERICAN JOURNAL OF PATHOLOGY, 179:903-914, AUG 2011
abstract, full text

Watanabe, H., Suzuki, M., Ito, N.
Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems
PROGRESS OF THEORETICAL PHYSICS, 126:203-235, AUG 2011
abstract, full text

Pietra, F.
On the Egress of Carbon Monoxide from Myoglobin
CHEMISTRY & BIODIVERSITY, 8:1410-1421, AUG 2011
abstract, full text

Maeda, S., Morokuma, K.
Finding Reaction Pathways of Type A+B -> X: Toward Systematic Prediction of Reaction Mechanisms
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2335-2345, AUG 2011
abstract, full text

Romo, T.D., Grossfield, A.
Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2464-2472, AUG 2011
abstract, full text

Srinivas, G., Cheng, X.L., Smith, J.C.
A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2539-2548, AUG 2011
abstract, full text

Cojocaru, V., Balali-Mood, K., Sansom, M.S.P., Wade, R.C.
Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002152, AUG 2011
abstract, full text

Matts, R.L., Dixit, A., Peterson, L.B., Sun, L., Voruganti, S., Kalyanaraman, P., Hartson, S.D., Verkhivker, G.M., Blagg, B.S.J.
Elucidation of the Hsp90 C-Terminal Inhibitor Binding Site
ACS CHEMICAL BIOLOGY, 6:800-807, AUG 2011
abstract, full text

Papadopoulos, P.M.
Extending clusters to Amazon EC2 using the Rocks toolkit
INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS, 25:317-327, AUG 2011
abstract, full text

Glykos, N.M.
On the application of structure-specific bulk-solvent models
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 67:739-741, AUG 2011
abstract, full text

Knapp, B., Frantal, S., Cibena, M., Schreiner, W., Bauer, P.
Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?
JOURNAL OF COMPUTATIONAL BIOLOGY, 18:997-1005, AUG 2011
abstract, full text

Du, H.B., Qian, X.H.
Molecular Dynamics Simulations of PNIPAM-co-PEGMA Copolymer Hydrophilic to Hydrophobic Transition in NaCl Solution
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 49:1112-1122, AUG 1 2011
abstract, full text

Pedretti, A., De Luca, L., Marconi, C., Regazzoni, L., Aldini, G., Vistoli, G.
Fragmental modeling of hPepT2 and analysis of its binding features by docking studies and pharmacophore mapping
BIOORGANIC & MEDICINAL CHEMISTRY, 19:4544-4551, AUG 2011
abstract, full text

Lin, T.L., Song, G.
Efficient mapping of ligand migration channel networks in dynamic proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2475-2490, AUG 2011
abstract, full text

Venkatesan, B.M., Polans, J., Comer, J., Sridhar, S., Wendell, D., Aksimentiev, A., Bashir, R.
Lipid bilayer coated Al2O3 nanopore sensors: towards a hybrid biological solid-state nanopore
BIOMEDICAL MICRODEVICES, 13:671-682, AUG 2011
abstract, full text

Caulfield, T.R.
Inter-ring rotation of apolipoprotein A-I protein monomers for the double-belt model using biased molecular dynamics
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:1006-1014, AUG 2011
abstract, full text

Klenin, K., Strode, B., Wales, D.J., Wenzel, W.
Modelling proteins: Conformational sampling and reconstruction of folding kinetics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:977-1000, AUG 2011
abstract, full text

McGeagh, J.D., Ranaghan, K.E., Mulholland, A.J.
Protein dynamics and enzyme catalysis: Insights from simulations
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:1077-1092, AUG 2011
abstract, full text

Romo, T.D., Bradney, L.A., Greathouse, D.V., Grossfield, A.
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2019-2030, AUG 2011
abstract, full text

Guerry, P., Herrmann, T.
Advances in automated NMR protein structure determination
QUARTERLY REVIEWS OF BIOPHYSICS, 44:257-309, AUG 2011
abstract, full text

Boresch, S., Bruckner, S.
Avoiding the van der Waals Endpoint Problem Using Serial Atomic Insertion
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2449-2458, AUG 2011
abstract, full text

Makowski, L., Gore, D., Mandava, S., Minh, D., Park, S., Rodi, D.J., Fischetti, R.F.
X-ray Solution Scattering Studies of the Structural Diversity Intrinsic to Protein Ensembles
BIOPOLYMERS, 95:531-542, AUG 2011
abstract, full text

Shintani, M., Yoshida, K., Sakuraba, S., Nakahara, M., Matubayasi, N.
NMR-NOE and MD Simulation Study on Phospholipid Membranes: Dependence on Membrane Diameter and Multiple Time Scale Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9106-9115, JUL 28 2011
abstract, full text

Karachevtsev, M.V., Karachevtsev, V.A.
Peculiarities of Homooligonucleotides Wrapping around Carbon Nanotubes: Molecular Dynamics Modeling
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9271-9279, JUL 28 2011
abstract, full text

Chundawat, S.P.S., Bellesia, G., Uppugundla, N., Sousa, L.D., Gao, D.H., Cheh, A.M., Agarwal, U.P., Bianchetti, C.M., Phillips, G.N., Langan, P., Balan, V., Gnanakaran, S., Dale, B.E.
Restructuring the Crystalline Cellulose Hydrogen Bond Network Enhances Its Depolymerization Rate
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:11163-11174, JUL 27 2011
abstract, full text

Rivalta, I., Amin, M., Luber, S., Vassiliev, S., Pokhrel, R., Umena, Y., Kawakami, K., Shen, J.R., Kamiya, N., Bruce, D., Brudvig, G.W., Gunner, M.R., Batista, V.S.
Structural-Functional Role of Chloride in Photosystem II
BIOCHEMISTRY, 50:6312-6315, JUL 26 2011
abstract, full text

He, Y.H., Scheicher, R.H., Grigoriev, A., Ahuja, R., Long, S.B., Huo, Z.L., Liu, M.
Enhanced DNA Sequencing Performance Through Edge-Hydrogenation of Graphene Electrodes
ADVANCED FUNCTIONAL MATERIALS, 21:2674-2679, JUL 22 2011
abstract, full text

Bond, P.J., Faraldo-Gomez, J.D.
Molecular Mechanism of Selective Recruitment of Syk Kinases by the Membrane Antigen-Receptor Complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:25872-25881, JUL 22 2011
abstract, full text

Ufimtsev, I.S., Luehr, N., Martinez, T.J.
Charge Transfer and Polarization in Solvated Proteins from Ab Initio Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1789-1793, JUL 21 2011
abstract, full text

Carr, R., Comer, J., Ginsberg, M.D., Aksimentiev, A.
Microscopic Perspective on the Adsorption Isotherm of a Heterogeneous Surface
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1804-1807, JUL 21 2011
abstract, full text

Zanuy, D., Hamley, I.W., Aleman, C.
Modeling the Tetraphenylalanine-PEG Hybrid Amphiphile: From DFT Calculations on the Peptide to Molecular Dynamics Simulations on the Conjugate
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8937-8946, JUL 21 2011
abstract, full text

Watt, E.D., Rivalta, I., Whittier, S.K., Batista, V.S., Loria, J.P.
Reengineering Rate-Limiting, Millisecond Enzyme Motions by Introduction of an Unnatural Amino Acid
BIOPHYSICAL JOURNAL, 101:411-420, JUL 20 2011
abstract, full text

Liu, J.J., Stockton, R.A., Gingras, A.R., Ablooglu, A.J., Han, J., Bobkov, A.A., Ginsberg, M.H.
A mechanism of Rap1-induced stabilization of endothelial cell-cell junctions
MOLECULAR BIOLOGY OF THE CELL, 22:2509-2519, JUL 15 2011
abstract, full text

Beretta, G., Artali, R., Facino, R.M., Gelmini, F.
An analytical and theoretical approach for the profiling of the antioxidant activity of essential oils: The case of Rosmarinus officinalis L.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 55:1255-1264, JUL 15 2011
abstract, full text

Denning, E.J., Priyakumar, U.D., Nilsson, L., Mackerell, A.D.
Impact of 2 '-Hydroxyl Sampling on the Conformational Properties of RNA: Update of the CHARMM All-Atom Additive Force Field for RNA
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1929-1943, JUL 15 2011
abstract, full text

Andersson, M., Freites, J.A., Tobias, D.J., White, S.H.
Structural Dynamics of the S4 Voltage-Sensor Helix in Lipid Bilayers Lacking Phosphate Groups
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8732-8738, JUL 14 2011
abstract, full text

Banerjee, R., Reynolds, N.M., Yadavalli, S.S., Rice, C., Roy, H., Banerjee, P., Alexander, R.W., Ibba, M.
Mitochondrial Aminoacyl-tRNA Synthetase Single-Nucleotide Polymorphisms That Lead to Defects in Refolding but Not Aminoacylation
JOURNAL OF MOLECULAR BIOLOGY, 410:280-293, JUL 8 2011
abstract, full text

Gamini, R., Sotomayor, M., Chipot, C., Schulten, K.
Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance
BIOPHYSICAL JOURNAL, 101:80-89, JUL 6 2011
abstract, full text, TCBG publications

Hamaneh, M.B., Zhang, L.Q., Buck, M.
A Direct Coupling between Global and Internal Motions in a Single Domain Protein? MD Investigation of Extreme Scenarios
BIOPHYSICAL JOURNAL, 101:196-204, JUL 6 2011
abstract, full text

Rommel, J.B., Kastner, J.
The Fragmentation-Recombination Mechanism of the Enzyme Glutamate Mutase Studied by QM/MM Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:10195-10203, JUL 6 2011
abstract, full text

Cristiani, A., Costa, G., Cozza, G., Meggio, F., Scapozza, L., Moro, S.
The Role of the N-Terminal Domain in the Regulation of the "Constitutively Active" Conformation of Protein Kinase CK2 alpha: Insight from a Molecular Dynamics Investigation
CHEMMEDCHEM, 6:1207-1216, JUL 4 2011
abstract, full text

Bettinelli, I., Graziani, D., Marconi, C., Pedretti, A., Vistoli, G.
The Approach of Conformational Chimeras to Model the Role of Proline-Containing Helices on GPCR Mobility: the Fertile Case of Cys-LTR1
CHEMMEDCHEM, 6:1217-1227, JUL 4 2011
abstract, full text

Kralikova, S., Budesinsky, M., Barvik, I., Masojidkova, M., Tocik, Z., Rosenberg, I.
SYNTHESIS AND PROPERTIES OF ApA ANALOGUES WITH SHORTENED PHOSPHONATE INTERNUCLEOTIDE LINKAGE
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 30:524-543, JUL-SEP 2011
abstract, full text

Amarasinghe, P.M., Anandarajah, A.
Influence of fabric variables on clay-water-air capillary meniscus
CANADIAN GEOTECHNICAL JOURNAL, 48:987-995, JUL 2011
abstract, full text

Wang, L.Z., Chen, D., Deng, Z., Huang, F.
Large scale distributed visualization on computational Grids: A review
COMPUTERS & ELECTRICAL ENGINEERING, 37:403-416, JUL 2011
abstract, full text

Parker, L.J., Italiano, L.C., Morton, C.J., Hancock, N.C., Ascher, D.B., Aitken, J.B., Harris, H.H., Campomanes, P., Rothlisberger, U., De Luca, A., Lo Bello, M., Ang, W.H., Dyson, P.J., Parker, M.W.
Studies of Glutathione Transferase P1-1 Bound to a Platinum(IV)-Based Anticancer Compound Reveal the Molecular Basis of Its Activation
CHEMISTRY-A EUROPEAN JOURNAL, 17:7806-7816, JUL 2011
abstract, full text

Romanowska, J., McCammon, J.A., Trylska, J.
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002099, JUL 2011
abstract, full text

Iacovache, I., Degiacomi, M.T., Pernot, L., Ho, S., Schiltz, M., Dal Peraro, M., van der Goot, F.G.
Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLOS PATHOGENS, 7: Art. No. e1002135, JUL 2011
abstract, full text

Kim, S.K., Huh, J., Kim, S.Y., Byun, Y., Lee, D.Y., Moon, H.T.
Physicochemical Conjugation with Deoxycholic Acid and Dimethylsulfoxide for Heparin Oral Delivery
BIOCONJUGATE CHEMISTRY, 22:1451-1458, JUL 2011
abstract, full text

Soriano-Ursua, M.A., Ocampo-Lopez, J.O., Ocampo-Mendoza, K., Trujillo-Ferrara, J.G., Correa-Basurto, J.
Theoretical study of 3-D molecular similarity and ligand binding modes of orthologous human and rat D-2 dopamine receptors
COMPUTERS IN BIOLOGY AND MEDICINE, 41:537-545, JUL 2011
abstract, full text

Splettstoesser, T., Holmes, K.C., Noe, F., Smith, J.C.
Structural modeling and molecular dynamics simulation of the actin filament
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2033-2043, JUL 2011
abstract, full text

Janosi, L., Keer, H., Cogdell, R.J., Ritz, T., Kosztin, I.
In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2306-2315, JUL 2011
abstract, full text

Lawrenz, M., Baron, R., Wang, Y., McCammon, J.A.
Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2224-2232, JUL 2011
abstract, full text

Perez-Siles, G., Morreale, A., Leo-Macias, A., Pita, G., Ortiz, A.R., Aragon, C., Lopez-Corcuera, B.
Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2
JOURNAL OF NEUROCHEMISTRY, 118:195-204, JUL 2011
abstract, full text

Savol, A.J., Burger, V.M., Agarwal, P.K., Ramanathan, A., Chennubhotla, C.S.
QAARM: quasi-anharmonic autoregressive model reveals molecular recognition pathways in ubiquitin
BIOINFORMATICS, 27:I52-I60, JUL 1 2011
abstract, full text

Hubner, M., Dixit, A., Mou, T.C., Lushington, G.H., Pinto, C., Gille, A., Geduhn, J., Konig, B., Sprang, S.R., Seifert, R.
Structural Basis for the High-Affinity Inhibition of Mammalian Membranous Adenylyl Cyclase by 2 ',3 '-O-(N-Methylanthraniloyl)-Inosine 5 '-Triphosphate
MOLECULAR PHARMACOLOGY, 80:87-96, JUL 2011
abstract, full text

Palmai, Z., Perahia, D., Lionne, C., Fidy, J., Balog, E., Chaloin, L.
Ligand chirality effects on the dynamics of human 3-phosphoglycerate kinase: Comparison between D- and L-nucleotides
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 511:88-100, JUL 2011
abstract, full text

Beassoni, P.R., Otero, L.H., Boetsch, C., Domenech, C.E., Gonzalez-Nilo, F.D., Lisa, A.T.
Site-directed mutations and kinetic studies show key residues involved in alkylammonium interactions and reveal two sites for phosphorylcholine in Pseudomonas aeruginosa phosphorylcholine phosphatase
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:858-863, JUL 2011
abstract, full text

Tavoosi, N., Davis-Harrison, R.L., Pogorelov, T.V., Ohkubo, Y.Z., Arcario, M.J., Clay, M.C., Rienstra, C.M., Tajkhorshid, E., Morrissey, J.H.
Molecular Determinants of Phospholipid Synergy in Blood Clotting
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:23247-23253, JUL 1 2011
abstract, full text

Jevnikar, Z., Obermajer, N., Doljak, B., Turk, S., Gobec, S., Svajger, U., Hailfinger, S., Thome, M., Kos, J.
Cathepsin X cleavage of the beta(2) integrin regulates talin-binding and LFA-1 affinity in T cells
JOURNAL OF LEUKOCYTE BIOLOGY, 90:99-109, JUL 2011
abstract, full text

Sokkar, P., Mohandass, S., Ramachandran, M.
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking
JOURNAL OF MOLECULAR MODELING, 17:1565-1577, JUL 2011
abstract, full text

Khrenova, M., Domratcheva, T., Grigorenko, B., Nemukhin, A.
Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1
JOURNAL OF MOLECULAR MODELING, 17:1579-1586, JUL 2011
abstract, full text

Strunk, T., Hamacher, K., Hoffgaard, F., Engelhardt, H., Zillig, M.D., Faist, K., Wenzel, W., Pfeifer, F.
Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo
MOLECULAR MICROBIOLOGY, 81:56-68, JUL 2011
abstract, full text

Mayo, D., Zhou, A., Sahu, I., McCarrick, R., Walton, P., Ring, A., Troxel, K., Coey, A., Hawn, J., Emwas, A.H., Lorigan, G.A.
Probing the structure of membrane proteins with electron spin echo envelope modulation spectroscopy
PROTEIN SCIENCE, 20:1100-1104, JUL 2011
abstract, full text

Raliou, M., Grauso, M., Hoffmann, B., Schlegel-Le-Poupon, C., Nespoulous, C., Debat, H., Belloir, C., Wiencis, A., Sigoillot, M., Bano, S.P., Trotier, D., Pernollet, J.C., Montmayeur, J.P., Faurion, A., Briand, L.
Human Genetic Polymorphisms in T1R1 and T1R3 Taste Receptor Subunits Affect Their Function
CHEMICAL SENSES, 36:527-537, JUL 2011
abstract, full text

Narayanan, S.S., Sokkar, P., Ramachandran, M., Nampoothiri, K.M.
Glycine in the conserved motif III modulates the thermostability and oxidative stress resistance of peptide deformylase in Mycobacterium tuberculosis
FEMS MICROBIOLOGY LETTERS, 320:40-47, JUL 2011
abstract, full text

Wu, B.J., Xin, B., Jin, M., Wei, T.D., Bai, Z.L.
Comparative and phylogenetic analyses of three TIR domain-containing adaptors in metazoans: Implications for evolution of TLR signaling pathways
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY, 35:764-773, JUL 2011
abstract, full text

Kleinekathofer, U., Isralewitz, B., Dittrich, M., Schulten, K.
Domain Motion of Individual F-1-ATPase beta-Subunits during Unbiased Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 115:7267-7274, JUN 30 2011
abstract, full text, TCBG publications

Schulz, R., Vargiu, A.V., Ruggerone, P., Kleinekathofer, U.
Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8278-8287, JUN 30 2011
abstract, full text

Bravaya, K.B., Khrenova, M.G., Grigorenko, B.L., Nemukhin, A.V., Krylov, A.I.
Effect of Protein Environment on Electronically Excited and Ionized States of the Green Fluorescent Protein Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8296-8303, JUN 30 2011
abstract, full text

White, K.H., Orzechowski, M., Fourmy, D., Visscher, K.
Mechanical Unfolding of the Beet Western Yellow Virus-1 Frameshift Signal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9775-9782, JUN 29 2011
abstract, full text

Kotsikorou, E., Madrigal, K.E., Hurst, D.P., Sharir, H., Lynch, D.L., Heynen-Genel, S., Milan, L.B., Chung, T.D.Y., Setzman, H.H., Bai, Y.S., Caron, M.G., Barak, L., Abood, M.E., Reggio, P.H.
Identification of the GPR55 Agonist Binding Site Using a Novel Set of High-Potency GPR55 Selective Ligands
BIOCHEMISTRY, 50:5633-5647, JUN 28 2011
abstract, full text

Lee, W., Luckner, S.R., Kisker, C., Tonge, P.J., Engels, B.
Elucidation of the Protonation States of the Catalytic Residues in mtKasA: Implications for Inhibitor Design
BIOCHEMISTRY, 50:5743-5756, JUN 28 2011
abstract, full text

Truong, K., Su, Y., Song, J., Chen, Y.
Entropy-Driven Mechanism of an E3 Ligase
BIOCHEMISTRY, 50:5757-5766, JUN 28 2011
abstract, full text

Furini, S., Domene, C.
Selectivity and Permeation of Alkali Metal Ions in K+-channels
JOURNAL OF MOLECULAR BIOLOGY, 409:867-878, JUN 24 2011
abstract, full text

Bleicher, L., Prates, E.T., Gomes, T.C.F., Silveira, R.L., Nascimento, A.S., Rojas, A.L., Golubev, A., Martinez, L., Skaf, M.S., Polikarpov, I.
Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7940-7949, JUN 23 2011
abstract, full text

Liu, Y.X., Hsin, J., Kim, H., Selvin, P.R., Schulten, K.
Extension of a Three-Helix Bundle Domain of Myosin VI and Key Role of Calmodulins
BIOPHYSICAL JOURNAL, 100:2964-2973, JUN 22 2011
abstract, full text, TCBG publications

Jones, P.M., George, A.M.
Molecular-Dynamics Simulations of the ATP/apo State of a Multidrug ATP-Binding Cassette Transporter Provide a Structural and Mechanistic Basis for the Asymmetric Occluded State
BIOPHYSICAL JOURNAL, 100:3025-3034, JUN 22 2011
abstract, full text

Frauer, C., Hoffmann, T., Bultmann, S., Casa, V., Cardoso, M.C., Antes, I., Leonhardt, H.
Recognition of 5-Hydroxymethylcytosine by the Uhrf1 SRA Domain
PLOS ONE, 6: Art. No. e21306, JUN 22 2011
abstract, full text

Buch, I., Giorgino, T., De Fabritiis, G.
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:10184-10189, JUN 21 2011
abstract, full text

Ziemys, A., Kojic, M., Milosevic, M., Kojic, N., Hussain, F., Ferrari, M., Grattoni, A.
Hierarchical modeling of diffusive transport through nanochannels by coupling molecular dynamics with finite element method
JOURNAL OF COMPUTATIONAL PHYSICS, 230:5722-5731, JUN 20 2011
abstract, full text

Pan, Z.Z., McCullagh, M., Schatz, G.C., Lewis, F.D.
Conformational Control of Thymine Photodimerization in Purine-Containing Trinucleotides
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1432-1438, JUN 16 2011
abstract, full text

Rose, F., Hodak, M., Bernholc, J.
Mechanism of copper(II)-induced misfolding of Parkinson's disease protein
SCIENTIFIC REPORTS, 1: Art. No. 11, JUN 14 2011
abstract, full text

Tian, J.H., Garcia, A.E.
Simulations of the confinement of ubiquitin in self-assembled reverse micelles
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 225101, JUN 14 2011
abstract, full text

Miller, Y., Ma, B.Y., Nussinov, R.
Synergistic Interactions between Repeats in Tau Protein and A beta Amyloids May Be Responsible for Accelerated Aggregation via Polymorphic States
BIOCHEMISTRY, 50:5172-5181, JUN 14 2011
abstract, full text

Dixit, P.D., Asthagiri, D.
An Elastic-Network-Based Local Molecular Field Analysis of Zinc Finger Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7374-7382, JUN 9 2011
abstract, full text

Schneider, C.P., Shukla, D., Trout, B.L.
Arginine and the Hofmeister Series: The Role of Ion-Ion Interactions in Protein Aggregation Suppression
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7447-7458, JUN 9 2011
abstract, full text

Serrano, A.L., Tucker, M.J., Gai, F.
Direct Assessment of the alpha-Helix Nucleation Time
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7472-7478, JUN 9 2011
abstract, full text

Tanner, D.E., Ma, W., Chen, Z.Z., Schulten, K.
Theoretical and Computational Investigation of Flagellin Translocation and Bacterial Flagellum Growth
BIOPHYSICAL JOURNAL, 100:2548-2556, JUN 8 2011
abstract, full text, TCBG publications

Sun, C.B., Tang, T., Uludag, H., Cuervo, J.E.
Molecular Dynamics Simulations of DNA/PEI Complexes: Effect of PEI Branching and Protonation State
BIOPHYSICAL JOURNAL, 100:2754-2763, JUN 8 2011
abstract, full text

Falvo, C., Meier, C.
A fluctuating quantum model of the CO vibration in carboxyhemoglobin
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 214106, JUN 7 2011
abstract, full text

Yu, X., Zheng, J.
Polymorphic Structures of Alzheimer's beta-Amyloid Globulomers
PLOS ONE, 6: Art. No. e20575, JUN 7 2011
abstract, full text

Matsushita, S., Inoue, Y., Hojo, M., Sokabe, M., Adachi, T.
Effect of tensile force on the mechanical behavior of actin filaments
JOURNAL OF BIOMECHANICS, 44:1776-1781, JUN 3 2011
abstract, full text

Zomot, E., Bahar, I.
Protonation of Glutamate 208 Induces the Release of Agmatine in an Outward-facing Conformation of an Arginine/Agmatine Antiporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:19693-19701, JUN 3 2011
abstract, full text

Dai, Z.W., Ling, J., Huang, X.J., Wan, L.S., Xu, Z.K.
Molecular Simulation on the Interactions of Water with Polypropylene Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 115:10702-10708, JUN 2 2011
abstract, full text

Balog, E., Perahia, D., Smith, J.C., Merzel, F.
Vibrational Softening of a Protein on Ligand Binding
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6811-6817, JUN 2 2011
abstract, full text

Madsen, J.J., Linderoth, L., Subramanian, A.K., Andresen, T.L., Peters, G.H.
Secretory Phospholipase A(2) Activity toward Diverse Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6853-6861, JUN 2 2011
abstract, full text

Arcario, M.J., Ohkubo, Y.Z., Tajkhorshid, E.
Capturing Spontaneous Partitioning of Peripheral Proteins Using a Biphasic Membrane-Mimetic Model
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7029-7037, JUN 2 2011
abstract, full text

Verde, A.V., Campen, R.K.
Disaccharide Topology Induces Slowdown in Local Water Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7069-7084, JUN 2 2011
abstract, full text

Ivetac, A., McCammon, J.A.
Molecular Recognition in the Case of Flexible Targets
CURRENT PHARMACEUTICAL DESIGN, 17:1663-1671, JUN 2011
abstract, full text

Li, C., Shen, J., Li, W.H., Lu, C.H., Liu, G.X., Tang, Y.
Possible ligand release pathway of dipeptidyl peptidase IV investigated by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1800-1809, JUN 2011
abstract, full text

Kim, S.K., Riley, L., Abrol, R., Jacobson, K.A., Goddard, W.A.
Predicted structures of agonist and antagonist bound complexes of adenosine A(3) receptor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1878-1897, JUN 2011
abstract, full text

Dong, H., Zhou, H.X.
Atomistic mechanism for the activation and desensitization of an AMPA-subtype glutamate receptor
NATURE COMMUNICATIONS, 2: Art. No. 354, JUN 2011
abstract, full text

Cristiani, A., Brisotto, N., Cedrati, F.C., Floris, M., Scapozza, L., Moro, S.
ClickMD: an intuitive web-oriented molecular dynamics platform
FUTURE MEDICINAL CHEMISTRY, 3:923-931, JUN 2011
abstract, full text

Liao, C.Z., Sitzmann, M., Pugliese, A., Nicklaus, M.C.
Software and resources for computational medicinal chemistry
FUTURE MEDICINAL CHEMISTRY, 3:1057-1085, JUN 2011
abstract, full text

Bourne, J.W., Torzilli, P.A.
Molecular simulations predict novel collagen conformations during cross-link loading
MATRIX BIOLOGY, 30:356-360, JUN 2011
abstract, full text

Baker, J.A., Hirst, J.D.
Molecular Dynamics Simulations Using Graphics Processing Units
MOLECULAR INFORMATICS, 30:498-504, JUN 2011
abstract, full text

Skulachev, M.V., Antonenko, Y.N., Anisimov, V.N., Chernyak, B.V., Cherepanov, D.A., Chistyakov, V.A., Egorov, M.V., Kolosova, N.G., Korshunova, G.A., Lyamzaev, K.G., Plotnikov, E.Y., Roginsky, V.A., Savchenko, A.Y., Severina, I.I., Severin, F.F., Shkurat, T.P., Tashlitsky, V.N., Shidlovsky, K.M., Vyssokikh, M.Y., Zamyatnin, A.A., Zorov, D.B., Skulachev, V.P.
Mitochondrial-Targeted Plastoquinone Derivatives. Effect on Senescence and Acute Age-Related Pathologies
CURRENT DRUG TARGETS, 12:800-826, JUN 2011
abstract, full text

Shin, A.J., Telesco, S.E., Choi, S.H., Lemmon, M.A., Radhakrishnan, R.
Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases
BIOCHEMICAL JOURNAL, 436:241-251, JUN 1 2011
abstract, full text

Hernandez-Ortega, A., Borrelli, K., Ferreira, P., Medina, M., Martinez, A.T., Guallar, V.
Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase
BIOCHEMICAL JOURNAL, 436:341-350, JUN 1 2011
abstract, full text

Liu, L., Liu, X.F., Gong, J.Y., Jiang, H.L., Li, H.L.
Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1595-1603, JUN 2011
abstract, full text

Grouleff, J., Jensen, F.
Searching Peptide Conformational Space
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1783-1790, JUN 2011
abstract, full text

Moya-Garcia, A.A., Rodriguez-Agudo, D., Hayashi, H., Medina, M.A., Urdiales, J.L., Sanchez-Jimenez, F.
Analysis of Mammalian Histidine Decarboxylase Dimerization Interface Reveals an Electrostatic Hotspot Important for Catalytic Site Topology and Function
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1935-1942, JUN 2011
abstract, full text

Giorgino, T., De Fabritiis, G.
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1943-1950, JUN 2011
abstract, full text

Mangold, M., Rolland, L., Costanzo, F., Sprik, M., Sulpizi, M., Blumberger, J.
Absolute pK(a) Values and Solvation Structure of Amino Acids from Density Functional Based Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1951-1961, JUN 2011
abstract, full text

Kenzaki, H., Koga, N., Hori, N., Kanada, R., Li, W.F., Okazaki, K., Yao, X.Q., Takada, S.
CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1979-1989, JUN 2011
abstract, full text

Librando, V., Pappalardo, M.
Computational study on the interaction of a ring-hydroxylating dioxygenase from Sphingomonas CHY-1 with PAHs
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:915-919, JUN 2011
abstract, full text

Chen, C., Li, W.Z., Song, Y.C., Weng, L.D.
Structure and Kinetics of Hydrogen Bonds in Aqueous Glucose Solutions
ACTA PHYSICO-CHIMICA SINICA, 27:1372-1378, JUN 2011
abstract, full text

Dai, W.M., You, Z.L., Zhou, H., Zhang, J., Hu, Y.Q.
Structure-function relationships of the human bitter taste receptor hTAS2R1: insights from molecular modeling studies
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:229-240, JUN 2011
abstract, full text

Floquet, N., Hernandez, J.F., Boucher, J.L., Martinez, J.
L-Arginine Binding to Human Inducible Nitric Oxide Synthase: An Antisymmetric Funnel Route toward Isoform-Specific Inhibitors?
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1325-1335, JUN 2011
abstract, full text

Pan, Y.P., Nussinov, R.
The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-beta Enhanceosome Example
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002077, JUN 2011
abstract, full text

Veldhuis, N.A., Kuiper, M.J., Dobson, R.C.J., Pearson, R.B., Camakaris, J.
In silico modeling of the Menkes copper-translocating P-type ATPase 3rd metal binding domain predicts that phosphorylation regulates copper-binding
BIOMETALS, 24:477-487, JUN 2011
abstract, full text

Yokota, R., Bardhan, J.P., Knepley, M.G., Barba, L.A., Hamada, T.
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
COMPUTER PHYSICS COMMUNICATIONS, 182:1272-1283, JUN 2011
abstract, full text

Kote-Jarai, Z., Al Olama, A.A., Leongamornlert, D., Tymrakiewicz, M., Saunders, E., Guy, M., Giles, G.G., Severi, G., Southey, M., Hopper, J.L., Sit, K.C., Harris, J.M., Batra, J., Spurdle, A.B., Clements, J.A., Hamdy, F., Neal, D., Donovan, J., Muir, K., Pharoah, P.D.P., Chanock, S.J., Brown, N., Benlloch, S., Castro, E., Mahmud, N., O'Brien, L., Hall, A., Sawyer, E., Wilkinson, R., Easton, D.F., Eeles, R.A.
Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript
HUMAN GENETICS, 129:687-694, JUN 2011
abstract, full text

Yang, M.J., Zhang, X.
Molecular dynamics simulations reveal structural coordination of Ffh-FtsY heterodimer toward GTPase activation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1774-1785, JUN 2011
abstract, full text

Karthik, S., Senapati, S.
Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1830-1840, JUN 2011
abstract, full text

Prates, E.T., Souza, P.C.T., Pickholz, M., Skaf, M.S.
CHARMM-Based Parameterization of Neutral Articaine-A Widely Used Local Anesthetic
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1339-1345, JUN-JUL 2011
abstract, full text

Hansson, A., Souza, P.C.T., Silveira, R.L., Martinez, L., Skaf, M.S.
CHARMM Force Field Parameterization of Rosiglitazone
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1346-1354, JUN-JUL 2011
abstract, full text

Poghosyan, A.H., Arsenyan, L.H., Gharabekyan, H.H., Falkenhagen, S., Koetz, J., Shahinyan, A.A.
Molecular dynamics simulations of inverse sodium dodecyl sulfate (SDS) micelles in a mixed toluene/pentanol solvent in the absence and presence of poly(diallyldimethylammonium chloride) (PDADMAC)
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 358:175-181, JUN 1 2011
abstract, full text

Qu, Z.W., Zhu, H., May, V.
Vibrational Spectral Signatures of Peptide Secondary Structures: N-methylation and Side chain Hydrogen Bond in Cyclosporin A
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1500-1518, JUN 2011
abstract, full text

Riihimaki, T.A., Kukkurainen, S., Varjonen, S., Horha, J., Nyholm, T.K.M., Kulomaa, M.S., Hytonen, V.P.
Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins
PLOS ONE, 6: Art. No. e20535, MAY 31 2011
abstract, full text

Timko, J., De Castro, A., Kuyucak, S.
Ab initio calculation of the potential of mean force for dissociation of aqueous Ca-Cl
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 204510, MAY 28 2011
abstract, full text

O'Connor, J.W., Klauda, J.B.
Lipid Membranes with a Majority of Cholesterol: Applications to the Ocular Lens and Aquaporin 0
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6455-6464, MAY 26 2011
abstract, full text

Satpati, P., Clavaguera, C., Ohanessian, G., Simonson, T.
Free Energy Simulations of a GTPase: GTP and GDP Binding to Archaeal Initiation Factor 2
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6749-6763, MAY 26 2011
abstract, full text

Huang, Y.M.M., Chang, C.E.A.
Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics
BMC BIOPHYSICS, 4: Art. No. 12, MAY 25 2011
abstract, full text

Sorensen, J., Palmer, D.S., Qvist, K.B., Schiott, B.
Initial Stage of Cheese Production: A Molecular Modeling Study of Bovine and Camel Chymosin Complexed with Peptides from the Chymosin-Sensitive Region of kappa-Casein
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 59:5636-5647, MAY 25 2011
abstract, full text

Kaye, M.D., Schmalzl, K., Nibali, V.C., Tarek, M., Rheinstadter, M.C.
Ethanol enhances collective dynamics of lipid membranes
PHYSICAL REVIEW E, 83: Art. No. 050907, MAY 25 2011
abstract, full text

Schreiner, E., Trabuco, L.G., Freddolino, P.L., Schulten, K.
Stereochemical errors and their implications for molecular dynamics simulations
BMC BIOINFORMATICS, 12: Art. No. 190, MAY 23 2011
abstract, full text, TCBG publications

Makowski, L., Bardhan, J., Gore, D., Lal, J., Mandava, S., Park, S., Rodi, D.J., Ho, N.T., Ho, C., Fischetti, R.F.
WAXS Studies of the Structural Diversity of Hemoglobin in Solution
JOURNAL OF MOLECULAR BIOLOGY, 408:909-921, MAY 20 2011
abstract, full text

Stewart, M.D., Morgan, B., Massi, F., Igumenova, T.I.
Probing the Determinants of Diacylglycerol Binding Affinity in the C1B Domain of Protein Kinase C alpha
JOURNAL OF MOLECULAR BIOLOGY, 408:949-970, MAY 20 2011
abstract, full text

Jiang, J., Mukamel, S.
Probing Amyloid Fibril Growth by Two-Dimensional Near-Ultraviolet Spectroscopy
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6321-6328, MAY 19 2011
abstract, full text

Bai, Q.F., Shen, Y.L., Yao, X.J., Wang, F., Du, Y.P., Wang, Q., Jin, N.Z., Hai, J., Hu, T.J., Yang, J.B.
Modeling a New Water Channel That Allows SET9 to Dimethylate p53
PLOS ONE, 6: Art. No. e19856, MAY 19 2011
abstract, full text

Ramachandran, A., Guo, Q.J., Iqbal, S.M., Liu, Y.L.
Coarse-Grained Molecular Dynamics Simulation of DNA Trans location in Chemically Modified Nanopores
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6138-6148, MAY 19 2011
abstract, full text

Wilson, M.A., Wei, C.Y., Bjelkmar, P., Wallace, B.A., Pohorille, A.
Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance
BIOPHYSICAL JOURNAL, 100:2394-2402, MAY 18 2011
abstract, full text

Chen, P.C., Kuyucak, S.
Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints
BIOPHYSICAL JOURNAL, 100:2466-2474, MAY 18 2011
abstract, full text

Gumbart, J., Chipot, C., Schulten, K.
Free Energy of Nascent-Chain Folding in the Translocon
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:7602-7607, MAY 18 2011
abstract, full text, TCBG publications

Verde, A.V., Beltramo, P.J., Maranas, J.K.
Adsorption of Homopolypeptides on Gold Investigated Using Atomistic Molecular Dynamics
LANGMUIR, 27:5918-5926, MAY 17 2011
abstract, full text

Maekawa, H., Ballano, G., Toniolo, C., Ge, N.H.
Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains
JOURNAL OF PHYSICAL CHEMISTRY B, 115:5168-5182, MAY 12 2011
abstract, full text

Weng, L.D., Chen, C., Zuo, J.G., Li, W.Z.
Molecular Dynamics Study of Effects of Temperature and Concentration on Hydrogen-Bond Abilities of Ethylene Glycol and Glycerol: Implications for Cryopreservation
JOURNAL OF PHYSICAL CHEMISTRY A, 115:4729-4737, MAY 12 2011
abstract, full text

Ketko, M.H., Kamath, G., Potoff, J.J.
Development of an Optimized Intermolecular Potential for Sulfur Dioxide
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4949-4954, MAY 5 2011
abstract, full text

Berryman, J.T., Radford, S.E., Harris, S.A.
Systematic Examination of Polymorphism in Amyloid Fibrils by Molecular-Dynamics Simulation
BIOPHYSICAL JOURNAL, 100:2234-2242, MAY 4 2011
abstract, full text

Gonidec, M., Biagi, R., Corradini, V., Moro, F., De Renzi, V., del Pennino, U., Summa, D., Muccioli, L., Zannoni, C., Amabilino, D.B., Veciana, J.
Surface Supramolecular Organization of a Terbium(III) Double-Decker Complex on Graphite and its Single Molecule Magnet Behavior
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6603-6612, MAY 4 2011
abstract, full text

Sonntag, Y., Musgaard, M., Olesen, C., Schiott, B., Moller, J.V., Nissen, P., Thogersen, L.
Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes
NATURE COMMUNICATIONS, 2: Art. No. 304, MAY 2011
abstract, full text

Vemparala, S., Mehrotra, S., Balaram, H.
Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: A molecular dynamics and normal mode analysis study
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:630-637, MAY 2011
abstract, full text

Aprikian, P., Interlandi, G., Kidd, B.A., Le Trong, I., Tchesnokova, V., Yakovenko, O., Whitfield, M.J., Bullitt, E., Stenkamp, R.E., Thomas, W.E., Sokurenko, E.V.
The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor
PLOS BIOLOGY, 9: Art. No. e1000617, MAY 2011
abstract, full text

Postila, P.A., Ylilauri, M., Pentikainen, O.T.
Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1037-1047, MAY 2011
abstract, full text

Camargo, H., Nusspaumer, G., Abia, D., Briceno, V., Remacha, M., Ballesta, J.P.G.
The amino terminal end determines the stability and assembling capacity of eukaryotic ribosomal stalk proteins P1 and P2
NUCLEIC ACIDS RESEARCH, 39:3735-3743, MAY 2011
abstract, full text

Lin, Y.W., Ying, T.L., Liao, L.F.
Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b (5)
JOURNAL OF MOLECULAR MODELING, 17:971-978, MAY 2011
abstract, full text

Chew, T.H., Joyce-Tan, K.H., Akma, F., Shamsir, M.S.
birgHPC: creating instant computing clusters for bioinformatics and molecular dynamics
BIOINFORMATICS, 27:1320-1321, MAY 1 2011
abstract, full text

Zhao, J., Yu, X., Liang, G.Z., Zheng, J.
Heterogeneous Triangular Structures of Human Islet Amyloid Polypeptide (Amylin) with Internal Hydrophobic Cavity and External Wrapping Morphology Reveal the Polymorphic Nature of Amyloid Fibrils
BIOMACROMOLECULES, 12:1781-1794, MAY 2011
abstract, full text

Kutzner, C., Czub, J., Grubmuller, H.
Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1381-1393, MAY 2011
abstract, full text

Schlick, T., Collepardo-Guevara, R., Halvorsen, L.A., Jung, S., Xiao, X.
Biomolecular modeling and simulation: a field coming of age
QUARTERLY REVIEWS OF BIOPHYSICS, 44:191-228, MAY 2011
abstract, full text

Khrenova, M.G., Domratcheva, T., Schlichting, I., Grigorenko, B.L., Nemukhin, A.V.
Computational Characterization of Reaction Intermediates in the Photocycle of the Sensory Domain of the AppA Blue Light Photoreceptor
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 87:564-573, MAY-JUN 2011
abstract, full text

Fezoua-Boubegtiten, Z., Desbat, B., Brisson, A., Gounou, C., Laguerre, M., Lecomte, S.
Effect of Mg2+ versus Ca2+ on the behavior of Annexin A5 in a membrane-bound state
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:641-649, MAY 2011
abstract, full text

Bellesia, G., Jewett, A.I., Shea, J.E.
Relative stability of de novo four-helix bundle proteins: Insights from coarse grained molecular simulations
PROTEIN SCIENCE, 20:818-826, MAY 2011
abstract, full text

Darian, E., Guvench, O., Yu, B., Qu, C.K., MacKerell, A.D.
Structural mechanism associated with domain opening in gain-of-function mutations in SHP2 phosphatase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1573-1588, MAY 2011
abstract, full text

Martinez, L., Malliavin, T.E., Blondel, A.
Mechanism of reactant and product dissociation from the anthrax edema factor: A locally enhanced sampling and steered molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1649-1661, MAY 2011
abstract, full text

Sapay, N., Tieleman, D.P.
Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1400-1410, MAY 2011
abstract, full text

Konig, G., Boresch, S.
Non-Boltzmann Sampling and Bennett's Acceptance Ratio Method: How to Profit from Bending the Rules
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1082-1090, APR 30 2011
abstract, full text

Lettieri, S., Mamonov, A.B., Zuckerman, D.M.
Extending Fragment-Based Free Energy Calculations with Library Monte Carlo Simulation: Annealing in Interaction Space
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1135-1143, APR 30 2011
abstract, full text

Busby, B., Oashi, T., Willis, C.D., Ackermann, M.A., Kontrogianni-Konstantopoulos, A., MacKerell, A.D., Bloch, R.J.
Electrostatic Interactions Mediate Binding of Obscurin to Small Ankyrin 1: Biochemical and Molecular Modeling Studies
JOURNAL OF MOLECULAR BIOLOGY, 408:321-334, APR 29 2011
abstract, full text

Conejo-Garcia, A., Pisani, L., Nunez, M.D.C., Catto, M., Nicolotti, O., Leonetti, F., Campos, J.M., Gallo, M.A., Espinosa, A., Carotti, A.
Homodimeric Bis-Quaternary Heterocyclic Ammonium Salts as Potent Acetyl- and Butyrylcholinesterase Inhibitors: A Systematic Investigation of the Influence of Linker and Cationic Heads over Affinity and Selectivity
JOURNAL OF MEDICINAL CHEMISTRY, 54:2627-2645, APR 28 2011
abstract, full text

Patra, N., Kral, P.
Controlled Self-Assembly of Filled Micelles on Nanotubes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6146-6149, APR 27 2011
abstract, full text

Murphy, D.L., Jaeger, J., Sweasy, J.B.
A Triad Interaction in the Fingers Subdomain of DNA Polymerase Beta Controls Polymerase Activity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6279-6287, APR 27 2011
abstract, full text

Swedberg, J.E., de Veer, S.J., Sit, K.C., Reboul, C.F., Buckle, A.M., Harris, J.M.
Mastering the Canonical Loop of Serine Protease Inhibitors: Enhancing Potency by Optimising the Internal Hydrogen Bond Network
PLOS ONE, 6: Art. No. e19302, APR 27 2011
abstract, full text

Walch, S.P.
Effect of Solvation on the Oxygen Reduction Reaction on Pt Catalyst
JOURNAL OF PHYSICAL CHEMISTRY C, 115:7377-7391, APR 21 2011
abstract, full text

Agirrezabala, X., Schreiner, E., Trabuco, L.G., Lei, J.L., Ortiz-Meoz, R.F., Schulten, K., Green, R., Frank, J.
Structural insights into cognate versus near-cognate discrimination during decoding
EMBO JOURNAL, 30:1497-1507, APR 20 2011
abstract, full text, TCBG publications

Reboul, C.F., Andrews, D.A., Nahar, M.F., Buckle, A.M., Roujeinikova, A.
Crystallographic and Molecular Dynamics Analysis of Loop Motions Unmasking the Peptidoglycan-Binding Site in Stator Protein MotB of Flagellar Motor
PLOS ONE, 6: Art. No. e18981, APR 20 2011
abstract, full text

Sun, G., Lu, K.Q., Kun, F.
Percolation-induced conductor-insulator transition in a system of metal spheres in a dielectric fluid
PHYSICAL REVIEW E, 83: Art. No. 041405, APR 15 2011
abstract, full text

Lian, P., Wei, D.Q., Wang, J.F., Chou, K.C.
An Allosteric Mechanism Inferred from Molecular Dynamics Simulations on Phospholamban Pentamer in Lipid Membranes
PLOS ONE, 6: Art. No. e18587, APR 15 2011
abstract, full text

Nurminen, E.M., Pihlavisto, M., Lazar, L., Pentikainen, U., Fulop, F., Pentikainen, O.T.
Novel Hydrazine Molecules as Tools To Understand the Flexibility of Vascular Adhesion Protein-1 Ligand-Binding Site: Toward More Selective Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 54:2143-2154, APR 14 2011
abstract, full text

Zhao, X.C.
Self-Assembly of DNA Segments on Graphene and Carbon Nanotube Arrays in Aqueous Solution: A Molecular Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 115:6181-6189, APR 14 2011
abstract, full text

Delemotte, L., Tarek, M., Klein, M.L., Amaral, C., Treptow, W.
Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:6109-6114, APR 12 2011
abstract, full text

Wei, C.Y., Pohorile, A.
Permeation of Nucleosides through Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 115:3681-3688, APR 7 2011
abstract, full text

Suyetin, M.V., Vakhrushev, A.V.
Guided Carbon Nanocapsules for Hydrogen Storage
JOURNAL OF PHYSICAL CHEMISTRY C, 115:5485-5491, APR 7 2011
abstract, full text

Narita, A., Oda, T., Maeda, Y.
Structural basis for the slow dynamics of the actin filament pointed end
EMBO JOURNAL, 30:1230-1237, APR 6 2011
abstract, full text

Jang, H., Arce, F.T., Mustata, M., Ramachandran, S., Capone, R., Nussinov, R., Lal, R.
Antimicrobial Protegrin-1 Forms Amyloid-Like Fibrils with Rapid Kinetics Suggesting a Functional Link
BIOPHYSICAL JOURNAL, 100:1775-1783, APR 6 2011
abstract, full text

Song, S.H., Freddolino, P.L., Nash, A.I., Carroll, E.C., Schulten, K., Gardner, K.H., Larsen, D.S.
Modulating LOV Domain Photodynamics with a Residue Alteration outside the Chromophore Binding Site
BIOCHEMISTRY, 50:2411-2423, APR 5 2011
abstract, full text, TCBG publications

Beckham, G.T., Bomble, Y.J., Bayer, E.A., Himmel, M.E., Crowley, M.F.
Applications of computational science for understanding enzymatic deconstruction of cellulose
CURRENT OPINION IN BIOTECHNOLOGY, 22:231-238, APR 2011
abstract, full text

Robinson, M.W., Corvo, I., Jones, P.M., George, A.M., Padula, M.P., To, J., Cancela, M., Rinaldi, G., Tort, J.F., Roche, L., Dalton, J.P.
Collagenolytic Activities of the Major Secreted Cathepsin L Peptidases Involved in the Virulence of the Helminth Pathogen, Fasciola hepatica
PLOS NEGLECTED TROPICAL DISEASES, 5: Art. No. e1012, APR 2011
abstract, full text

Cardinali, A., Tursi, N., Ligorio, A., Giuffrida, M.G., Napolitano, L., Caliandro, R., Sergio, L., Di Venere, D., Lattanzio, V., Sonnante, G.
Purification, biochemical characterization and cloning of a new cationic peroxidase isoenzyme from artichoke
PLANT PHYSIOLOGY AND BIOCHEMISTRY, 49:395-403, APR 2011
abstract, full text

Chodera, J.D., Mobley, D.L., Shirts, M.R., Dixon, R.W., Branson, K., Pande, V.S.
Alchemical free energy methods for drug discovery: progress and challenges
CURRENT OPINION IN STRUCTURAL BIOLOGY, 21:150-160, APR 2011
abstract, full text

Vorob'ev, Y.N.
Molecular dynamics method for proteins with ionization-conformation coupling and equilibrium titration
MOLECULAR BIOLOGY, 45:309-317, APR 2011
abstract, full text

Bucher, D., Grant, B.J., Markwick, P.R., McCammon, J.A.
Accessing a Hidden Conformation of the Maltose Binding Protein Using Accelerated Molecular Dynamics
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002034, APR 2011
abstract, full text

Wang, J., Wang, Y., Chu, X.K., Hagen, S.J., Han, W., Wang, E.K.
Multi-Scaled Explorations of Binding-Induced Folding of Intrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1001118, APR 2011
abstract, full text

Xie, L., Evangelidis, T., Xie, L., Bourne, P.E.
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002037, APR 2011
abstract, full text

Andronico, A., Randall, A., Benz, R.W., Baldi, P.
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:760-776, APR 2011
abstract, full text

Bahrami, M., Kalantarinejad, R., Aghaei, M.J., Azadi, N.
Simulation of the Interaction of Carbon Nanotubes and External Flow
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8:563-567, APR 2011
abstract, full text

Roth, M.W., Balasubramanya, M.K., Bergmann, P., Karl, M., Connolly, M.J., Gray, P.A.
Predicted Anomalous Behavior of C-60 Fullerenes on Graphite at Low Temperature: A New Hindered Cooperative Rotational Transition
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8:795-799, APR 2011
abstract, full text

Ghosh-Kumar, M., Alam, T.I., Draper, B., Stack, J.D., Rao, V.B.
Regulation by interdomain communication of a headful packaging nuclease from bacteriophage T4
NUCLEIC ACIDS RESEARCH, 39:2742-2755, APR 2011
abstract, full text

Buch, I., Tsai, C.J., Wolfson, H.J., Nussinov, R.
Symmetry-Based Self-assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers
PROTEIN AND PEPTIDE LETTERS, 18:362-372, APR 2011
abstract, full text

Liang, H., Liu, T., Chen, F.J., Liu, Z.Q., Liu, S.J.
A full-length 3D structure for MAPK/ERK kinase 2 (MEK2)
SCIENCE CHINA-LIFE SCIENCES, 54:336-341, APR 2011
abstract, full text

Lee, J.H., Park, H., Park, S.J., Kim, H.J., Eom, S.H.
The structural flexibility of the shank1 PDZ domain is important for its binding to different ligands
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 407:207-212, APR 1 2011
abstract, full text

Preat, J., Zanuy, D., Perpete, E.A., Aleman, C.
Binding of Cationic Conjugated Polymers to DNA: Atomistic Simulations of Adducts Involving the Dickerson's Dodecamer
BIOMACROMOLECULES, 12:1298-1304, APR 2011
abstract, full text

Staritzbichler, R., Anselmi, C., Forrest, L.R., Faraldo-Gomez, J.D.
GRIFFIN: A Versatile Methodology for Optimization of Protein-Lipid Interfaces for Membrane Protein Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1167-1176, APR 2011
abstract, full text

Firlej, L., Kuchta, B., Roth, M.W., Wexler, C.
Molecular simulations of intermediate and long alkanes adsorbed on graphite: Tuning of non-bond interactions
JOURNAL OF MOLECULAR MODELING, 17:811-816, APR 2011
abstract, full text

Vattulainen, I., Rog, T.
Lipid Simulations: A Perspective on Lipids in Action
COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY, 3: Art. No. a004655, APR 2011
abstract, full text

Moss, C.L., Chung, T.W., Wyer, J.A., Nielsen, S.B., Hvelplund, P., Turecek, F.
Dipole-Guided Electron Capture Causes Abnormal Dissociations of Phosphorylated Pentapeptides
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22:731-751, APR 2011
abstract, full text

Wada, M., Nishiyama, Y., Bellesia, G., Forsyth, T., Gnanakaran, S., Langan, P.
Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during the treatment of cellulose with ammonia
CELLULOSE, 18:191-206, APR 2011
abstract, full text

Olmez, E.O., Alakent, B.
Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:675-693, APR 2011
abstract, full text

Strzelecki, J.W., Strzelecka, J., Mikulska, K., Tszydel, M., Balter, A., Nowak, W.
Nanomechanics of new materials - AFM and computer modelling studies of trichoptera silk
CENTRAL EUROPEAN JOURNAL OF PHYSICS, 9:482-491, APR 2011
abstract, full text

Kosevich, M.V., Zobnina, V.G., Chagovets, V.V., Boryak, O.A.
Observation of poly(ethylene glycol) clusters with the chlorine anion in the gas phase under electrospray conditions
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 25:713-718, MAR 30 2011
abstract, full text

Jones, M.K., Gu, F.F., Catte, A., Li, L., Segrest, J.P.
"Sticky" and "Promiscuous", the Yin and Yang of Apolipoprotein A-I Termini in Discoidal High-Density Lipoproteins: A Combined Computational-Experimental Approach
BIOCHEMISTRY, 50:2249-2263, MAR 29 2011
abstract, full text

Boettcher, J.M., Davis-Harrison, R.L., Clay, M.C., Nieuwkoop, A.J., Ohkubo, Y.Z., Tajkhorshid, E., Morrissey, J.H., Rienstra, C.M.
Atomic View of Calcium-Induced Clustering of Phosphatidylserine in Mixed Lipid Bilayers
BIOCHEMISTRY, 50:2264-2273, MAR 29 2011
abstract, full text

Geppert, T., Hoy, B., Wessler, S., Schneider, G.
Context-Based Identification of Protein-Protein Interfaces and "Hot-Spot" Residues
CHEMISTRY & BIOLOGY, 18:344-353, MAR 25 2011
abstract, full text

Ozboyaci, M., Gursoy, A., Erman, B., Keskin, O.
Molecular Recognition of H3/H4 Histone Tails by the Tudor Domains of JMJD2A: A Comparative Molecular Dynamics Simulations Study
PLOS ONE, 6: Art. No. e14765, MAR 25 2011
abstract, full text

Shukla, D., Zamolo, L., Cavallotti, C., Trout, B.L.
Understanding the Role of Arginine as an Eluent in Affinity Chromatography via Molecular Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:2645-2654, MAR 24 2011
abstract, full text

Dalosto, S.D., Tinte, S.
Fluctuation Effects of the Electric Field Induced by Water on a Graphene Dot Band Gap
JOURNAL OF PHYSICAL CHEMISTRY C, 115:4381-4386, MAR 24 2011
abstract, full text

Radadia, A.D., Stavis, C.J., Carr, R., Zeng, H.J., King, W.P., Carlisle, J.A., Aksimentiev, A., Hamers, R.J., Bashir, R.
Control of Nanoscale Environment to Improve Stability of Immobilized Proteins on Diamond Surfaces
ADVANCED FUNCTIONAL MATERIALS, 21:1040-1050, MAR 22 2011
abstract, full text

Zhao, C.F., Noskov, S.Y.
The Role of Local Hydration and Hydrogen-Bonding Dynamics in Ion and Solute Release from Ion-Coupled Secondary Transporters
BIOCHEMISTRY, 50:1848-1856, MAR 22 2011
abstract, full text

Sinha, S.K., Bandyopadhyay, S.
Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 115101, MAR 21 2011
abstract, full text

Bhattacharya, S., Muzard, J., Payet, L., Mathe, J., Bockelmann, U., Aksimentiev, A., Viasnoff, V.
Rectification of the Current in alpha-Hemolysin Pore Depends on the Cation Type: The Alkali Series Probed by Molecular Dynamics Simulations and Experiments
JOURNAL OF PHYSICAL CHEMISTRY C, 115:4255-4264, MAR 17 2011
abstract, full text

Mihailescu, M., Vaswani, R.G., Jardon-Valadez, E., Castro-Roman, F., Freites, J.A., Worcester, D.L., Chamberlin, A.R., Tobias, D.J., White, S.H.
Acyl-Chain Methyl Distributions of Liquid-Ordered and -Disordered Membranes
BIOPHYSICAL JOURNAL, 100:1455-1462, MAR 16 2011
abstract, full text

Dixit, P.D., Asthagiri, D.
The Role of Bulk Protein in Local Models of Ion-Binding to Proteins: Comparative Study of KcsA, Its Semisynthetic Analog with a Locked-in Binding Site, and Valinomycin
BIOPHYSICAL JOURNAL, 100:1542-1549, MAR 16 2011
abstract, full text

Parthasarathy, S., Long, F., Miller, Y., Xiao, Y.L., McElheny, D., Thurber, K., Ma, B.Y., Nussinov, R., Ishii, Y.
Molecular-Level Examination of Cu2+ Binding Structure for Amyloid Fibrils of 40-Residue Alzheimer's beta by Solid-State NMR Spectroscopy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3390-3400, MAR 16 2011
abstract, full text

McCullagh, M., Franco, I., Ratner, M.A., Schatz, G.C.
DNA-Based Optomechanical Molecular Motor
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3452-3459, MAR 16 2011
abstract, full text

Lee, O.S., Stupp, S.I., Schatz, G.C.
Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3677-3683, MAR 16 2011
abstract, full text

Wedberg, R., O'Connell, J.P., Peters, G.H., Abildskov, J.
Total and direct correlation function integrals from molecular simulation of binary systems
FLUID PHASE EQUILIBRIA, 302:32-42, MAR 15 2011
abstract, full text

Haspel, N., Zanuy, D., Nussinov, R., Teesalu, T., Ruoslahti, E., Aleman, C.
Binding of a C-End Rule Peptide to the Neuropilin-1 Receptor: A Molecular Modeling Approach
BIOCHEMISTRY, 50:1755-1762, MAR 15 2011
abstract, full text

Zhang, Q.C., Yeh, T.L., Leyva, A., Frank, L.G., Miller, J., Kim, Y.E., Langen, R., Finkbeiner, S., Amzel, M.L., Ross, C.A., Poirier, M.A.
A Compact beta Model of huntingtin Toxicity
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:8188-8196, MAR 11 2011
abstract, full text

Grafmuller, A., Voth, G.A.
Intrinsic Bending of Microtubule Protofilaments
STRUCTURE, 19:409-417, MAR 9 2011
abstract, full text

Akgun, U., Khademi, S.
Periplasmic vestibule plays an important role for solute recruitment, selectivity, and gating in the Rh/Amt/MEP superfamily
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:3970-3975, MAR 8 2011
abstract, full text

Uhart, M., Iglesias, A.A., Bustos, D.M.
Structurally Constrained Residues Outside the Binding Motif Are Essential in the Interaction of 14-3-3 and Phosphorylated Partner
JOURNAL OF MOLECULAR BIOLOGY, 406:552-557, MAR 4 2011
abstract, full text

Ayuso-Tejedor, S., Garcia-Fandino, R., Orozco, M., Sancho, J., Bernado, P.
Structural Analysis of an Equilibrium Folding Intermediate in the Apoflavodoxin Native Ensemble by Small-Angle X-ray Scattering
JOURNAL OF MOLECULAR BIOLOGY, 406:604-619, MAR 4 2011
abstract, full text

Khan, N.S., Perez-Aguilar, J.M., Kaufmann, T., Hill, P.A., Taratula, O., Lee, O.S., Carroll, P.J., Saven, J.G., Dmochowski, I.J.
Multiple Hindered Rotators in a Gyroscope-Inspired Tribenzylamine Hemicryptophane
JOURNAL OF ORGANIC CHEMISTRY, 76:1418-1424, MAR 4 2011
abstract, full text

Miller, Y., Ma, B.Y., Nussinov, R.
The Unique Alzheimer's beta-Amyloid Triangular Fibril Has a Cavity along the Fibril Axis under Physiological Conditions
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:2742-2748, MAR 2 2011
abstract, full text

Cui, H.S., Lyman, E., Voth, G.A.
Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins
BIOPHYSICAL JOURNAL, 100:1271-1279, MAR 2 2011
abstract, full text

Wallrapp, F.H., Guallar, V.
Mixed quantum mechanics and molecular mechanics methods: Looking inside proteins
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:315-322, MAR-APR 2011
abstract, full text

Prasad, N.K., Vindal, V., Kumar, V., Kabra, A., Phogat, N., Kumar, M.
Structural and docking studies of Leucaena leucocephala Cinnamoyl CoA reductase
JOURNAL OF MOLECULAR MODELING, 17:533-541, MAR 2011
abstract, full text

Cai, W.S., Wang, T., Liu, Y.Z., Liu, P., Chipot, C., Shao, X.G.
Free Energy Calculations for Cyclodextrin Inclusion Complexes
CURRENT ORGANIC CHEMISTRY, 15:839-847, MAR 2011
abstract, full text

Gonzalez, A., Murcia, M., Benhamu, B., Campillo, M., Lopez-Rodriguez, M.L., Pardo, L.
The importance of solvation in the design of ligands targeting membrane proteins
MEDCHEMCOMM, 2:160-164, MAR 2011
abstract, full text

Mazars, M.
Long ranged interactions in computer simulations and for quasi-2D systems
PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS, 500:43-116, MAR 2011
abstract, full text

Heroux, M.S., Mohan, A.D., Olsen, K.W.
Ligand Migration in the Truncated Hemoglobin of Mycobacterium tuberculosis
IUBMB LIFE, 63:214-220, MAR 2011
abstract, full text

Patra, N., Song, Y.B., Kral, P.
Self-Assembly of Graphene Nanostructures on Nanotubes
ACS NANO, 5:1798-1804, MAR 2011
abstract, full text

Perez-Sanchez, H., Wenzel, W.
Optimization Methods for Virtual Screening on Novel Computational Architectures
CURRENT COMPUTER-AIDED DRUG DESIGN, 7:44-52, MAR 2011
abstract, full text

Singh, L.R., Poddar, N.K., Dar, T.A., Rahman, S., Kumar, R., Ahmad, F.
Forty Years of Research on Osmolyte-Induced Protein Folding and Stability
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 8:1-23, MAR 2011
abstract, full text

Janovec, L., Kozurkova, M., Sabolova, D., Ungvarsky, J., Paulikova, H., Plsikova, J., Vantova, Z., Imrich, J.
Cytotoxic 3,6-bis((imidazolidinone)imino)acridines: Synthesis, DNA binding and molecular modeling
BIOORGANIC & MEDICINAL CHEMISTRY, 19:1790-1801, MAR 1 2011
abstract, full text

Beretta, G., Artali, R., Caneva, E., Facino, R.M.
Conformation of the tridimensional structure of 1,2,3,4,6-pentagalloyl-beta-D-glucopyranose (PGG) by H-1 NMR, NOESY and theoretical study and membrane interaction in a simulated phospholipid bilayer: a first insight
MAGNETIC RESONANCE IN CHEMISTRY, 49:132-136, MAR 2011
abstract, full text

Qiu, H., Shen, R., Guo, W.L.
Vibrating carbon nanotubes as water pumps
NANO RESEARCH, 4:284-289, MAR 2011
abstract, full text

Lin, Y.W.
Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:679-684, MAR 2011
abstract, full text

Chennamsetty, N., Voynov, V., Kayser, V., Helk, B., Trout, B.L.
Prediction of protein binding regions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:888-897, MAR 2011
abstract, full text

Fogolari, F., Corazza, A., Varini, N., Rotter, M., Gumral, D., Codutti, L., Rennella, E., Viglino, P., Bellotti, V., Esposito, G.
Molecular dynamics simulation of beta(2)-microglobulin in denaturing and stabilizing conditions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:986-1001, MAR 2011
abstract, full text

Tsoulos, I.G., Stavrakoudis, A.
Eucb: A C plus plus program for molecular dynamics trajectory analysis
COMPUTER PHYSICS COMMUNICATIONS, 182:834-841, MAR 2011
abstract, full text

Corry, B.
Water and ion transport through functionalised carbon nanotubes: implications for desalination technology
ENERGY & ENVIRONMENTAL SCIENCE, 4:751-759, MAR 2011
abstract, full text

Trabuco, L.G., SchreineR, E., Gumbart, J., Hsin, J., Villa, E., Schulten, K.
Applications of the molecular dynamics flexible fitting method
JOURNAL OF STRUCTURAL BIOLOGY, 173:420-427, MAR 2011
abstract, full text, TCBG publications

Wang, X., Lee, H.W., Liu, Y.Z., Prestegard, J.H.
Structural NMR of protein oligomers using hybrid methods
JOURNAL OF STRUCTURAL BIOLOGY, 173:515-529, MAR 2011
abstract, full text

Min, S.K., Kim, W.Y., Cho, Y., Kim, K.S.
Fast DNA sequencing with a graphene-based nanochannel device
NATURE NANOTECHNOLOGY, 6:162-165, MAR 2011
abstract, full text

Silvestre-Ryan, J., Lin, Y.C., Chu, J.W.
"Fluctuograms'' Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002023, MAR 2011
abstract, full text

Gumbart, J., Chipot, C., Schulten, K.
Free-energy cost for translocon-assisted insertion of membrane proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:3596-3601, MAR 1 2011
abstract, full text, TCBG publications

Peplowski, L., Sikora, M., Nowak, W., Cieplak, M.
Molecular jamming-The cystine slipknot mechanical clamp in all-atom simulations
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 085102, FEB 28 2011
abstract, full text

NategholEslam, M., Holland, B.W., Gray, C.G., Tomberli, B.
Drift-oscillatory steering with the forward-reverse method for calculating the potential of mean force
PHYSICAL REVIEW E, 83: Art. No. 021114, FEB 28 2011
abstract, full text

Megow, J., Roder, B., Kulesza, A., Bonacic-Koutecky, V., May, V.
A Mixed Quantum-Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Forster Theory and beyond
CHEMPHYSCHEM, 12:645-656, FEB 25 2011
abstract, full text

Su, C.C., Long, F., Zimmermann, M.T., Rajashankar, K.R., Jernigan, R.L., Yu, E.W.
Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli
NATURE, 470:558-U153, FEB 24 2011
abstract, full text

Li, X.C., Tobacman, L.S., Mun, J.Y., Craig, R., Fischer, S., Lehman, W.
Tropomyosin Position on F-Actin Revealed by EM Reconstruction and Computational Chemistry
BIOPHYSICAL JOURNAL, 100:1005-1013, FEB 16 2011
abstract, full text

Spiriti, J., Binder, J.K., Levitus, M., van der Vaart, A.
Cy3-DNA Stacking Interactions Strongly Depend on the Identity of the Terminal Basepair
BIOPHYSICAL JOURNAL, 100:1049-1057, FEB 16 2011
abstract, full text

Hsin, J., Schulten, K.
Improved Resolution of Tertiary Structure Elasticity in Muscle Protein
BIOPHYSICAL JOURNAL, 100:L22-L24, FEB 16 2011
abstract, full text, TCBG publications

Santiso, E.E., Trout, B.L.
A general set of order parameters for molecular crystals
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 064109, FEB 14 2011
abstract, full text

Liu, Y.Z., Chipot, C., Shao, X.G., Cai, W.S.
Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide
JOURNAL OF PHYSICAL CHEMISTRY C, 115:1851-1856, FEB 10 2011
abstract, full text

Su, Z.Y., Wang, Y.T.
Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:796-802, FEB 10 2011
abstract, full text

Mroginski, M.A., Kaminski, S., von Stetten, D., Ringsdorf, S., Gartner, W., Essen, L.O., Hildebrandt, P.
Structure of the Chromophore Binding Pocket in the Pr State of Plant Phytochrome phyA
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1220-1231, FEB 10 2011
abstract, full text

Zhou, R.H., Li, J.Y., Hua, L., Yang, Z.X., Berne, B.J.
Comment on "Urea-Mediated Protein Denaturation: A Consensus View"
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1323-1326, FEB 10 2011
full text

Oliveira, A.F., Gemming, S., Seifert, G.
Conformational Analysis of Aqueous BMP-2 Using Atomistic Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1122-1130, FEB 10 2011
abstract, full text

Shukla, D., Trout, B.L.
Preferential Interaction Coefficients of Proteins in Aqueous Arginine Solutions and Their Molecular Origins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1243-1253, FEB 10 2011
abstract, full text

Garate, J.A., English, N.J., MacElroy, J.M.D.
Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 055110, FEB 7 2011
abstract, full text

Yeh, I.C., Wallqvist, A.
On the proper calculation of electrostatic interactions in solid-supported bilayer systems
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 055109, FEB 7 2011
abstract, full text

Martinez, A.V., DeSensi, S.C., Dominguez, L., Rivera, E., Straub, J.E.
Protein folding in a reverse micelle environment: The role of confinement and dehydration
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 055107, FEB 7 2011
abstract, full text

Sapir, L., Harries, D.
Linking Trehalose Self-Association with Binary Aqueous Solution Equation of State
JOURNAL OF PHYSICAL CHEMISTRY B, 115:624-634, FEB 3 2011
abstract, full text

Olbrich, C., Strumpfer, J., Schulten, K., Kleinekathofer, U.
Quest for Spatially Correlated Fluctuations in the FMO Light-Harvesting Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 115:758-764, FEB 3 2011
abstract, full text, TCBG publications

Bastug, T., Kuyucak, S.
Comparative Study of the Energetics of Ion Permeation in Kv1.2 and KcsA Potassium Channels
BIOPHYSICAL JOURNAL, 100:629-636, FEB 2 2011
abstract, full text

Kokhan, O., Shinkarev, V.P.
All-Atom Molecular Dynamics Simulations Reveal Significant Differences in Interaction between Antimycin and Conserved Amino Acid Residues in Bovine and Bacterial bc(1) Complexes
BIOPHYSICAL JOURNAL, 100:720-728, FEB 2 2011
abstract, full text

Skjevik, A.A., Haug, B.E., Lygre, H., Teigen, K.
Intramolecular hydrogen bonding in articaine can be related to superior bone tissue penetration: A molecular dynamics study
BIOPHYSICAL CHEMISTRY, 154:18-25, FEB 2011
abstract, full text

Grasso, G., Pietropaolo, A., Spoto, G., Pappalardo, G., Tundo, G.R., Ciaccio, C., Coletta, M., Rizzarelli, E.
Copper(I) and Copper(II) Inhibit A beta Peptides Proteolysis by Insulin-Degrading Enzyme Differently: Implications for Metallostasis Alteration in Alzheimer's Disease
CHEMISTRY-A EUROPEAN JOURNAL, 17:2752-2762, FEB 2011
abstract, full text

Morales-Quintana, L., Fuentes, L., Gaete-Eastman, C., Herrera, R., Moya-Leon, M.A.
Structural characterization and substrate specificity of VpAAT1 protein related to ester biosynthesis in mountain papaya fruit
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:635-642, FEB 2011
abstract, full text

Gossett, J.J., Harvey, S.C.
Computational Screening and Design of DNA-Linked Molecular Nanowires
NANO LETTERS, 11:604-608, FEB 2011
abstract, full text

Falconi, M., Oteri, F., Di Palma, F., Pandey, S., Battistoni, A., Desideri, A.
Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:181-194, FEB 2011
abstract, full text

Kamisetty, H., Ramanathan, A., Bailey-Kellogg, C., Langmead, C.J.
Accounting for conformational entropy in predicting binding free energies of protein-protein interactions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:444-462, FEB 2011
abstract, full text

Novak, B.R., Moldovan, D., Waldrop, G.L., de Queiroz, M.S.
Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:622-632, FEB 2011
abstract, full text

Chakrabarti, B., Bairagya, H.R., Mallik, P., Mukhopadhyay, B.P., Bera, A.K.
An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn+2 ions in Matrix Metalloproteinase 13 of Human
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:503-516, FEB 2011
abstract, full text

Niazi, U.H.K., Bibby, J., Sutcliffe, M.J.
In-silico characterization of the effects of phosphorylated tyrosines 86 and 106 on structure and binding of MAL: insight into hyperinflammatory response to infection by the human malaria parasites
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:53-65, FEB 2011
abstract, full text

Chen, W., Lou, J.Z., Hsin, J., Schulten, K., Harvey, S.C., Zhu, C.
Molecular Dynamics Simulations of Forced Unbending of Integrin alpha(V)beta(3)
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1001086, FEB 2011
abstract, full text, TCBG publications

Calderon, C.P.
Estimation and Inference of Diffusion Coefficients in Complex Biomolecular Environments
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:280-290, FEB 2011
abstract, full text

Kawatsu, T., Lundberg, M., Morokuma, K.
Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:390-401, FEB 2011
abstract, full text

Qu, Y.Y., Zhou, H., Li, A., Ma, F., Zhou, J.T.
Nitroreductase activity of ferredoxin reductase BphA4 from Dyella ginsengisoli LA-4 by catalytic and structural properties analysis
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 89:655-663, FEB 2011
abstract, full text

Gushchin, I.Y., Gordeliy, V.I., Grudinin, S.
Role of the HAMP Domain Region of Sensory Rhodopsin Transducers in Signal Transduction
BIOCHEMISTRY, 50:574-580, FEB 1 2011
abstract, full text

Kalikka, J., Akola, J.
Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:181-194, FEB 2011
abstract, full text

Mustata, G., Li, M., Zevola, N., Bakan, A., Zhang, L., Epperly, M., Greenberger, J.S., Yu, J., Bahar, I.
Development of Small-Molecule PUMA Inhibitors for Mitigating Radiation-Induced Cell Death
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 11:281-290, FEB 2011
abstract, full text

Yan, Q., Murphy-Ullrich, J.E., Song, Y.H.
Molecular and Structural Insight into the Role of Key Residues of Thrombospondin-1 and Calreticulin in Thrombospondin-1-Calreticulin Binding
BIOCHEMISTRY, 50:566-573, FEB 1 2011
abstract, full text

Khurana, E., DeVane, R.H., Dal Peraro, M., Klein, M.L.
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:530-537, FEB 2011
abstract, full text

Kotsikorou, E., Lynch, D.L., Abood, M.E., Reggio, P.H.
Lipid bilayer molecular dynamics study of lipid-derived agonists of the putative cannabinoid receptor, GPR55
CHEMISTRY AND PHYSICS OF LIPIDS, 164:131-143, FEB 2011
abstract, full text

Zhang, J.L., Zheng, Q.C., Zhang, H.X.
Theoretical improvement of the specific inhibitor of human carbonic anhydrase VII
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 35:50-56, FEB 2011
abstract, full text

Bowman, G.R., Voelz, V.A., Pande, V.S.
Taming the complexity of protein folding
CURRENT OPINION IN STRUCTURAL BIOLOGY, 21:4-11, FEB 2011
abstract, full text

Kim, S.K., Li, Y.Y., Abrol, R., Heo, J., Goddard, W.A.
Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:420-433, FEB 2011
abstract, full text

Nowosieski, M., Hoffmann, M., Wyrwicz, L.S., Stepniak, P., Plewczynski, D.M., Lazniewski, M., Ginalski, K., Rychlewski, L.
Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:455-462, FEB 2011
abstract, full text

Arsawang, U., Saengsawang, O., Rungrotmongkol, T., Sornmee, P., Wittayanarakul, K., Remsungnen, T., Hannongbua, S.
How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system?
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:591-596, FEB 2011
abstract, full text

Yun, S.J., Guy, H.R.
Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:663-675, FEB 2011
abstract, full text

Olbrich, C., Liebers, J., Kleinekathofer, U.
Modeling of light-harvesting in purple bacteria using a time-dependent Hamiltonian approach
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, 248:393-398, FEB 2011
abstract, full text

Huang, D.Z., Caflisch, A.
The Free Energy Landscape of Small Molecule Unbinding
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002002, FEB 2011
abstract, full text

Henriques, E.S., Brito, R.M.M., Soares, H., Ventura, S., de Oliveira, V.L., Parkhouse, R.M.E.
Modeling of the Toll-like receptor 3 and a putative Toll-like receptor 3 antagonist encoded by the African swine fever virus
PROTEIN SCIENCE, 20:247-255, FEB 2011
abstract, full text

Emileh, A., Abrams, C.F.
A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain alpha 1 helix in an engineered HIV-1 gp120
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:537-546, FEB 2011
abstract, full text

Shim, J.Y., Rudd, J., Ding, T.T.
Distinct second extracellular loop structures of the brain cannabinoid CB1 receptor: Implication in ligand binding and receptor function
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:581-597, FEB 2011
abstract, full text

Cruz, F.A., Knepley, M.G., Barba, L.A.
PetFMM-A dynamically load-balancing parallel fast multipole library
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, 85:403-428, JAN 28 2011
abstract, full text

Hilder, T.A., Gordon, D., Chung, S.H.
Synthetic cation-selective nanotube: Permeant cations chaperoned by anions
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 045103, JAN 28 2011
abstract, full text

Karino, Y., Matubayasi, N.
Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 041105, JAN 28 2011
abstract, full text

Ramanathan, A., Savol, A.J., Langmead, C.J., Agarwal, P.K., Chennubhotla, C.S.
Discovering Conformational Sub-States Relevant to Protein Function
PLOS ONE, 6: Art. No. e15827, JAN 28 2011
abstract, full text

Panecka, J., Mura, C., Trylska, J.
Molecular Dynamics of Potential rRNA Binders: Single-Stranded Nucleic Acids and Some Analogues
JOURNAL OF PHYSICAL CHEMISTRY B, 115:532-546, JAN 27 2011
abstract, full text

Shan, J.F., Javitch, J.A., Shi, L., Weinstein, H.
The Substrate-Driven Transition to an Inward-Facing Conformation in the Functional Mechanism of the Dopamine Transporter
PLOS ONE, 6: Art. No. e16350, JAN 27 2011
abstract, full text

Ko, E., Liu, J., Perez, L.M., Lu, G.L., Schaefer, A., Burgess, K.
Universal Peptidomimetics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:462-477, JAN 26 2011
abstract, full text

Zuniga, L., Marquez, V., Gonzalez-Nilo, F.D., Chipot, C., Cid, L.P., Sepulveda, F.V., Niemeyer, M.I.
Gating of a pH-Sensitive K-2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter
PLOS ONE, 6: Art. No. e16141, JAN 25 2011
abstract, full text

Liu, L., Fang, Y., Huang, Q.S., Wu, J.H.
A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic alpha-Helical Peptide HP(2-20) and Its Four Analogues
PLOS ONE, 6: Art. No. e16441, JAN 24 2011
abstract, full text

Zerbetto, M., Buck, M., Meirovitch, E., Polimeno, A.
Integrated Computational Approach to the Analysis of NMR Relaxation in Proteins: Application to ps-ns Main Chain N-15-H-1 and Global Dynamics of the Rho GTPase Binding Domain of Plexin-B1
JOURNAL OF PHYSICAL CHEMISTRY B, 115:376-388, JAN 20 2011
abstract, full text

Jiang, W., Hardy, D.J., Phillips, J.C., MacKerell, A.D., Schulten, K., Roux, B.
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:87-92, JAN 20 2011
abstract, full text, TCBG publications

Nury, H., Van Renterghem, C., Weng, Y., Tran, A., Baaden, M., Dufresne, V., Changeux, J.P., Sonner, J.M., Delarue, M., Corringer, P.J.
X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
NATURE, 469:428-+, JAN 20 2011
abstract, full text

Fritsch, S., Ivanov, I., Wang, H.L., Cheng, X.L.
Ion Selectivity Mechanism in a Bacterial Pentameric Ligand-Gated Ion Channel
BIOPHYSICAL JOURNAL, 100:390-398, JAN 19 2011
abstract, full text

Brubaker, W.D., Freites, J.A., Golchert, K.J., Shapiro, R.A., Morikis, V., Tobias, D.J., Martin, R.W.
Separating Instability from Aggregation Propensity in gamma S-Crystallin Variants
BIOPHYSICAL JOURNAL, 100:498-506, JAN 19 2011
abstract, full text

Dendzik, Z., Gorny, K., Gwizdala, W., Gburski, Z.
Dipolar relaxation of propylene glycol molecular cluster confined in carbon nanotubes of different chiralities-computer simulation study
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:575-579, JAN 15 2011
abstract, full text

Kieslich, C.A., Gorham, R.D., Morikis, D.
Is the rigid-body assumption reasonable? Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:707-716, JAN 15 2011
abstract, full text

Sun, S., Yin, G.Y., Lee, Y.K., Wong, J.T.Y., Zhang, T.Y.
Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:684-688, JAN 14 2011
abstract, full text

Wang, C.H., Ye, F.B., Velardez, G.F., Peters, G.H., Westh, P.
Affinity of Four Polar Neurotransmitters for Lipid Bilayer Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:196-203, JAN 13 2011
abstract, full text

Venkatramani, R., Davis, K.L., Wierzbinski, E., Bezer, S., Balaeff, A., Keinan, S., Paul, A., Kocsis, L., Beratan, D.N., Achim, C., Waldeck, D.H.
Evidence for a Near-Resonant Charge Transfer Mechanism for Double-Stranded Peptide Nucleic Acid
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:62-72, JAN 12 2011
abstract, full text

Hilder, T.A., Chung, S.H.
Carbon nanotube as a gramicidin analogue
CHEMICAL PHYSICS LETTERS, 501:423-426, JAN 7 2011
abstract, full text

Bossis, F., Palese, L.L.
Molecular dynamics in cytochrome c oxidase Mossbauer spectra deconvolution
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:438-442, JAN 7 2011
abstract, full text

Sakata, T., Kawashima, Y., Nakano, H.
Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 014501, JAN 7 2011
abstract, full text

Koksal, M., Jin, Y.H., Coates, R.M., Croteau, R., Christianson, D.W.
Taxadiene synthase structure and evolution of modular architecture in terpene biosynthesis
NATURE, 469:116-U138, JAN 6 2011
abstract, full text

Thomas, M., Jayatilaka, D., Corry, B.
Mapping the Importance of Four Factors in Creating Monovalent Ion Selectivity in Biological Molecules
BIOPHYSICAL JOURNAL, 100:60-69, JAN 5 2011
abstract, full text

Wang, T., Chipot, C., Shao, X.G., Cai, W.S.
Structural Characterization of Micelles Formed of Cholesteryl-Functionalized Cyclodextrins
LANGMUIR, 27:91-97, JAN 4 2011
abstract, full text

Merchant, B.A., Madura, J.D.
A Review of Coarse-Grained Molecular Dynamics Techniques to Access Extended Spatial and Temporal Scales in Biomolecular Simulations
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 7, 7:67-87, 2011
abstract, full text

Tiber, P.M., Orun, O., Nacar, C., Sezerman, U.O., Severcan, F., Severcan, M., Matagne, A., Kan, B.
Structural characterization of recombinant bovine Go alpha by spectroscopy and homology modeling
SPECTROSCOPY-BIOMEDICAL APPLICATIONS, 26:213-229, 2011
abstract, full text

Jolley, C.C., Lucon, J., Uchida, M., Reichhardt, C., Vaughn, M.J., Lafrance, B.J., Douglas, T.
Structure, dynamics, and solvation in a disordered metal-organic coordination polymer: a multiscale study
JOURNAL OF COORDINATION CHEMISTRY, 64:4301-4317, 2011
abstract, full text

Kass, I., Reboul, C.F., Buckle, A.M.
COMPUTATIONAL METHODS FOR STUDYING SERPIN CONFORMATIONAL CHANGE AND STRUCTURAL PLASTICITY
METHODS IN ENZYMOLOGY, VOL 501: SERPIN STRUCTURE AND EVOLUTION, 501:295-323, 2011
abstract, full text

Chipot, C., Lelievre, T.
ENHANCED SAMPLING OF MULTIDIMENSIONAL FREE-ENERGY LANDSCAPES USING ADAPTIVE BIASING FORCES
SIAM JOURNAL ON APPLIED MATHEMATICS, 71:1673-1695, 2011
abstract, full text

Dong, X.L., Qi, W., Tao, W., Ma, L.Y., Fu, C.X.
The dynamic behaviours of protein BMP-2 on hydroxyapatite nanoparticles
MOLECULAR SIMULATION, 37:1097-1104, 2011
abstract, full text

Hughes, M., Xu, H.X., Frederix, P.W.J.M., Smith, A.M., Hunt, N.T., Tuttle, T., Kinloch, I.A., Ulijn, R.V.
Biocatalytic self-assembly of 2D peptide-based nanostructures
SOFT MATTER, 7:10032-10038, 2011
abstract, full text

Khelashvili, G., Rappolt, M., Chiu, S.W., Pabst, G., Harries, D.
Impact of sterol tilt on membrane bending rigidity in cholesterol and 7DHC-containing DMPC membranes
SOFT MATTER, 7:10299-10312, 2011
abstract, full text

Engelbrecht, T., Hauss, T., Suss, K., Vogel, A., Roark, M., Feller, S.E., Neubert, R.H.H., Dobner, B.
Characterisation of a new ceramide EOS species: synthesis and investigation of the thermotropic phase behaviour and influence on the bilayer architecture of stratum corneum lipid model membranes
SOFT MATTER, 7:8998-9011, 2011
abstract, full text

Zhao, Y.P., Wang, F.C., Chi, M.
Molecular Dynamics Simulation and Molecular Orbital Method
HANDBOOK OF ADHESION TECHNOLOGY, VOL 1 AND 2, DOI 10.1007/978-3-642-01169-6_52, 2011
abstract, full text

Asghar, W., Billo, J.A., Iqbal, S.M.
Solid State Nanopores for Selective Sensing of DNA
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, DOI 10.1007/978-1-4419-8252-0_5, 2011
abstract, full text

Gracheva, M.E., Leroux, A., Destine, J., Leburton, J.P.
Simulation of Electronic Sensing of Biomolecules in Translocation Through a Nanopore in a Semiconductor Membrane
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, DOI 10.1007/978-1-4419-8252-0_7, 2011
abstract, full text

Comer, J., Aksimentiev, A.
Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations
NANOPORES: SENSING AND FUNDAMENTAL BIOLOGICAL INTERACTIONS, DOI 10.1007/978-1-4419-8252-0_14, 2011
abstract, full text

Stavrakoudis, A.
Molecular dynamics study of the human insulin B peptide SHLVEALYLVCGERGG complexed with HLA-DQ8 reveals important hydrogen bond interactions
MOLECULAR SIMULATION, 37:837-845, 2011
abstract, full text

Nishizawa, K.
Atomistic Molecular Simulation of Gating Modifier Venom Peptides - Two Binding Modes and Effects of Lipid Structure
MECHANOSENSITIVITY AND MECHANOTRANSDUCTION, 4:167-190, 2011
abstract, full text

Wang, F., Akin-Ojo, O., Pinnick, E., Song, Y.
Approaching post-Hartree-Fock quality potential energy surfaces with simple pair-wise expressions: parameterising point-charge-based force fields for liquid water using the adaptive force matching method
MOLECULAR SIMULATION, 37:591-605, 2011
abstract, full text

Abroshan, H., Akbarzadeh, H., Taherkhani, F., Parsafar, G.
Effect of water-methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamics study
MOLECULAR PHYSICS, 109:709-724, 2011
abstract, full text

Carr, R., Comer, J., Ginsberg, M.D., Aksimentiev, A.
Modeling Pressure-Driven Transport of Proteins Through a Nanochannel
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 10:75-82, JAN 2011
abstract, full text

Calero, C., Faraudo, J., Aguilella-Arzo, M.
Molecular dynamics simulations of concentrated aqueous electrolyte solutions
MOLECULAR SIMULATION, 37:123-134, 2011
abstract, full text

Cazade, P.A., Bordat, P., Baraille, I., Brown, R., Smith, W., Todorov, I.T.
DL_POLY_2 adaptations for solvation studies
MOLECULAR SIMULATION, 37:43-52, 2011
abstract, full text

Orozco, M., Orellana, L., Hospital, A., Naganathan, A.N., Emperador, A., Carrillo, O., Gelpi, J.L.
COARSE-GRAINED REPRESENTATION OF PROTEIN FLEXIBILITY. FOUNDATIONS, SUCCESSES, AND SHORTCOMINGS
ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, VOL 85: COMPUTATIONAL CHEMISTRY METHODS IN STRUCTURAL BIOLOGY, 85:183-215, 2011
abstract, full text

Friddle, R.W., Battle, K., Trubetskoy, V., Tao, J.H., Salter, E.A., Moradian-Oldak, J., De Yoreo, J.J., Wierzbicki, A.
Single-Molecule Determination of the Face-Specific Adsorption of Amelogenin's C-Terminus on Hydroxyapatite
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50:7541-7545, 2011
full text

Hsin, J., Strumpfer, J., Lee, E.H., Schulten, K.
Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory
ANNUAL REVIEW OF BIOPHYSICS, VOL 40, 40:187-203, 2011
abstract, full text, TCBG publications

Jamadagni, S.N., Godawat, R., Garde, S.
Hydrophobicity of Proteins and Interfaces: Insights from Density Fluctuations
ANNUAL REVIEW OF CHEMICAL AND BIOMOLECULAR ENGINEERING, VOL 2, 2:147-171, 2011
abstract, full text

Kortagere, S., Cheng, S.Y., Antonio, T., Zhen, J.A., Reith, M.E.A., Dutta, A.K.
Interaction of novel hybrid compounds with the D3 dopamine receptor: Site-directed mutagenesis and homology modeling studies
BIOCHEMICAL PHARMACOLOGY, 81:157-163, JAN 1 2011
abstract, full text

Kaila, V.R.I., Sharma, V., Wikstrom, M.
The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:80-84, JAN 2011
abstract, full text

Lim, J.B., Klauda, J.B.
Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:323-331, JAN 2011
abstract, full text

Zhao, J., Yu, X.A., Liang, G.Z., Zheng, J.
Structural Polymorphism of Human Islet Amyloid Polypeptide (hIAPP) Oligomers Highlights the Importance of Interfacial Residue Interactions
BIOMACROMOLECULES, 12:210-220, JAN 2011
abstract, full text

Lee, O.S., Schatz, G.C.
Computational Simulations of the Interaction of Lipid Membranes with DNA-Functionalized Gold Nanoparticles
BIOMEDICAL NANOETECHNOLOGY: METHODS AND PROTOCOLS, 726:283-296, 2011
abstract, full text

Kayser, V., Chennamsetty, N., Voynov, V., Forrer, K., Helk, B., Trout, B.L.
Glycosylation influences on the aggregation propensity of therapeutic monoclonal antibodies
BIOTECHNOLOGY JOURNAL, 6:38-44, JAN 2011
abstract, full text

Milac, A.L., Anishkin, A., Fatakia, S.N., Chow, C.C., Sukharev, S., Guy, H.R.
Structural models of TREK channels and their gating mechanism
CHANNELS, 5:23-33, JAN-FEB 2011
abstract, full text

Papadopoulos, T.A., Muccioli, L., Athanasopoulos, S., Walker, A.B., Zannoni, C., Beljonne, D.
Does supramolecular ordering influence exciton transport in conjugated systems? Insight from atomistic simulations
CHEMICAL SCIENCE, 2:1025-1032, 2011
abstract, full text

Moss, C.L., Chung, T.W., Cerovsky, V., Turecek, F.
ELECTRON TRANSFER DISSOCIATION OF A MELECTIN PEPTIDE: CORRELATING THE PRECURSOR ION STRUCTURE WITH PEPTIDE BACKBONE DISSOCIATIONS
COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, 76:295-309, 2011
abstract, full text

Cashman, D.J., Mamonov, A.B., Bhatt, D., Zuckerman, D.M.
Thermal Motions of the E. coli Glucose-Galactose Binding Protein Studied Using Well-Sampled Semi-Atomistic Simulations
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 11:211-220, JAN 2011
abstract, full text

Comer, J.R., Wells, D.B., Aksimentiev, A.
Modeling Nanopores for Sequencing DNA
DNA NANOTECHNOLOGY: METHODS AND PROTOCOLS, 749:317-358, 2011
abstract, full text

Aguilella, V.M., Queralt-Martin, M., Aguilella-Arzo, M., Alcaraz, A.
Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity
INTEGRATIVE BIOLOGY, 3:159-172, 2011
abstract, full text

Wagner, C., Olbrich, C., Brutzer, H., Salomo, M., Kleinekathofer, U., Keyser, U.F., Kremer, F.
DNA condensation by TmHU studied by optical tweezers, AFM and molecular dynamics simulations
JOURNAL OF BIOLOGICAL PHYSICS, 37:117-131, JAN 2011
abstract, full text

Kayser, V., Chennamsetty, N., Voynov, V., Helk, B., Trout, B.L.
Tryptophan-Tryptophan Energy Transfer and Classification of Tryptophan Residues in Proteins Using a Therapeutic Monoclonal Antibody as a Model
JOURNAL OF FLUORESCENCE, 21:275-288, JAN 2011
abstract, full text

Pizzirusso, A., Savini, M., Muccioli, L., Zannoni, C.
An atomistic simulation of the liquid-crystalline phases of sexithiophene
JOURNAL OF MATERIALS CHEMISTRY, 21:125-133, 2011
abstract, full text

Schow, E.V., Freites, J.A., Cheng, P., Bernsel, A., von Heijne, G., White, S.H., Tobias, D.J.
Arginine in Membranes: The Connection Between Molecular Dynamics Simulations and Translocon-Mediated Insertion Experiments
JOURNAL OF MEMBRANE BIOLOGY, 239:35-48, JAN 2011
abstract, full text

Bairagya, H.R., Mukhopadhyay, B.P., Bera, A.K.
Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II
JOURNAL OF MOLECULAR RECOGNITION, 24:35-44, JAN-FEB 2011
abstract, full text

Gangupomu, V.K., Capaldi, F.M.
Interactions of Carbon Nanotube with Lipid Bilayer Membranes
JOURNAL OF NANOMATERIALS, Art. No. 830436, 2011
abstract, full text

Chung, T.W., Moss, C.L., Zimnicka, M., Johnson, R.S., Moritz, R.L., Turecek, F.
Electron-Capture and -Transfer Dissociation of Peptides Tagged with Tunable Fixed-Charge Groups: Structures and Dissociation Energetics
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22:13-30, JAN 2011
abstract, full text

Lynch, R.M., Rong, R., Boliar, S., Sethi, A., Li, B., Mulenga, J., Allen, S., Robinson, J.E., Gnanakaran, S., Derdeyn, C.A.
The B Cell Response Is Redundant and Highly Focused on V1V2 during Early Subtype C Infection in a Zambian Seroconverter
JOURNAL OF VIROLOGY, 85:905-915, JAN 2011
abstract, full text

Carr, R., Comer, J., Ginsberg, M.D., Aksimentiev, A.
Atoms-to-microns model for small solute transport through sticky nanochannels
LAB ON A CHIP, 11:3766-3773, 2011
abstract, full text

Gill, J.P., Shaw, K.M., Rountree, B.L., Kehl, C.E., Chiel, H.J.
Simulating Kinetic Processes in Time and Space on a Lattice
MATHEMATICAL MODELLING OF NATURAL PHENOMENA, 6:159-197, 2011
abstract, full text

Suyetin, M.V., Vakhrushev, A.V.
Temperature-sensitive nanocapsule for drug delivery
MICRO & NANO LETTERS, 6:39-42, JAN 2011
abstract, full text

Tsaousis, A.D., Gaston, D., Stechmann, A., Walker, P.B., Lithgow, T., Roger, A.J.
A Functional Tom70 in the Human Parasite Blastocystis sp.: Implications for the Evolution of the Mitochondrial Import Apparatus
MOLECULAR BIOLOGY AND EVOLUTION, 28:781-791, JAN 2011
abstract, full text

Telesco, S.E., Shih, A.J., Jia, F., Radhakrishnan, R.
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network
MOLECULAR BIOSYSTEMS, 7:2066-2080, 2011
abstract, full text

Figueira, A.C.M., Saidemberg, D.M., Souza, P.C.T., Martinez, L., Scanlan, T.S., Baxter, J.D., Skaf, M.S., Palma, M.S., Webb, P., Polikarpov, I.
Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange
MOLECULAR ENDOCRINOLOGY, 25:15-31, JAN 2011
abstract, full text

Chan, H., Kral, P.
Self-standing nanoparticle membranes and capsules
NANOSCALE, 3:1881-1886, 2011
abstract, full text

Chakrapani, S., Cordero-Morales, J.F., Jogini, V., Pan, A.C., Cortes, D.M., Roux, B., Perozo, E.
On the structural basis of modal gating behavior in K+ channels
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 18:67-+, JAN 2011
abstract, full text

Pazos, E., Perez, M., Gutierrez-de-Teran, H., Orzaez, M., Guevara, T., Mascarenas, J.L., Vazquez, M.E.
Rational design of a cyclin A fluorescent peptide sensor
ORGANIC & BIOMOLECULAR CHEMISTRY, 9:7629-7632, 2011
abstract, full text

Gubbins, K.E., Liu, Y.C., Moore, J.D., Palmer, J.C.
The role of molecular modeling in confined systems: impact and prospects
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:58-85, 2011
abstract, full text

Wang, T., Shao, X.G., Cai, W.S., Xue, Y.L., Wang, S.A., Feng, X.Z.
Predicting the coordination geometry for Mg2+ in the p53 DNA-binding domain: insights from computational studies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:1140-1151, 2011
abstract, full text

Jiang, J., Mukamel, S.
Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:2394-2400, 2011
abstract, full text

Bernini, C., Pogni, R., Ruiz-Duenas, F.J., Martinez, A.T., Basosia, R., Sinicropi, A.
EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:5078-5098, 2011
abstract, full text

Chen, L.Y.
Exploring the free-energy landscapes of biological systems with steered molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6176-6183, 2011
abstract, full text

Guest, W.C., Cashman, N.R., Plotkin, S.S.
A theory for the anisotropic and inhomogeneous dielectric properties of proteins
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6286-6295, 2011
abstract, full text

Venturini, A., Zerbetto, F.
Dynamics of a lipid bilayer induced by electric fields
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9216-9222, 2011
abstract, full text

Suyetin, M.V., Vakhrushev, A.V.
Nanocapsule with pump for methane storage
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9863-9870, 2011
abstract, full text

Revilla-Lopez, G., Torras, J., Nussinov, R., Aleman, C., Zanuy, D.
Exploring the energy landscape of a molecular engineered analog of a tumor-homing peptide
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9986-9994, 2011
abstract, full text

Deplazes, E., Jayatilaka, D., Corry, B.
Testing the use of molecular dynamics to simulate fluorophore motions and FRET
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:11045-11054, 2011
abstract, full text

Kawashima, Y., Nakano, H., Jung, J., Ten-no, S.
A combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals: implementation for electronic excited states
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:11731-11738, 2011
abstract, full text

Wang, Q.M., Shah, N., Zhao, J., Wang, C.S., Zhao, C., Liu, L.Y., Li, L.Y., Zhou, F.M., Zheng, J.
Structural, morphological, and kinetic studies of beta-amyloid peptide aggregation on self-assembled monolayers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:15200-15210, 2011
abstract, full text

Yamamoto, T., Ohnishi, S.
Molecular dynamics study on helium nanobubbles in water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:16142-16145, 2011
abstract, full text

Reith, D., Mirny, L., Virnau, P.
GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling
PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT, Issue 191, 135-145, 2011
abstract, full text

Romo, T.D., Grossfield, A.
Validating and improving elastic network models with molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:23-34, JAN 2011
abstract, full text

Mustafa, M., Mirza, A., Kannan, N.
Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:99-114, JAN 2011
abstract, full text

Banu, M., Patriche, S., Coman, M., Matsushita, S., Tofan, A., Epureanu, A.
Investigation of ubiquitin deformation mechanism under induced stretch-compression loads
ROMANIAN JOURNAL OF MORPHOLOGY AND EMBRYOLOGY, 52:449-454, 2011
abstract, full text

Lyubartsev, A.P., Rabinovich, A.L.
Recent development in computer simulations of lipid bilayers
SOFT MATTER, 7:25-39, 2011
abstract, full text

Sun, S., Wong, J.T.Y., Zhang, T.Y.
Molecular dynamics simulations of phase transition of lamellar lipid membrane in water under an electric field
SOFT MATTER, 7:147-152, 2011
abstract, full text

Feng, J., Pandey, R.B., Berry, R.J., Farmer, B.L., Naik, R.R., Heinz, H.
Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules
SOFT MATTER, 7:2113-2120, 2011
abstract, full text

Arce, F.T., Jang, H.B., Ramachandran, S., Landon, P.B., Nussinov, R., Lal, R.
Polymorphism of amyloid beta peptide in different environments: implications for membrane insertion and pore formation
SOFT MATTER, 7:5267-5273, 2011
abstract, full text

Shinoda, W., DeVane, R., Klein, M.L.
Coarse-grained force field for ionic surfactants
SOFT MATTER, 7:6178-6186, 2011
abstract, full text

Teixeira-Dias, B., Zanuy, D., Poater, J., Sola, M., Estrany, F., del Valle, L.J., Aleman, C.
Binding of 6-mer single-stranded homo-nucleotides to poly(3,4-ethylenedioxythiophene): specific hydrogen bonds with guanine
SOFT MATTER, 7:9922-9932, 2011
abstract, full text

Castelletto, V., Moulton, C.M., Cheng, G., Hamley, I.W., Hicks, M.R., Rodger, A., Lopez-Perez, D.E., Revilla-Lopez, G., Aleman, C.
Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif
SOFT MATTER, 7:11405-11415, 2011
abstract, full text

Wang, Y., Dewdney, T.G., Liu, Z.G., Reiter, S.J., Brunzelle, J.S., Kovari, I.A., Kovari, L.C.
X-RAY CRYSTAL STRUCTURE AND DYNAMICS REVEAL HIV-1 PROTEASE DRUG INTERACTIONS
STUDIA UNIVERSITATIS BABES-BOLYAI CHEMIA, 56:221-230, 2011
abstract, full text

Zhang, M.H., Lu, S.Q., Li, G.W., Mao, Z.L., Yu, X., Sun, W.N., Tang, Z.C., Long, M.A., Su, W.A.
Identification of a Residue in Helix 2 of Rice Plasma Membrane Intrinsic Proteins That Influences Water Permeability
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:41982-41992, DEC 31 2010
abstract, full text

Luan, B.Q., Afzali, A., Harrer, S., Peng, H.B., Waggoner, P., Polonsky, S., Stolovitzky, G., Martyna, G.
Tribological Effects on DNA Translocation in a Nanochannel Coated with a Self-Assembled Monolayer
JOURNAL OF PHYSICAL CHEMISTRY B, 114:17172-17176, DEC 30 2010
abstract, full text

Neumann, A., Baginski, M., Czub, J.
How Do Sterols Determine the Antifungal Activity of Amphotericin B? Free Energy of Binding between the Drug and Its Membrane Targets
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:18266-18272, DEC 29 2010
abstract, full text

Jia, X.B., Zhang, J., Sun, H.W., Chen, L., Shen, R.X., Lai, C.M.
Molecular Dynamics Simulation Study on the Interaction Mode of Auxin Perception
ACTA CHIMICA SINICA, 68:2500-2508, DEC 28 2010
abstract, full text

Buch, I., Fishelovitch, D., London, N., Raveh, B., Wolfson, H.J., Nussinov, R.
Allosteric Regulation of Glycogen Synthase Kinase 3 beta: A Theoretical Study
BIOCHEMISTRY, 49:10890-10901, DEC 28 2010
abstract, full text

Jones, M.K., Zhang, L., Catte, A., Li, L., Oda, M.N., Ren, G., Segrest, J.P.
Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:41161-41171, DEC 24 2010
abstract, full text

Kaminski, S., Mroginski, M.A.
Molecular Dynamics of Phycocyanobilin Binding Bacteriophytochromes: A Detailed Study of Structural and Dynamic Properties
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16677-16686, DEC 23 2010
abstract, full text

Patapati, K.K., Glykos, N.M.
Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study
PLOS ONE, 5: Art. No. e15290, DEC 20 2010
abstract, full text

Kim, T., Cooper, J.A., Sept, D.
The Interaction of Capping Protein with the Barbed End of the Actin Filament
JOURNAL OF MOLECULAR BIOLOGY, 404:794-802, DEC 17 2010
abstract, full text

Jang, H., Arce, F.T., Ramachandran, S., Capone, R., Lal, R., Nussinov, R.
beta-Barrel Topology of Alzheimer's beta-Amyloid Ion Channels
JOURNAL OF MOLECULAR BIOLOGY, 404:917-934, DEC 17 2010
abstract, full text

DeVane, R., Jusufi, A., Shinoda, W., Chiu, C.C., Nielsen, S.O., Moore, P.B., Klein, M.L.
Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16364-16372, DEC 16 2010
abstract, full text

Du, H.B., Wickramasinghe, R., Qian, X.H.
Effects of Salt on the Lower Critical Solution Temperature of Poly (N-Isopropylacrylamide)
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16594-16604, DEC 16 2010
abstract, full text

Watanabe, A., Choe, S., Chaptal, V., Rosenberg, J.M., Wright, E.M., Grabe, M., Abramson, J.
The mechanism of sodium and substrate release from the binding pocket of vSGLT
NATURE, 468:988-U162, DEC 16 2010
abstract, full text

Turgut, D., Atilgan, A.R., Atilgan, C.
Assortative Mixing in Close-Packed Spatial Networks
PLOS ONE, 5: Art. No. e15551, DEC 16 2010
abstract, full text

Chen, K., Eargle, J., Sarkar, K., Gruebele, M., Luthey-Schulten, Z.
Functional Role of Ribosomal Signatures
BIOPHYSICAL JOURNAL, 99:3930-3940, DEC 15 2010
abstract, full text

Kaila, V.R.I., Johansson, M.P., Sundholm, D., Wikstrom, M.
Interheme electron tunneling in cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:21470-21475, DEC 14 2010
abstract, full text

Mirza, A., Mustafa, M., Talevich, E., Kannan, N.
Co-Conserved Features Associated with cis Regulation of ErbB Tyrosine Kinases
PLOS ONE, 5: Art. No. e14310, DEC 13 2010
abstract, full text

Carnevale, V., Fiorin, G., Levine, B.G., DeGrado, W.F., Klein, M.L.
Multiple Proton Confinement in the M2 Channel from the Influenza A Virus
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20856-20863, DEC 9 2010
abstract, full text

Nonella, M., Seeger, S.
Monitoring peptide-surface interaction by means of molecular dynamics simulation
CHEMICAL PHYSICS, 378:73-81, DEC 9 2010
abstract, full text

Davis, W.B., Bjorklund, C.C., Cho, P.S.
Hole Transport Dynamics in Mixed Sequence DNA Can Vary with Salt Concentration: An Experimental and Theoretical Analysis
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20821-20833, DEC 9 2010
abstract, full text

Lu, S.Q., Zhang, Y., Long, M.A.
Visualization of Allostery in P-Selectin Lectin Domain Using MD Simulations
PLOS ONE, 5: Art. No. e15417, DEC 8 2010