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

David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten.
Multilevel Summation Method for Electrostatic Force Evaluation.
Journal of Chemical Theory and Computation, 2014. In Press.
abstract, journal

Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot.
Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules.
Journal of Chemical Theory and Computation, 2014. In Press.
abstract, journal

James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laximant V. Kale.
Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.
In Proceedings of the 2014 International Conference for High Performance Computing, Networking, Storage, and Analysis (SC14), 2014.
abstract, conference, journal

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten.
Petascale Tcl with NAMD, VMD, and Swift/T.
In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. IEEE Press, 2014.
abstract, journal

Wei Jiang, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James Gumbart, Yun Luo, Klaus Schulten, and Benoit Roux.
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.
Computational Physics Communications, 185:908-916, 2014.
abstract, journal

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, journal

David E. Tanner, James C. Phillips, and Klaus Schulten.
GPU/CPU algorithm for generalized Born / solvent-accessible surface area implicit solvent calculations.
Journal of Chemical Theory and Computation, 8:2521-2530, 2012.
abstract, journal

David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten.
Parallel generalized Born implicit solvent calculations with NAMD.
Journal of Chemical Theory and Computation, 7:3635-3642, 2011.
abstract, journal

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, journal

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.

6043 citations found May 11, 2015.

Guerra, Fernando P.; Reyes, Luz; Vergara-Jaque, Ariela; Campos-Hernandez, Carola; Gutierrez, Adelina; Perez-Diaz, Jorge; Perez-Diaz, Ricardo; Blaudez, Damien; Ruiz-Lara, Simon
Populus deltoides Kunitz trypsin inhibitor 3 confers metal tolerance and binds copper, revealing a new defensive role against heavy metal stress
ENVIRONMENTAL AND EXPERIMENTAL BOTANY, 115:28-37, JUL 2015
abstract, full text, DOI:10.1016/j.envexpbot.2015.02.005

Hu, Benfeng; Ge, Zhenpeng; Li, Xiaoyi
Interface Adsorption Taking the Most Advantageous Conformation for Electron Transfer Between Graphene and Cytochrome c
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 15:4863-4869, JUL 2015
abstract, full text, DOI:10.1166/jnn.2015.9853

Sieradzan, Adam K.
Introduction of Periodic Boundary Conditions into UNRES Force Field
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:940-946, MAY 5 2015
abstract, full text, DOI:10.1002/jcc.23864

Azamat, Jafar; Khataee, Alireza; Joob, Sang Woo
Molecular dynamics simulation of trihalomethanes separation from water by functionalized nanoporous graphene under induced pressure
CHEMICAL ENGINEERING SCIENCE, 127:285-292, MAY 4 2015
abstract, full text, DOI:10.1016/j.ces.2015.01.048

Ko, Jeong-Ahn; Ambrosia, Matthew; Ha, Man Yeong
A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces
COMPUTERS & FLUIDS, 112:19-34, MAY 2 2015
abstract, full text, DOI:10.1016/j.compfluid.2015.02.005

Akcapinar, Gunseli Bayram; Kappel, Lisa; Sezerman, Osman Ugur; Seidl-Seiboth, Verena
Molecular diversity of LysM carbohydrate-binding motifs in fungi
CURRENT GENETICS, 61:103-113, MAY 2015
abstract, full text, DOI:10.1007/s00294-014-0471-9

Gaete-Eastman, Carlos; Morales-Quintana, Luis; Herrera, Raul; Alejandra Moya-Leon, Maria
In-silico analysis of the structure and binding site features of an alpha-expansin protein from mountain papaya fruit (VpEXPA2), through molecular modeling, docking, and dynamics simulation studies
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 115, MAY 2015
abstract, full text, DOI:10.1007/s00894-015-2656-7

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel
A theoretical study of the unfolding pathway of reduced Human serum albumin
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 106, MAY 2015
abstract, full text, DOI:10.1007/s00894-015-2659-4

Nanda, Hirsh; Heinrich, Frank; Loesche, Mathias
Membrane association of the PTEN tumor suppressor: Neutron scattering and MD simulations reveal the structure of protein-membrane complexes
METHODS, 77-78:136-146, MAY 1 2015
abstract, full text, DOI:10.1016/j.ymeth.2014.10.014

Jackson, Brian C.; Reigan, Philip; Miller, Bettina; Thompson, David C.; Vasiliou, Vasilis
Human ALDH1B1 Polymorphisms may Affect the Metabolism of Acetaldehyde and All-trans retinaldehyde-In Vitro Studies and Computational Modeling
PHARMACEUTICAL RESEARCH, 32:1648-1662, MAY 2015
abstract, full text, DOI:10.1007/s11095-014-1564-3

Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Li, Hung-Sheng; Hou, Tsai-Yi; Chu, Wen-Yuan; Shen, Po-Chuan; Chen, Ying-Yu; Tan, Chun-Jui; Hu, Jia-Cheng; Chiu, Chih-Chiang
Geometrical effects of phospholipid olefinic bonds on the structure and dynamics of membranes: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1234-1247, MAY 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.02.016

Begau, Christoph; Sutmann, Godehard
Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations
COMPUTER PHYSICS COMMUNICATIONS, 190:51-61, MAY 2015
abstract, full text, DOI:10.1016/j.cpc.2015.01.009

Nakamura, Takenobu; Kawamoto, Shuhei; Shinoda, Wataru
Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS
COMPUTER PHYSICS COMMUNICATIONS, 190:120-128, MAY 2015
abstract, full text, DOI:10.1016/j.cpc.2014.11.017

Vanommeslaeghe, K.; MacKerell, A. D., Jr.
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:861-871, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.08.004

Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
Enhanced sampling techniques in molecular dynamics simulations of biological systems
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:872-877, MAY 2015
abstract, full text, TCBG publications, DOI:10.1016/j.bbagen.2014.10.019

Batchelor, Matthew; Gowdy, James; Paci, Emanuele
Effect of external pulling forces on the length distribution of peptides
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:903-910, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.019

Lynch, Gillian C.; Perkyns, John S.; Bao Linh Nguyen; Pettitt, B. Montgomery
Solvation and cavity occupation in biomolecules
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:923-931, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.020

Cazade, Pierre-Andre; Berezovska, Ganna; Meuwly, Markus
Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:996-1005, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.008

Simonson, Thomas; Aleksandrov, Alexey; Satpati, Priyadarshi
Electrostatic free energies in translational GTPases: Classic allostery and the rest
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:1006-1016, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.07.006

Grauffel, Cedric; Stote, Roland H.; Dejaegere, Annick
Molecular dynamics for computational proteomics of methylated histone H3
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:1026-1040, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.015

Babcock, Jeremiah J.; Brancaleon, Lorenzo
The Effect of Local Dynamics of Atto 390-Labeled Lysozyme on Fluorescence Anisotropy Modeling
BIOPOLYMERS, 103:285-295, MAY 2015
abstract, full text, DOI:10.1002/bip.22596

Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.
Pairwise amino acid secondary structural propensities
PHYSICAL REVIEW E, 91 Art. No. 042709, APR 15 2015
abstract, full text, DOI:10.1103/PhysRevE.91.042709

Yuan, Yunyun; Zaidi, Saheem A.; Stevens, David L.; Scoggins, Krista L.; Mosier, Philip D.; Kellogg, Glen E.; Dewey, William L.; Selley, Dana E.; Zhang, Yan
Design, syntheses, and pharmacological characterization of 17-cyclopropylmethyl-3,14 beta-dihydroxy-4,5 alpha-epoxy-6 alpha-(isoquinoline-3 '-carboxamido)morphinan analogues as opioid receptor ligands
BIOORGANIC & MEDICINAL CHEMISTRY, 23:1701-1715, APR 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.02.055

Wang, Beibei; Weng, Jingwei; Wang, Wenning
Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB
FRONTIERS IN MICROBIOLOGY, 6 Art. No. 302, APR 13 2015
abstract, full text, DOI:10.3389/fmicb.2015.00302

Jang, Hyunbum; Abraham, Sherwin J.; Chavan, Tanmay S.; Hitchinson, Ben; Khavrutskii, Lyuba; Tarasova, Nadya I.; Nussinov, Ruth; Gaponenko, Vadim
Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:9465-9477, APR 10 2015
abstract, full text, DOI:10.1074/jbc.M114.620724

Krammer, Eva-Maria; Giang Thi Vu; Homble, Fabrice; Prevost, Martine
Dual Mechanism of Ion Permeation through VDAC Revealed with Inorganic Phosphate Ions and Phosphate Metabolites
PLOS ONE, 10 Art. No. e0121746, APR 10 2015
abstract, full text, DOI:10.1371/journal.pone.0121746

Kuttel, Michelle M.; Jackson, Graham E.; Mafata, Mpho; Ravenscroft, Neil
Capsular polysaccharide conformations in pneumococcal serotypes 19F and 19A
CARBOHYDRATE RESEARCH, 406:27-33, APR 10 2015
abstract, full text, DOI:10.1016/j.carres.2014.12.013

Preti, Delia; Baraldi, Pier Giovanni; Saponaro, Giulia; Romagnoli, Romeo; Tabrizi, Mojgan Aghazadeh; Baraldi, Stefania; Cosconati, Sandro; Bruno, Agostino; Novellino, Ettore; Vincenzi, Fabrizio; Ravani, Annalisa; Borea, Pier Andrea; Varani, Katia
Design, Synthesis, and Biological Evaluation of Novel 2-((2-4-(Substituted)phenylpiperazin-1-yl)ethyl)amino)-5 '-N-ethylcarboxamidoadenosines as Potent and Selective Agonists of the A(2A) Adenosine Receptor
JOURNAL OF MEDICINAL CHEMISTRY, 58:3253-3267, APR 9 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b00215

Semino, Rocio; Rodriguez, Javier
Molecular Dynamics Study of Ionic Liquids Complexation within beta-Cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4865-4872, APR 9 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00909

Denisov, Ilia G.; Grinkova, Yelena V.; Baylon, Javier L.; Tajkhorshid, Emad; Sligar, Stephen G.
Mechanism of Drug-Drug Interactions Mediated by Human Cytochrome P450 CYP3A4 Monomer
BIOCHEMISTRY, 54:2227-2239, APR 7 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00079

Michel Espinoza-Fonseca, L.; Autry, Joseph M.; Lizbeth Ramirez-Salinas, G.; Thomas, David D.
Atomic-Level Mechanisms for Phospholamban Regulation of the Calcium Pump
BIOPHYSICAL JOURNAL, 108:1697-1708, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.004

Davis, Brittny C.; Brown, Jodian A.; Thorpe, Ian F.
Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase
BIOPHYSICAL JOURNAL, 108:1785-1795, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.005

Miao, Yinglong; Caliman, Alisha D.; McCammon, J. Andrew
Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor
BIOPHYSICAL JOURNAL, 108:1796-1806, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.003

Lockhart, Christopher; Klimov, Dmitri K.
Calcium Enhances Binding of A beta Monomer to DMPC Lipid Bilayer
BIOPHYSICAL JOURNAL, 108:1807-1818, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.001

Tsutakawa, Susan E.; Yan, Chunli; Xu, Xiaojun; Weinacht, Christopher P.; Freudenthal, Bret D.; Yang, Kun; Zhuang, Zhihao; Washington, M. Todd; Tainer, John A.; Ivanov, Ivaylo
Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response
STRUCTURE, 23:724-733, APR 7 2015
abstract, full text, DOI:10.1016/j.str.2015.02.008

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
Accuracy Assessment of the Linear Poisson-Boltzmann Equation and Reparametrization of the OBC Generalized Born Model for Nucleic Acids and Nucleic Acid-Protein Complexes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:585-596, APR 5 2015
abstract, full text, DOI:10.1002/jcc.23832

Elmes, Matthew W.; Kaczocha, Martin; Berger, William T.; Leung, KwanNok; Ralph, Brian P.; Wang, Liqun; Sweeney, Joseph M.; Miyauchi, Jeremy T.; Tsirka, Stella E.; Ojima, Iwao; Deutsch, Dale G.
Fatty Acid-binding Proteins (FABPs) Are Intracellular Carriers for Delta(9)-Tetrahydrocannabinol (THC) and Cannabidiol (CBD)
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:8711-8721, APR 3 2015
abstract, full text, DOI:10.1074/jbc.M114.618447

Gillet, Jean-Numa
Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:690-705, APR 3 2015
abstract, full text, DOI:10.1080/07391102.2014.907544

Jimenez, Veronica A.; Alderete, Joel B.; Navarrete, Karen R.
Structural insight into epothilones antitumor activity based on the conformational preferences and tubulin binding modes of epothilones A and B obtained from molecular dynamics simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:789-803, APR 3 2015
abstract, full text, DOI:10.1080/07391102.2014.911702

Dokainish, Hisham M.; Gauld, James W.
Formation of a Stable Iminol Intermediate in the Redox Regulation Mechanism of Protein Tyrosine Phosphatase 1B (PTP1B)
ACS CATALYSIS, 5:2195-2202, APR 2015
abstract, full text, DOI:10.1021/cs501707h

Wang, Zhiming; Qiao, Zhu; Ye, Sheng; Zhang, Rongguang
Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71:779-789, APR 2015
abstract, full text, DOI:10.1107/S1399004715001169

Johnson, Jennifer L.; Entzminger, Kevin C.; Hyun, Jeongmin; Kalyoncu, Sibel; Heaner, David P., Jr.; Morales, Ivan A.; Sheppard, Aly; Gumbart, James C.; Maynard, Jennifer A.; Lieberman, Raquel L.
Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71:896-906, APR 2015
abstract, full text, DOI:10.1107/S1399004715001856

Lehman, William; Medlock, Greg; Li, Xiaochuan (Edward); Suphamungmee, Worawit; Tu, An-Yue; Schmidtmann, Anja; Ujfalusi, Zoltan; Fischer, Stefan; Moore, Jeffrey R.; Geeves, Michael A.; Regnier, Michael
Phosphorylation of Ser283 enhances the stiffness of the tropomyosin head-to-tail overlap domain
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 571:10-15, APR 1 2015
abstract, full text, DOI:10.1016/j.abb.2015.02.026

Kwon, Tae Woo; Ambrosia, Matthew Stanley; Jang, Joonkyoung; Ha, Man Yeong
Dynamic hydrophobicity of heterogeneous pillared surfaces at the nano-scale
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 29:1663-1671, APR 2015
abstract, full text, DOI:10.1007/s12206-015-0338-0

Nguyen, Phuong T. V.; Yu, Haibo; Keller, Paul A.
Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:1-8, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.001

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo; Yin, Binfeng
Removal of trihalomethanes from aqueous solution through armchair carbon nanotubes: A molecular dynamics study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:70-75, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.008

Behera, Pabitra Mohan; Behera, Deepak Kumar; Satpati, Suresh; Agnihotri, Geetanjali; Nayak, Sanghamitra; Padhi, Payodhar; Dixit, Anshuman
Molecular modeling and identification of novel glucokinase activators through stepwise virtual screening
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:122-130, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.012

Viricel, Clement; Ahmed, Marawan; Barakat, Khaled
Human PD-1 binds differently to its human ligands: A comprehensive modeling study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:131-142, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.015

Tarasevich, Barbara J.; Philo, John S.; Maluf, Nasib Karl; Krueger, Susan; Buchko, Garry W.; Lin, Genyao; Shaw, Wendy J.
The leucine-rich amelogenin protein (LRAP) is primarily monomeric and unstructured in physiological solution
JOURNAL OF STRUCTURAL BIOLOGY, 190:81-91, APR 2015
abstract, full text, DOI:10.1016/j.jsb.2014.10.007

Pedretti, Alessandro; Mazzolari, Angelica; Ricci, Chiara; Vistoli, Giulio
Enhancing the Reliability of GPCR Models by Accounting for Flexibility of Their Pro-Containing Helices: the Case of the Human mAChR1 Receptor
MOLECULAR INFORMATICS, 34:216-227, APR 2015
abstract, full text, DOI:10.1002/minf.201400159

Kaczor, Agnieszka A.; Guixa-Gonzalez, Ramon; Carrio, Pau; Poso, Antti; Dove, Stefan; Pastor, Manuel; Selent, Jana
Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors
MOLECULAR INFORMATICS, 34:246-255, APR 2015
abstract, full text, DOI:10.1002/minf.201400088

Jorgensen, Christian; Darre, Leonardo; Vanommeslaeghe, Kenno; Omoto, Kiyoyuki; Pryde, David; Domene, Carmen
In Silico Identification of PAP-1 Binding Sites in the Kv1.2 Potassium Channel
MOLECULAR PHARMACEUTICS, 12:1299-1307, APR 2015
abstract, full text, DOI:10.1021/acs.molpharmaceut.5b00023

D'Avino, Gabriele; Muccioli, Luca; Zannoni, Claudio
From Chiral Islands to Smectic Layers: A Computational Journey Across Sexithiophene Morphologies on C-60
ADVANCED FUNCTIONAL MATERIALS, 25:1985-1995, APR 1 2015
abstract, full text, DOI:10.1002/adfm.201402609

Comitani, Federico; Melis, Claudio; Molteni, Carla
Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations
BIOCHEMICAL SOCIETY TRANSACTIONS, 43:151-156, APR 2015
abstract, full text, DOI:10.1042/BST20140259

Mitra, Suranjita; Mukhopadhyay, Bidhan Chandra; Mandal, Anisur Rahaman; Arukha, Ananta Prasad; Chakrabarty, Kuheli; Das, Gourab Kanti; Chakrabartty, Pran Krishna; Biswas, Swadesh Ranjan
Cloning, overexpression, and characterization of a novel alkali-thermostable xylanase from Geobacillus sp WBI
JOURNAL OF BASIC MICROBIOLOGY, 55:527-537, APR 2015
abstract, full text, DOI:10.1002/jobm.201400495

Aitha, Mahesh; Moritz, Lindsay; Sahu, Indra D.; Sanyurah, Omar; Roche, Zahilyn; McCarrick, Robert; Lorigan, Gary A.; Bennett, Brian; Crowder, Michael W.
Conformational dynamics of metallo-beta-lactamase CcrA during catalysis investigated by using DEER spectroscopy
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 20:585-594, APR 2015
abstract, full text, DOI:10.1007/s00775-015-1244-8

Montanez, Mara I.; Najera, Francisco; Mayorga, Cristobalina; Ruiz-Sanchez, Antonio J.; Vida, Yolanda; Collado, Daniel; Blanca, Miguel; Torres, Maria J.; Perez-Inestrosa, Ezequiel
Recognition of multiepitope dendrimeric antigens by human immunoglobulin E
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE, 11:579-588, APR 2015
abstract, full text, DOI:10.1016/j.nano.2015.01.006

Dong, Sijia S.; Abrol, Ravinder; Goddard, William A.
The Predicted Ensemble of Low-Energy Conformations of Human Somatostatin Receptor Subtype 5 and the Binding of Antagonists
CHEMMEDCHEM, 10:650-661, APR 2015
abstract, full text, DOI:10.1002/cmdc.201500023

Sfyroera, Georgia; Ricklin, Daniel; Reis, Edimara S.; Chen, Hui; Wu, Emilia L.; Kaznessis, Yiannis N.; Ekdahl, Kristina N.; Nilsson, Bo; Lambris, John D.
Rare Loss-of-Function Mutation in Complement Component C3 Provides Insight into Molecular and Pathophysiological Determinants of Complement Activity
JOURNAL OF IMMUNOLOGY, 194:3305-3316, APR 1 2015
abstract, full text, DOI:10.4049/jimmunol.1402781

Qu, Tao; Verma, Devendra; Shahidi, Mehran; Pichler, Bernhard; Hellmich, Christian; Tomar, Vikas
Mechanics of organic-inorganic biointerfaces-Implications for strength and creep properties
MRS BULLETIN, 40:349-358, APR 2015
abstract, full text, DOI:10.1557/mrs.2015.70

Mernea, Maria; Ionescu, Alina; Vasile, Ionut; Nica, Cristina; Stoian, Gheorghe; Dascalu, Traian; Mihailescu, Dan Florin
In vitro human serum albumin glycation monitored by Terahertz spectroscopy
OPTICAL AND QUANTUM ELECTRONICS, 47:961-973, APR 2015
abstract, full text, DOI:10.1007/s11082-015-0129-y

Mornon, Jean-Paul; Hoffmann, Brice; Jonic, Slavica; Lehn, Pierre; Callebaut, Isabelle
Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics
CELLULAR AND MOLECULAR LIFE SCIENCES, 72:1377-1403, APR 2015
abstract, full text, DOI:10.1007/s00018-014-1749-2

Zhang, Peng; Deng, Yuefan; Feng, Rui; Luo, Xingguo; Wu, Jiangxing
Evaluation of Various Networks Configurated by Adding Bypass or Torus Links
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 26:984-996, APR 2015
abstract, full text, DOI:10.1109/TPDS.2014.2315201

Sharma, Anurag; Payne, Scott; Katti, Kalpana S.; Katti, Dinesh R.
Evaluating Molecular Interactions in Polycaprolactone-Biomineralized Hydroxyapatite Nanocomposites using Steered Molecular Dynamics
JOM, 67:733-743, APR 2015
abstract, full text, DOI:10.1007/s11837-015-1361-4

Zhang, Pu-pu; Zhao, Li; Long, Shi-yang; Tian, Pu
The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 72, APR 2015
abstract, full text, DOI:10.1007/s00894-015-2625-1

Alaybeyoglu, Begum; Sariyar Akbulut, Berna; Ozkirimli, Elif
A novel chimeric peptide with antimicrobial activity
JOURNAL OF PEPTIDE SCIENCE, 21:294-301, APR 2015
abstract, full text, DOI:10.1002/psc.2739

Sensoy, Ozge; Weinstein, Hare
A mechanistic role of Helix 8 in GPCRs: Computational modeling of the dopamine D2 receptor interaction with the GIPC1-PDZ-domain
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:976-983, APR 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.12.002

Rogers, David M.; Kent, Michael S.; Rempe, Susan B.
Molecular basis of endosomal-membrane association for the dengue virus envelope protein
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1041-1052, APR 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.12.018

Trung Dac Nguyen; Plimpton, Steven J.
Accelerating dissipative particle dynamics simulations for soft matter systems
COMPUTATIONAL MATERIALS SCIENCE, 100:173-180, APR 1 2015
abstract, full text, DOI:10.1016/j.commatsci.2014.10.068

Feroz, Shevin R.; Teoh, Yue Jun; Mohamad, Saharuddin B.; Hong, Sok Lai; Malek, Sri Na.; Tayyab, Saad
Interaction of flavokawain B with lysozyme: A photophysical and molecular simulation study
JOURNAL OF LUMINESCENCE, 160:101-109, APR 2015
abstract, full text, DOI:10.1016/j.jlumin.2014.11.053

Garcia, Pamela Soto; Dario Moreau, Alberto Luis; Magalhaes Ierich, Jessica Cristiane; Araujo Vig, Ana Carolina; Higa, Akemi Martins; Oliveira, Guedmiller S.; Abdalla, Fabio Camargo; Hausen, Moema; Leite, Fabio L.
A Nanobiosensor Based on 4-Hydroxyphenylpyruvate Dioxygenase Enzyme for Mesotrione Detection
IEEE SENSORS JOURNAL, 15:2106-2113, APR 2015
abstract, full text, DOI:10.1109/JSEN.2014.2371773

Vermaas, Josh V.; Taguchi, Alexander T.; Dikanov, Sergei A.; Wraight, Colin A.; Tajkhorshid, Emad
Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter sphaeroides
BIOCHEMISTRY, 54:2104-2116, MAR 31 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00033

Impellizzeri, Agata Antonina Rita; Pappalardo, Matteo; Basile, Livia; Manfra, Ornella; Andressen, Kjetil Wessel; Krobert, Kurt Allen; Messina, Angela; Levy, Finn Olav; Guccione, Salvatore
Identification of essential residues for binding and activation in the human 5-HT7(a) serotonin receptor by molecular modeling and site-directed mutagenesis
FRONTIERS IN BEHAVIORAL NEUROSCIENCE, 9 Art. No. 92, MAR 31 2015
abstract, full text, DOI:10.3389/fnbeh.2015.00092

Ho, Jianghai; Perez-Aguilar, Jose Manuel; Gao, Lu; Saven, Jeffery G.; Matsunami, Hiroaki; Eckenhoff, Roderic G.
Molecular recognition of ketamine by a subset of olfactory G protein-coupled receptors
SCIENCE SIGNALING, 8 Art. No. ra33, MAR 31 2015
abstract, full text, DOI:10.1126/scisignal.2005912

Chandramouli, Balasubramanian; Di Maio, Danilo; Mancini, Giordano; Barone, Vincenzo; Brancato, Giuseppe
Breaking the Hydrophobicity of the MscL Pore: Insights into a Charge-Induced Gating Mechanism
PLOS ONE, 10 Art. No. e0120196, MAR 31 2015
abstract, full text, DOI:10.1371/journal.pone.0120196

Lai, Pin-Kuang; Lin, Shiang-Tai
Internal Coordinate Density of State from Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:507-517, MAR 30 2015
abstract, full text, DOI:10.1002/jcc.23822

Padhi, Siladitya; Ramakrishna, Siddabattula; Priyakumar, U. Deva
Prediction of the Structures of Helical Membrane Proteins Based on a Minimum Unfavorable Contacts Approach
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:539-552, MAR 30 2015
abstract, full text, DOI:10.1002/jcc.23828

Loerbroks, Claudia; Boulanger, Eliot; Thiel, Walter
Solvent Influence on Cellulose 1,4-beta-Glycosidic Bond Cleavage: A Molecular Dynamics and Metadynarnics Study
CHEMISTRY-A EUROPEAN JOURNAL, 21:5477-5487, MAR 27 2015
abstract, full text, DOI:10.1002/chem.201405507

Martinez, Leandro
Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis
PLOS ONE, 10 Art. No. e0119264, MAR 27 2015
abstract, full text, DOI:10.1371/journal.pone.0119264

Sanchez-Rodriguez, Jorge E.; Khalili-Araghi, Fatemeh; Miranda, Pablo; Roux, Benoit; Holmgren, Miguel; Bezanilla, Francisco
A Structural Rearrangement of the Na+/K+-ATPase Traps Ouabain within the External Ion Permeation Pathway
JOURNAL OF MOLECULAR BIOLOGY, 427:1335-1344, MAR 27 2015
abstract, full text, DOI:10.1016/j.jmb.2015.01.011

Girdhar, Anuj; Sathe, Chaitanya; Schulten, Klaus; Leburton, Jean-Pierre
Tunable graphene quantum point contact transistor for DNA detection and characterization
NANOTECHNOLOGY, 26 Art. No. 134005, MAR 27 2015
abstract, full text, TCBG publications, DOI:10.1088/0957-4484/26/13/134005

Savelyev, Alexey; MacKerell, Alexander D., Jr.
Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4428-4440, MAR 26 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00683

Rheault, Jean-Francois; Gagne, Eve; Guertin, Michel; Lamoureux, Guillaume; Auger, Michele; Laguee, Patrick
Molecular Model of Hemoglobin N from Mycobacterium tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study
BIOCHEMISTRY, 54:2073-2084, MAR 24 2015
abstract, full text, DOI:10.1021/bi5010624

Guo, Jiqing; Cheng, Yen May; Lees-Miller, James P.; Perissinotti, Laura L.; Claydon, Tom W.; Hull, Christina M.; Thouta, Samrat; Roach, Daniel E.; Durdagi, Serdar; Noskov, Sergei Y.; Duff, Henry J.
NS1643 Interacts around L529 of hERG to Alter Voltage Sensor Movement on the Path to Activation
BIOPHYSICAL JOURNAL, 108:1400-1413, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2014.12.055

Morgan, Brittany R.; Deveau, Laura M.; Massi, Francesca
Probing the Structural and Dynamical Effects of the Charged Residues of the TZF Domain of TIS11d
BIOPHYSICAL JOURNAL, 108:1503-1515, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2015.01.039

Burmann, Bjoern M.; Holdbrook, Daniel A.; Callon, Morgane; Bond, Peter J.; Hiller, Sebastian
Revisiting the Interaction between the Chaperone Skp and Lipopolysaccharide
BIOPHYSICAL JOURNAL, 108:1516-1526, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2015.01.029

Plascencia-Villa, German; Torrente, Daniel; Marucho, Marcelo; Jose-Yacaman, Miguel
Biodirected Synthesis and Nanostructural Characterization of Anisotropic Gold Nanoparticles
LANGMUIR, 31:3527-3536, MAR 24 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b00084

Ren, Baiping; Gao, Huipeng; Cao, Yafeng; Jia, Lingyun
In Silico understanding of the cyclodextrin-phenanthrene hybrid assemblies in both aqueous medium and bacterial membranes
JOURNAL OF HAZARDOUS MATERIALS, 285:148-156, MAR 21 2015
abstract, full text, DOI:10.1016/j.jhazmat.2014.12.001

Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli
A Model of Lipid-Free Apolipoprotein A-I Revealed by Iterative Molecular Dynamics Simulation
PLOS ONE, 10 Art. No. e0120233, MAR 20 2015
abstract, full text, DOI:10.1371/journal.pone.0120233

Andrijchenko, Natalya N.; Ermilov, Alexander Yu.; Khriachtchev, Leonid; Rasanen, Markku; Nemukhin, Alexander V.
Toward Molecular Mechanism of Xenon Anesthesia: A Link to Studies of Xenon Complexes with Small Aromatic Molecules
JOURNAL OF PHYSICAL CHEMISTRY A, 119:2517-2521, MAR 19 2015
abstract, full text, DOI:10.1021/jp508800k

Shilov, Ignat Yu.
Molecular dynamics simulation of dielectric constant and cluster structure of liquid methanol: the role of cluster-cluster dipole correlations
MOLECULAR PHYSICS, 113:570-576, MAR 19 2015
abstract, full text, DOI:10.1080/00268976.2014.960496

Mehta, Jatin; Asthana, Shailendra; Mandal, Chandi Charan; Saxena, Sunita
A Molecular Analysis Provides Novel Insights into Androgen Receptor Signalling in Breast Cancer
PLOS ONE, 10 Art. No. e0120622, MAR 17 2015
abstract, full text, DOI:10.1371/journal.pone.0120622

Bruno, Agostino; Scrima, Mario; Novellino, Ettore; D'Errico, Gerardino; D'Ursi, Anna Maria; Limongelli, Vittorio
The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)
SCIENTIFIC REPORTS, 5 Art. No. 9200, MAR 17 2015
abstract, full text, DOI:10.1038/srep09200

Blair, Jessica M. A.; Bavro, Vassiliy N.; Ricci, Vito; Modi, Niraj; Cacciotto, Pierpaolo; Kleinekathoefer, Ulrich; Ruggerone, Paolo; Vargiu, Attilio V.; Baylay, Alison J.; Smith, Helen E.; Brandon, Yvonne; Galloway, David; Piddock, Laura J. V.
AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:3511-3516, MAR 17 2015
abstract, full text, DOI:10.1073/pnas.1419939112

Kinoshita, Mikitaka; Okada, Tetsuji
Structural conservation among the rhodopsin-like and other G protein-coupled receptors
SCIENTIFIC REPORTS, 5 Art. No. 9176, MAR 17 2015
abstract, full text, DOI:10.1038/srep09176

Mizuguchi, Tomoko; Ishizuka, Ryosuke; Matubayasi, Nobuyuki
Effect of diffuseness of micelle boundary on the solute distribution upon solubilization
CHEMICAL PHYSICS LETTERS, 624:19-23, MAR 16 2015
abstract, full text, DOI:10.1016/j.cplett.2015.02.001

Hameau, Aurelien; Fruchon, Severine; Bijani, Christian; Barducci, Alessandro; Blanzat, Muriel; Poupot, Remy; Pavan, Giovanni M.; Caminade, Anne-Marie; Turrin, Cedric-Olivier
Theoretical and Experimental Characterization of Amino-PEG-Phosphonate-Terminated Polyphosphorhydrazone Dendrimers: Influence of Size and PEG Capping on Cytotoxicity Profiles
JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY, 53:761-774, MAR 15 2015
abstract, full text, DOI:10.1002/pola.27501

Hanasaki, Itsuo; Nagura, Ryo; Kawano, Satoyuki
Coarse-grained picture of Brownian motion in water: Role of size and interaction distance range on the nature of randomness
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 104301, MAR 14 2015
abstract, full text, DOI:10.1063/1.4913748

Megow, Joerg; Roehr, Merle I. S.; Busch, Marcel Schmidt am; Renger, Thomas; Mitric, Roland; Kirstein, Stefan; Rabe, Juergen P.; May, Volkhard
Site-dependence of van der Waals interaction explains exciton spectra of double-walled tubular J-aggregates
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6741-6747, MAR 14 2015
abstract, full text, DOI:10.1039/c4cp05945j

Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Kang, Ying; Ge, Zhongxue
Interactions of carbon nanotubes with the nitromethane-water mixture governing selective adsorption of energetic molecules from aqueous solution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6995-7001, MAR 14 2015
abstract, full text, DOI:10.1039/c4cp05909c

Hu, Yunfei; Wu, Yujie; Li, Qianwen; Zhang, Wenbo; Jin, Changwen
Solution Structure of Yeast Rpn9 INSIGHTS INTO PROTEASOME LID ASSEMBLY
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:6878-6889, MAR 13 2015
abstract, full text, DOI:10.1074/jbc.M114.626762

Islam, Shahidul M.; Roux, Benoit
Simulating the Distance Distribution between Spin-Labels Attached to Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3901-3911, MAR 12 2015
abstract, full text, DOI:10.1021/jp510745d

Lee, Cheng-Kuang; Pao, Chun-Wei; Smit, Berend
PSII-LHCII Supercomplex Organizations in Photosynthetic Membrane by Coarse-Grained Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3999-4008, MAR 12 2015
abstract, full text, DOI:10.1021/jp511277c

Dubiez, Etienne; Aleksandrov, Alexey; Lazennec-Schurdevin, Christine; Mechulam, Yves; Schmitt, Emmanuelle
Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2
NUCLEIC ACIDS RESEARCH, 43:2946-2957, MAR 11 2015
abstract, full text, DOI:10.1093/nar/gkv053

Serratos, Iris N.; Castellanos, Pilar; Pastor, Nina; Millan-Pacheco, Cesar; Rembao, Daniel; Perez-Montfort, Ruy; Cabrera, Nallely; Reyes-Espinosa, Francisco; Diaz-Garrido, Paulina; Lopez-Macay, Ambar; Martinez-Flores, Karina; Lopez-Reyes, Alberto; Sanchez-Garcia, Aurora; Cuevas, Elvis; Santamaria, Abel
Modeling the Interaction between Quinolinate and the Receptor for Advanced Glycation End Products (RAGE): Relevance for Early Neuropathological Processes
PLOS ONE, 10 Art. No. UNSP e0120221, MAR 10 2015
abstract, full text, DOI:10.1371/journal.pone.0120221

Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He
Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase
BIOCHEMISTRY, 54:1841-1848, MAR 10 2015
abstract, full text, DOI:10.1021/bi5015612

Leone, Vanessa; Pogoryelov, Denys; Meier, Thomas; Faraldo-Gomez, Jose D.
On the principle of ion selectivity in Na+/H+-coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E1057-E1066, MAR 10 2015
abstract, full text, DOI:10.1073/pnas.1421202112

Lee, Hui Sun; Qi, Yifei; Im, Wonpil
Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study
SCIENTIFIC REPORTS, 5 Art. No. 8926, MAR 9 2015
abstract, full text, DOI:10.1038/srep08926

Mendoza-Martinez, Cesar; Galindo-Sevilla, Norma; Correa-Basurto, Jose; Manuel Ugalde-Saldivar, Victor; Georgina Rodriguez-Delgado, Rosa; Hernandez-Pineda, Jessica; Padierna-Mota, Cecilia; Flores-Alamo, Marcos; Hernandez-Luis, Francisco
Antileishmanial activity of quinazoline derivatives: Synthesis, docking screens, molecular dynamic simulations and electrochemical studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 92:314-331, MAR 6 2015
abstract, full text, DOI:10.1016/j.ejmech.2014.12.051

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji
Origin of 1/f noise in hydration dynamics on lipid membrane surfaces
SCIENTIFIC REPORTS, 5 Art. No. 8876, MAR 6 2015
abstract, full text, DOI:10.1038/srep08876

Weng, Jingwei; Yang, Yanhong; Wang, Wenning
Lipid Regulated Conformational Dynamics of the Longin SNARE Protein Ykt6 Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 119:1554-1562, MAR 5 2015
abstract, full text, DOI:10.1021/jp5075708

Guzman, Irisbel; Ghaemi, Zhaleh; Baranger, Anne; Luthey-Schulten, Zaida; Gruebele, Martin
Native Conformational Dynamics of the Spliceosomal U1A Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3651-3661, MAR 5 2015
abstract, full text, DOI:10.1021/jp511760m

Zenn, Roland K.; Abad, Enrique; Kaestner, Johannes
Influence of the Environment on the Oxidative Deamination of p-Substituted Benzylamines in Monoamine Oxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3678-3686, MAR 5 2015
abstract, full text, DOI:10.1021/jp512470a

Nierzwicki, Lukasz; Czub, Jacek
Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:784-790, MAR 5 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b00197

Miyashita, Naoyuki; Re, Suyong; Sugita, Yuji
REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:325-332, MAR 5 2015
abstract, full text, DOI:10.1002/qua.24785

Yoshii, Noriyuki; Andoh, Yoshimichi; Fujimoto, Kazushi; Kojima, Hidekazu; Yamada, Atsushi; Okazaki, Susumu
MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:342-348, MAR 5 2015
abstract, full text, DOI:10.1002/qua.24841

Ma, Wen; Schulten, Klaus
Mechanism of Substrate Trans location by a Ring-Shaped ATPase Motor at Millisecond Resolution
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:3031-3040, MAR 4 2015
abstract, full text, TCBG publications, DOI:10.1021/ja512605w

Yu, Tang-Qing; Lapelosa, Mauro; Vanden-Eijnden, Eric; Abrams, Cameron F.
Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:3041-3050, MAR 4 2015
abstract, full text, DOI:10.1021/ja512484q

Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang
HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation
SCIENTIFIC REPORTS, 5 Art. No. 8741, MAR 4 2015
abstract, full text, DOI:10.1038/srep08741

Yao, Huili; Rui, Huan; Kumar, Ritesh; Eshelman, Kate; Lovell, Scott; Battaile, Kevin P.; Im, Wonpil; Rivera, Mario
Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic
BIOCHEMISTRY, 54:1611-1627, MAR 3 2015
abstract, full text, DOI:10.1021/bi501255r

Fetics, Susan K.; Guterres, Hugo; Kearney, Bradley M.; Buhrman, Greg; Ma, Buyong; Nussinov, Ruth; Mattos, Carla
Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD
STRUCTURE, 23:505-516, MAR 3 2015
abstract, full text, DOI:10.1016/j.str.2014.12.017

Duran-Lara, Esteban F.; Avila-Salas, Fabian; Galaz, Sebastian; John, Amalraj; Marican, Adolfo; Gutierrez, Margarita; Nachtigall, Fabiane M.; Gonzalez-Nilo, Fernando D.; Santos, Leonardo S.
Nano-Detoxification of Organophosphate Agents by PAMAM Derivatives
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 26:580-591, MAR 2015
abstract, full text, DOI:10.5935/0103-5053.20150013

Yuan, Li; Nerngchamnong, Nisachol; Cao, Liang; Hamoudi, Hicham; del Barco, Enrique; Roemer, Max; Sriramula, Ravi K.; Thompson, Damien; Nijhuis, Christian A.
Controlling the direction of rectification in a molecular diode
NATURE COMMUNICATIONS, 6 Art. No. 6324, MAR 2015
abstract, full text, DOI:10.1038/ncomms7324

Wu, Di
Proline puckering parameters for collagen structure simulations
AIP ADVANCES, 5 Art. No. 037124, MAR 2015
abstract, full text, DOI:10.1063/1.4915295

Schiro, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Haertlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin
Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins
NATURE COMMUNICATIONS, 6 Art. No. 6490, MAR 2015
abstract, full text, DOI:10.1038/ncomms7490

Miguel, Amanda; Hsin, Jen; Liu, Tianyun; Tang, Grace; Altman, Russ B.; Huang, Kerwyn Casey
Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004117, MAR 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004117

Izanloo, C.
Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study
CANADIAN JOURNAL OF CHEMISTRY, 93:348-361, MAR 2015
abstract, full text, DOI:10.1139/cjc-2014-0371

Chen, Qi; Cheng, Xiaolin; Wei, Dongqing; Xu, Qin
Molecular Dynamics Simulation Studies of the Wild Type and E92Q/N155H Mutant of Elvitegravir-resistance HIV-1 Integrase
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 7:36-42, MAR 2015
abstract, full text, DOI:10.1007/s12539-014-0235-8

Feng, Zhiwei; Pearce, Larry V.; Xu, Xiaomeng; Yang, Xiaole; Yang, Peng; Blumberg, Peter M.; Xie, Xiang-Qun
Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening, and Bioassay Validations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:572-588, MAR 2015
abstract, full text, DOI:10.1021/ci5007189

Tsigelny, Igor F.; Sharikov, Yuriy; Kouznetsova, Valentina L.; Greenberg, Jerry P.; Wrasidlo, Wolf; Overk, Cassia; Gonzalez, Tania; Trejo, Margarita; Spencer, Brian; Kosberg, Kori; Masliah, Eliezer
Molecular Determinants of alpha-Synuclein Mutants' Oligomerization and Membrane Interactions
ACS CHEMICAL NEUROSCIENCE, 6:403-416, MAR 2015
abstract, full text, DOI:10.1021/cn500332w

Tofoleanu, Florentina; Brooks, Bernard R.; Buchete, Nicolae-Viorel
Modulation of Alzheimer's A beta Protofilament-Membrane Interactions by Lipid Headgroups
ACS CHEMICAL NEUROSCIENCE, 6:446-455, MAR 2015
abstract, full text, DOI:10.1021/cn500277f

Pietra, Francesco
From the Sequence to the Conformation of the Unabridged Transmembrane Domains TM1 and TM2 of the cASIC1a Ion Channel - A Parallel Tempering Approach
CHEMISTRY & BIODIVERSITY, 12:350-357, MAR 2015
abstract, full text, DOI:10.1002/cbdv.201400298

Pothapragada, Seetha; Zhang, Peng; Sheriff, Jawaad; Livelli, Mark; Slepian, Marvin J.; Deng, Yuefan; Bluestein, Danny
A phenomenological particle-based platelet model for simulating filopodia formation during early activation
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, 31 Art. No. e02702, MAR 2015
abstract, full text, DOI:10.1002/cnm.2702

Ko, Jeong-Ahn; Kwon, Tae Woo; Ambrosia, Matthew; Ha, Man Yeong
Study of the wetting characteristics of water droplet on a heterogeneous pillared surface
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 29:1243-1256, MAR 2015
abstract, full text, DOI:10.1007/s12206-015-0238-3

Tovstun, S. A.; Ivanchikhina, A. V.; Nikolenko, L. M.; Nevidimov, A. V.; Brichkin, S. B.; Razumov, V. F.
J-aggregation of a thiacarbocyanine dye in reverse microemulsions
HIGH ENERGY CHEMISTRY, 49:111-116, MAR 2015
abstract, full text, DOI:10.1134/S0018143915020113

Lindert, Steffen; McCammon, J. Andrew
Improved cryoEM-Guided Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:1337-1346, MAR 2015
abstract, full text, DOI:10.1021/ct500995d

Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.
A robust all-atom model for LCAT generated by homology modeling
JOURNAL OF LIPID RESEARCH, 56:620-634, MAR 2015
abstract, full text, DOI:10.1194/jlr.M056382

Miller, John H., Jr.; Villagrau, Martha Y. Suarez; Mark, Sladjana; Briggs, James M.
Normal and impaired charge transport in biological systems
PHYSICA B-CONDENSED MATTER, 460:119-125, MAR 1 2015
abstract, full text, DOI:10.1016/j.physb.2014.11.052

Chen, Liao Y.
Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin
BIOPHYSICAL CHEMISTRY, 198:14-21, MAR 2015
abstract, full text, DOI:10.1016/j.bpc.2015.01.004

Nicolas, Aurelie; Raguenes-Nicol, Celine; Ben Yaou, Rabah; Ameziane-Le Hir, Sarah; Cheron, Angelique; Vie, Veronique; Claustres, Mireille; Leturcq, France; Delalande, Olivier; Hubert, Jean-Francois; Tuffery-Giraud, Sylvie; Giudice, Emmanuel; Le Rumeur, Elisabeth
Becker muscular dystrophy severity is linked to the structure of dystrophin
HUMAN MOLECULAR GENETICS, 24:1267-1279, MAR 1 2015
abstract, full text, DOI:10.1093/hmg/ddu537

Marek, Ale; Shaffer, Christopher J.; Pepin, Robert; Slovakova, Kristina; Laszlo, Kenneth J.; Bush, Matthew F.; Turecek, Frantiek
Electron Transfer Reduction of the Diazirine Ring in Gas-Phase Peptide Ions. On the Peculiar Loss of [NH4O] from Photoleucine
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 26:415-431, MAR 2015
abstract, full text, DOI:10.1007/s13361-014-1047-0

Cheatham, Thomas E., I.I.I.; Roe, Daniel R.
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
COMPUTING IN SCIENCE & ENGINEERING, 17:30-39, MAR-APR 2015
abstract, full text

Mondal, Manas; Choudhury, Devapriya; Chakrabarti, Jaydeb; Bhattacharyya, Dhananjay
Role of indirect readout mechanism in TATA box binding protein-DNA interaction
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:283-295, MAR 2015
abstract, full text, DOI:10.1007/s10822-014-9828-x

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Kang, Ying; Ge, Zhongxue
Ordered and layered structure of liquid nitromethane within a graphene bilayer: toward stabilization of energetic materials through nanoscale confinement
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 40, MAR 2015
abstract, full text, DOI:10.1007/s00894-015-2588-2

Paudyal, Samridhdi; Alfonso-Prieto, Mercedes; Carnevale, Vincenzo; Redhu, Shiv K.; Klein, Michael L.; Nicholson, Allen W.
Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:459-472, MAR 2015
abstract, full text, DOI:10.1002/prot.24751

Baker, Christopher M.
Polarizable force fields for molecular dynamics simulations of biomolecules
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 5:241-254, MAR-APR 2015
abstract, full text, DOI:10.1002/wcms.1215

Zhang, Peng; Zhang, Na; Deng, Yuefan; Bluestein, Danny
A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma
JOURNAL OF COMPUTATIONAL PHYSICS, 284:668-686, MAR 1 2015
abstract, full text, DOI:10.1016/j.jcp.2015.01.004

Ai, Haixin; Zheng, Fangliang; Deng, Fangbo; Zhu, Chunyu; Gu, Ying; Zhang, Li; Li, Xuejiao; Chang, Alan K.; Zhao, Jian; Zhu, Junfeng; Liu, Hongsheng
Structure-Based Virtual Screening for Potential Inhibitors of Influenza A Virus RNA Polymerase PA Subunit
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 21:149-156, MAR 2015
abstract, full text, DOI:10.1007/s10989-014-9442-8

Mohan, Rohith R.; Gorham, Ronald D., Jr.; Morikis, Dimitrios
A theoretical view of the C3d:CR2 binding controversy
MOLECULAR IMMUNOLOGY, 64:112-122, MAR 2015
abstract, full text, DOI:10.1016/j.molimm.2014.11.006

Mahboobi, Seyed Hanif; Javanpour, Alex A.; Mofrad, Mohammad R. K.
The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle
PLOS ONE, 10 Art. No. e0112969, FEB 27 2015
abstract, full text, DOI:10.1371/journal.pone.0112969

Shinobu, Ai; Agmon, Noam
The Hole in the Barrel: Water Exchange at the GFP Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3464-3478, FEB 26 2015
abstract, full text, DOI:10.1021/jp5127255

Cai, Kaicong; Du, Fenfen; Liu, Jia; Su, Tingting
Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 137:701-710, FEB 25 2015
abstract, full text, DOI:10.1016/j.saa.2014.08.126

Johnson, Quentin R.; Lindsay, Richard J.; Nellas, Ricky B.; Fernandez, Elias J.; Shen, Tongye
Mapping Allostery through Computational Glycine Scanning and Correlation Analysis of Residue-Residue Contacts
BIOCHEMISTRY, 54:1534-1541, FEB 24 2015
abstract, full text, DOI:10.1021/bi501152d

Francisca Aguayo, M.; Carlos Caceres, Juan; Fuentealba, Matias; Munoz, Rodrigo; Stange, Claudia; Cabrera, Ricardo; Handford, Michael
Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling
FRONTIERS IN PLANT SCIENCE, 6 Art. No. 91, FEB 23 2015
abstract, full text, DOI:10.3389/fpls.2015.00091

Singh, Rajesh; Ahalawat, Navjeet; Murarka, Rajesh K.
Activation of Corticotropin-Releasing Factor 1 Receptor: Insights from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2806-2817, FEB 19 2015
abstract, full text, DOI:10.1021/jp509814n

Mirjalili, Vahid; Feig, Michael
Interactions of Amino Acid Side-Chain Analogs within Membrane Environments
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2877-2885, FEB 19 2015
abstract, full text, DOI:10.1021/jp511712u

Korchowiec, Beata; Korchowiec, Jacek; Gorczyca, Marcelina; de Vains, Jean-Bernard Regnouf; Rogalska, Ewa
Molecular Organization of Nalidixate Conjugated Calixarenes in Bacterial Model Membranes Probed by Molecular Dynamics Simulation and Langmuir Mono layer Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2990-3000, FEB 19 2015
abstract, full text, DOI:10.1021/jp567151r

Bertran, Oscar; Zhang, Baozhong; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Modeling Nanosized Single Molecule Objects: Dendronized Polymers Adsorbed onto Mica
JOURNAL OF PHYSICAL CHEMISTRY C, 119:3746-3753, FEB 19 2015
abstract, full text, DOI:10.1021/jp510586r

Farimani, A. Barati; Heiranian, M.; Aluru, N. R.
Electromechanical Signatures for DNA Sequencing through a Mechanosensitive Nanopore
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:650-657, FEB 19 2015
abstract, full text, DOI:10.1021/jz5025417

Plaschka, C.; Lariviere, L.; Wenzeck, L.; Seizl, M.; Hemann, M.; Tegunov, D.; Petrotchenko, E. V.; Borchers, C. H.; Baumeister, W.; Herzog, F.; Villa, E.; Cramer, P.
Architecture of the RNA polymerase II-Mediator core initiation complex
NATURE, 518, FEB 19 2015
abstract, full text, DOI:10.1038/nature14229

Huggins, David J.
Quantifying the Entropy of Binding for Water Molecules in Protein Cavities by Computing Correlations
BIOPHYSICAL JOURNAL, 108:928-936, FEB 17 2015
abstract, full text, DOI:10.1016/j.bpj.2014.12.035

Sharma, Vivek; Enkavi, Giray; Vattulainen, Ilpo; Rog, Tomasz; Wikstrom, Marten
Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:2040-2045, FEB 17 2015
abstract, full text, DOI:10.1073/pnas.1409543112

Wade, Kristin R.; Hotze, Eileen M.; Kuiper, Michael J.; Morton, Craig J.; Parker, Michael W.; Tweten, Rodney K.
An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:2204-2209, FEB 17 2015
abstract, full text, DOI:10.1073/pnas.1423754112

Cronin, Melissa; Coolbaugh, Michael J.; Nellis, David; Zhu, Jianwei; Wood, David W.; Nussinov, Ruth; Ma, Buyong
Dynamics differentiate between active and inactive inteins
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 91:51-62, FEB 16 2015
abstract, full text, DOI:10.1016/j.ejmech.2014.07.094

Aguayo, Daniel; Pacheco, Nicolas; Morales, Eduardo H.; Collao, Bernardo; Luraschi, Roberto; Cabezas, Carolina; Calderon, Paulina; Gonzalez-Nilo, Fernando; Gil, Fernando; Calderon, Ivan L.; Saavedra, Claudia P.
Hydrogen peroxide and hypochlorous acid influx through the major S. Typhimurium porin OmpD is affected by substitution of key residues of the channel
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 568:38-45, FEB 15 2015
abstract, full text, DOI:10.1016/j.abb.2015.01.005

Hatano, Hiroko; Shaw, Jacqueline; Marquardt, Kaitlin; Zhang, Zhiyong; Gauthier, Laurent; Chanteux, Stephanie; Rossi, Benjamin; Li, Demin; Mitchell, Julie; Kollnberger, Simon
The D0 Ig-like Domain Plays a Central Role in the Stronger Binding of KIR3DL2 to B27 Free H Chain Dimers
JOURNAL OF IMMUNOLOGY, 194:1591-1601, FEB 15 2015
abstract, full text, DOI:10.4049/jimmunol.1402214

Lu, Shouqin; Chen, Shenbao; Mao, Debin; Zhang, Yan; Long, Mian
Contribution of the CR Domain to P-Selectin Lectin Domain Allostery by Regulating the Orientation of the EGF Domain
PLOS ONE, 10 Art. No. e0118083, FEB 12 2015
abstract, full text, DOI:10.1371/journal.pone.0118083

Houari, Ymene; Chibani, Siwar; Jacquemin, Denis; Laurent, Adele D.
TD-DFT Assessment of the Excited State Intramolecular Proton Transfer in Hydroxyphenylbenzimidazole (HBI) Dyes
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2180-2192, FEB 12 2015
abstract, full text, DOI:10.1021/jp505036d

Banerjee, Shouvik; Wilson, James; Shim, Jiwook; Shankla, Manish; Corbin, Elise A.; Aksimentiev, Aleksei; Bashir, Rashid
Slowing DNA Transport Using Graphene-DNA Interactions
ADVANCED FUNCTIONAL MATERIALS, 25:936-946, FEB 11 2015
abstract, full text, DOI:10.1002/adfm.201403719

Zhao, Yuqi; Wang, Yanjie; Gao, Yuedong; Li, Gonghua; Huang, Jingfei
Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins
PLOS ONE, 10 Art. No. e0117506, FEB 11 2015
abstract, full text, DOI:10.1371/journal.pone.0117506

Diaz, Natalia; Suarez, Dimas
Extensive Simulations of the Full-Length Matrix Metalloproteinase-2 Enzyme in a Prereactive Complex with a Collagen Triple-Helical Peptide
BIOCHEMISTRY, 54:1243-1258, FEB 10 2015
abstract, full text, DOI:10.1021/bi501014w

Mouchlis, Varnavas D.; Bucher, Denis; McCammon, J. Andrew; Dennis, Edward A.
Membranes serve as allosteric activators of phospholipase A(2), enabling it to extract, bind, and hydrolyze phospholipid substrates
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E516-E525, FEB 10 2015
abstract, full text, DOI:10.1073/pnas.1424651112

Goldau, Thomas; Murayama, Keiji; Brieke, Clara; Steinwand, Sabrina; Mondal, Padmabati; Biswas, Mithun; Burghardt, Irene; Wachtveitl, Josef; Asanuma, Hiroyuki; Heckel, Alexander
Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C-Nucleoside
CHEMISTRY-A EUROPEAN JOURNAL, 21:2845-2854, FEB 9 2015
abstract, full text, DOI:10.1002/chem.201405840

Pal, Somedatta; Chakraborty, Kaushik; Khatua, Prabir; Bandyopadhyay, Sanjoy
Microscopic dynamics of water around unfolded structures of barstar at room temperature
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 055102, FEB 7 2015
abstract, full text, DOI:10.1063/1.4907007

Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H.
Effect of surface free energies on the heterogeneous nucleation of water droplet: A molecular dynamics simulation approach
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 054701, FEB 7 2015
abstract, full text, DOI:10.1063/1.4906877

Burger, Pieter B.; Williams, Marni; Sprenger, Janina; Reeksting, Shaun B.; Botha, Mariette; Mueller, Ingrid B.; Joubert, Fourie; Birkholtz, Lyn-Marie; Louw, Abraham I.
A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail
MALARIA JOURNAL, 14 Art. No. 54, FEB 5 2015
abstract, full text, DOI:10.1186/s12936-015-0572-z

Calero, C.; Marti, J.; Guardia, E.
H-1 Nuclear Spin Relaxation of Liquid Water from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1966-1973, FEB 5 2015
abstract, full text, DOI:10.1021/jp510013q

Luan, Binquan; Tien Huynh; Zhou, Ruhong
Nanopore-Based Sensors for Ligand Receptor Lead Optimization
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:331-337, FEB 5 2015
abstract, full text, DOI:10.1021/jz5025614

Martin, Daniel R.; Matyushov, Dmitry V.
Dipolar Nanodomains in Protein Hydration Shells
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:407-412, FEB 5 2015
abstract, full text, DOI:10.1021/jz5025433

Akyuz, Nurunisa; Georgieva, Elka R.; Zhou, Zhou; Stolzenberg, Sebastian; Cuendet, Michel A.; Khelashvili, George; Altman, Roger B.; Terry, Daniel S.; Freed, Jack H.; Weinstein, Harel; Boudker, Olga; Blanchard, Scott C.
Transport domain unlocking sets the uptake rate of an aspartate transporter
NATURE, 518:68-+, FEB 5 2015
abstract, full text, DOI:10.1038/nature14158

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei
BROMOC Suite: Monte Carlo/Brownian Dynamics Suite for Studies of Ion Permeation and DNA transport in Biological and Artificial Pores with Effective Potentials
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:264-271, FEB 5 2015
abstract, full text, DOI:10.1002/jcc.23799

Jahangiri, Soran; Legris-Falardeau, Valery; Peslherbe, Gilles H.
Computational investigation of the hydration of alkyl diammonium cations in water clusters
CHEMICAL PHYSICS LETTERS, 621:85-90, FEB 4 2015
abstract, full text, DOI:10.1016/j.cplett.2014.12.045

Cheung, Luthur Siu-Lun; Shea, Daniel J.; Nicholes, Nathan; Date, Amol; Ostermeier, Marc; Konstantopoulos, Konstantinos
Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics
SCIENTIFIC REPORTS, 5 Art. No. 8247, FEB 4 2015
abstract, full text, DOI:10.1038/srep08247

Eddy, Matthew T.; Andreas, Loren; Teijido, Oscar; Su, Yongchao; Clark, Lindsay; Noskov, Sergei Y.; Wagner, Gerhard; Rostovtseva, Tatiana K.; Griffin, Robert G.
Magic Angle Spinning Nuclear Magnetic Resonance Characterization of Voltage-Dependent Anion Channel Gating in Two-Dimensional Lipid Crystalline Bilayers
BIOCHEMISTRY, 54:994-1005, FEB 3 2015
abstract, full text, DOI:10.1021/bi501260r

Mastrangelo, Eloise; Vachette, Patrice; Cossu, Federica; Malvezzi, Francesca; Bolognesi, Martino; Milani, Mario
The Activator of Apoptosis Smac-DIABLO Acts as a Tetramer in Solution
BIOPHYSICAL JOURNAL, 108:714-723, FEB 3 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.3471

Hackwon, Do; Kim, Soo Jin; Lee, Chang Woo; Kim, Han-Woo; Park, Hyun Ho; Kim, Ho Min; Park, Hyun; Park, HaJeung; Lee, Jun Hyuck
Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes
SCIENTIFIC REPORTS, 5 Art. No. 8196, FEB 3 2015
abstract, full text, DOI:10.1038/srep08196

Bertran, Oscar; del Valle, Luis J.; Revilla-Lopez, Guillermo; Rivas, Manuel; Chaves, Gustavo; Casas, Maria T.; Casanovas, Jordi; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
Synergistic Approach to Elucidate the Incorporation of Magnesium Ions into Hydroxyapatite
CHEMISTRY-A EUROPEAN JOURNAL, 21:2537-2546, FEB 2 2015
abstract, full text, DOI:10.1002/chem.201405428

Park, Yeonju; Seo, Yongil; Chae, Boknam; Pyo, Dongjin; Chung, Hoeil; Hwang, Hyonseok; Jung, Young Mee
Understanding the Structural Differences between Spherical and Rod-Shaped Human Insulin Nanoparticles Produced by Supercritical Fluids Precipitation
CHEMPHYSCHEM, 16:476-482, FEB 2 2015
abstract, full text, DOI:10.1002/cphc.201402504

Li Wenzhao; Meng Wei; Tian Pu
Impact of Stable Protein-protein Interaction on Protein Conformational Space
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 31:149-155, FEB 2015
abstract, full text, DOI:10.1007/s40242-015-3402-5

Chen, Xin; Duan, Danhui; Zhu, Shuyan; Zhang, Jinglai
Investigation of alanine mutations affecting insulin-like growth factor (IGF) I binding to IGF binding proteins
GROWTH FACTORS, 33:40-49, FEB 2015
abstract, full text, DOI:10.3109/08977194.2014.964868

Barakat, Khaled H.; Anwar-Mohamed, Anwar; Tuszynski, Jack A.; Robins, Morris J.; Tyrrell, D. Lorne; Houghton, Michael
A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:362-373, FEB 2015
abstract, full text, DOI:10.1021/ci400631n

Sandberg, Robert B.; Banchelli, Martina; Guardiani, Carlo; Menichetti, Stefano; Caminati, Gabriella; Procacci, Piero
Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:423-435, FEB 2015
abstract, full text, DOI:10.1021/ct500964e

Hardy, David J.; Wu, Zhe; Phillips, James C.; Stone, John E.; Skeel, Robert D.; Schulten, Klaus
Multilevel Summation Method for Electrostatic Force Evaluation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:766-779, FEB 2015
abstract, full text, TCBG publications, DOI:10.1021/ct5009075

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suarez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.
WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:800-809, FEB 2015
abstract, full text, DOI:10.1021/ct5010615

Sieradzan, Adam K.; Krupa, Pawel; Scheraga, Harold A.; Liwo, Adam; Czaplewski, Cezary
Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:817-831, FEB 2015
abstract, full text, DOI:10.1021/ct500736a

Fibriansah, Guntur; Tan, Joanne L.; Smith, Scott A.; de Alwis, Ruklanthi; Ng, Thiam-Seng; Kostyuchenko, Victor A.; Jadi, Ramesh S.; Kukkaro, Petra; de Silva, Aravinda M.; Crowe, James E.; Lok, Shee-Mei
A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins
NATURE COMMUNICATIONS, 6 Art. No. 6341, FEB 2015
abstract, full text, DOI:10.1038/ncomms7341

Modi, Niraj; Barcena-Uribarri, Ivan; Bains, Manjeet; Benz, Roland; Hancock, Robert E. W.; Kleinekathoefer, Ulrich
Tuning the Affinity of Anion Binding Sites in Porin Channels with Negatively Charged Residues: Molecular Details for OprP
ACS CHEMICAL BIOLOGY, 10:441-451, FEB 2015
abstract, full text, DOI:10.1021/cb500399j

Li, Chen-Yu; Hemmig, Elise A.; Kong, Jinglin; Yoo, Jejoong; Hernandez-Ainsa, Silvia; Keyser, Ulrich F.; Aksimentiev, Aleksei
Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field
ACS NANO, 9:1420-1433, FEB 2015
abstract, full text, DOI:10.1021/nn505825z

Li Jun-Wei; Xiao Shao-Ying; Xie Xiao-Xiao; Yu Hui; Zhang Hai-Lin; Zhan Yong; An Hai-Long
Identification of Three Interactions to Determine the Conformation Change and to Maintain the Function of Kir2.1 Channel Protein
CHINESE PHYSICS LETTERS, 32 Art. No. 028702, FEB 2015
abstract, full text, DOI:10.1088/0256-307X/32/2/028702

Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud
Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 55:13-24, FEB 2015
abstract, full text, DOI:10.1016/j.jmgm.2014.10.011

Madsen, J. J.; Persson, E.; Olsen, O. H.
Tissue factor activates allosteric networks in factor VIIa through structural and dynamic changes
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 13:262-267, FEB 2015
abstract, full text, DOI:10.1111/jth.12791

Yu, Xiaofeng; Cojocaru, Vlad; Mustafa, Ghulam; Salo-Ahen, Outi M. H.; Lepesheva, Galina I.; Wade, Rebecca C.
Dynamics of CYP51: implications for function and inhibitor design
JOURNAL OF MOLECULAR RECOGNITION, 28:59-73, FEB 2015
abstract, full text, DOI:10.1002/jmr.2412

Davis, Adam S.; Federici, Thais; Ray, William C.; Boulis, Nicholas M.; O'Connor, Deirdre; Clark, K. Reed; Bartlett, Jeffrey S.
Rational Design and Engineering of a Modified Adeno-Associated Virus (AAV1)-Based Vector System for Enhanced Retrograde Gene Delivery
NEUROSURGERY, 76:216-225, FEB 2015
abstract, full text, DOI:10.1227/NEU.0000000000000589

Zhang, Rui; Bhattacharjee, Anirban; Field, Martin J.; Salahub, Dennis R.
Multiple proton relay routes in the reaction mechanism of RNAP II: Assessing the effect of structural model
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:268-281, FEB 2015
abstract, full text, DOI:10.1002/prot.24732

Langley, David R.; Kimura, S. Roy; Sivaprakasam, Prasanna; Zhou, Nannan; Dicker, Ira; McAuliffe, Brian; Wang, Tao; Kadow, John F.; Meanwell, Nicholas A.; Krystal, Mark
Homology models of the HIV-1 attachment inhibitor BMS-626529 bound to gp120 suggest a unique mechanism of action
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:331-350, FEB 2015
abstract, full text, DOI:10.1002/prot.24726

Noto, Rosina; Santangelo, Maria Grazia; Levantino, Matteo; Cupane, Antonio; Mangione, Maria Rosalia; Parisi, Daniele; Ricagno, Stefano; Bolognesi, Martino; Manno, Mauro; Martorana, Vincenzo
Functional and dysfunctional conformers of human neuroserpin characterized by optical spectroscopies and Molecular Dynamics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1854:110-117, FEB 2015
abstract, full text, DOI:10.1016/j.bbapap.2014.10.002

Moreau, Adrien; Gosselin-Badaroudine, Pascal; Delemotte, Lucie; Klein, Michael L.; Chahine, Mohamed
Gating pore currents are defects in common with two Na(v)1.5 mutations in patients with mixed arrhythmias and dilated cardiomyopathy
JOURNAL OF GENERAL PHYSIOLOGY, 145:93-106, FEB 2015
abstract, full text, DOI:10.1085/jgp.201411304

Zhang, Chongqian; Du, Chunmiao; Feng, Zhiwei; Zhu, Jingyu; Li, Youyong
Hologram Quantitative Structure Activity Relationship, Docking, and Molecular Dynamics Studies of Inhibitors for CXCR4
CHEMICAL BIOLOGY & DRUG DESIGN, 85:119-136, FEB 2015
abstract, full text, DOI:10.1111/cbdd.12377

Kolsek, Katra; Gobec, Martina; Rascan, Irena Minaric; Dolenc, Marija Sollner
Screening of bisphenol A, triclosan and paraben analogues as modulators of the glucocorticoid and androgen receptor activities
TOXICOLOGY IN VITRO, 29:8-15, FEB 2015
abstract, full text, DOI:10.1016/j.tiv.2014.08.009

Wang, Beibei; Opron, Kristopher; Burton, Zachary F.; Cukier, Robert I.; Feig, Michael
Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details
NUCLEIC ACIDS RESEARCH, 43:1133-1146, JAN 30 2015
abstract, full text, DOI:10.1093/nar/gku1370

Sormanni, Pietro; Aprile, Francesco A.; Vendruscolo, Michele
The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility
JOURNAL OF MOLECULAR BIOLOGY, 427:478-490, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.09.026

Zheng, Fan; Jewell, Heather; Fitzpatrick, Jeremy; Zhang, Jian; Mierke, Dale F.; Grigoryan, Gevorg
Computational Design of Selective Peptides to Discriminate between Similar PDZ Domains in an Oncogenic Pathway
JOURNAL OF MOLECULAR BIOLOGY, 427:491-510, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.10.014

Darre, Leonardo; Furini, Simone; Domene, Carmen
Permeation and Dynamics of an Open-Activated TRPV1 Channel
JOURNAL OF MOLECULAR BIOLOGY, 427:537-549, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.11.016

Freudenthal, Bret D.; Beard, William A.; Perera, Lalith; Shock, David D.; Kim, Taejin; Schlick, Tamar; Wilson, Samuel H.
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide
NATURE, 517:635-U261, JAN 29 2015
abstract, full text, DOI:10.1038/nature13886

Li, Jun; Deng, Mingsen; Voronine, Dmitri V.; Mukamel, Shaul; Jiang, Jun
Two-Dimensional Near Ultraviolet (2DNUV) Spectroscopic Probe of Structural-Dependent Exciton Dynamics in a Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1314-1322, JAN 29 2015
abstract, full text, DOI:10.1021/jp509314y

Meng, Yilin; Lin, Yen-lin; Roux, Benoit
Computational Study of the "DFG-Flip" Conformational Transition in c-Abl and c-Src Tyrosine Kinases
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1443-1456, JAN 29 2015
abstract, full text, DOI:10.1021/jp511792a

Samoylova, Olga N.; Calixte, Emvia I.; Shuford, Kevin L.
Molecular Dynamics Simulations of Ion Transport in Carbon Nanotube Channels
JOURNAL OF PHYSICAL CHEMISTRY C, 119:1659-1666, JAN 29 2015
abstract, full text, DOI:10.1021/jp5103669

Luedemann, Gesa; Solov'yov, Ilia A.; Kubar, Tomas; Elstner, Marcus
Solvent Driving Force Ensures Fast Formation of a Persistent and Well-Separated Radical Pair in Plant Cryptochrome
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:1147-1156, JAN 28 2015
abstract, full text, DOI:10.1021/ja510550g

Chakraborty, Srirupa; Zheng, Wenjun
Decrypting the Structural, Dynamic, and Energetic Basis of a Monomeric Kinesin Interacting with a Tubulin Dimer in Three ATPase States by All-Atom Molecular Dynamics Simulation
BIOCHEMISTRY, 54:859-869, JAN 27 2015
abstract, full text, DOI:10.1021/bi501056h

Francois-Heude, Marc; Mendez-Ardoy, Alejandro; Cendret, Virginie; Lafite, Pierre; Daniellou, Richard; Ortiz Mellet, Carmen; Garcia Fernandez, Jose M.; Moreau, Vincent; Djedaini-Pilard, Florence
Synthesis of High-Mannose Oligosaccharide Analogues through Click Chemistry: True Functional Mimics of Their Natural Counterparts Against Lectins?
CHEMISTRY-A EUROPEAN JOURNAL, 21:1978-1991, JAN 26 2015
abstract, full text, DOI:10.1002/chem.201405481

Poblete, Horacio; Oyarzun, Ingrid; Olivero, Pablo; Comer, Jeffrey; Zuniga, Matias; Sepulveda, Ronnina V.; Baez-Nieto, David; Gonzalez Leon, Carlos; Gonzalez-Nilo, Fernando; Latorre, Ramon
Molecular Determinants of Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P-2) Binding to Transient Receptor Potential V1 (TRPV1) Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:2086-2098, JAN 23 2015
abstract, full text, DOI:10.1074/jbc.M114.613620

Patel, Dhilon S.; He, Xibing; MacKerell, Alexander D., Jr.
Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
JOURNAL OF PHYSICAL CHEMISTRY B, 119:637-652, JAN 22 2015
abstract, full text, DOI:10.1021/jp412696m

Krzeminska, Agnieszka; Paneth, Piotr; Moliner, Vicent; Swiderek, Katarzyna
Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT
JOURNAL OF PHYSICAL CHEMISTRY B, 119:917-927, JAN 22 2015
abstract, full text, DOI:10.1021/jp506119h

Ellingson, Sally R.; Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.
Multi-Conformer Ensemble Docking to Difficult Protein Targets
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1026-1034, JAN 22 2015
abstract, full text, DOI:10.1021/jp506511p

Craft, John W., Jr.; Shen, Tsai-wei; Brier, Lindsey M.; Briggs, James M.
Biophysical Characteristics of Cholera Toxin and Escherichia coli Heat-Labile Enterotoxin Structure and Chemistry Lead to Differential Toxicity
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1048-1061, JAN 22 2015
abstract, full text, DOI:10.1021/jp506509c

Comer, Jeffrey; Gumbart, James C.; Henin, Jerome; Lelievre, Tony; Pohorille, Andrew; Chipot, Christophe
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1129-1151, JAN 22 2015
abstract, full text, DOI:10.1021/jp506633n

Gianti, Eleonora; Carnevale, Vincenzo; DeGrado, William F.; Klein, Michael L.; Fiorin, Giacomo
Hydrogen-Bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-Based Inhibitors
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1173-1183, JAN 22 2015
abstract, full text, DOI:10.1021/jp506807y

Gleed, Mitchell L.; Busath, David D.
Why Bound Amantadine Fails to Inhibit Proton Conductance According to Simulations of the Drug-Resistant Influenza A M2 (S31N)
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1225-1231, JAN 22 2015
abstract, full text, DOI:10.1021/jp508545d

Holden, Jeffrey K.; Kang, Soosung; Hollingsworth, Scott A.; Li, Huiying; Lim, Nathan; Chen, Steven; Huang, He; Xue, Fengtian; Tang, Wei; Silverman, Richard B.; Poulos, Thomas L.
Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 58:994-1004, JAN 22 2015
abstract, full text, DOI:10.1021/jm501723p

Schur, Florian K. M.; Hagen, Wim J. H.; Rumlova, Michaela; Ruml, Tomas; Mueller, Barbara; Kraeusslich, Hans-Georg; Briggs, John A. G.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 angstrom resolution
NATURE, 517:505-+, JAN 22 2015
abstract, full text, DOI:10.1038/nature13838

Gun'ko, Vladimir M.; Nasiri, Rasoul; Sazhin, Sergei S.
Effects of the surroundings and conformerisation of n-dodecane molecules on evaporation/condensation processes
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 034502, JAN 21 2015
abstract, full text, DOI:10.1063/1A905496

Harrach, Michael F.; Klameth, Felix; Drossel, Barbara; Vogel, Michael
Effect of the hydroaffinity and topology of pore walls on the structure and dynamics of confined water
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 034703, JAN 21 2015
abstract, full text, DOI:10.1063/1.4905557

Lindert, Steffen; Cheng, Yuanhua; Kekenes-Huskey, Peter; Regnier, Michael; McCammon, J. Andrew
Effects of HCM cTnI Mutation R145G on Troponin Structure and Modulation by PKA Phosphorylation Elucidated by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 108:395-407, JAN 20 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.3461

Yan, Si; Zhang, Huilan; Hou, Guangjin; Ahmed, Shubbir; Williams, John C.; Polenova, Tatyana
Internal Dynamics of Dynactin CAP-Gly Is Regulated by Microtubules and Plus End Tracking Protein EB1
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:1607-1622, JAN 16 2015
abstract, full text, DOI:10.1074/jbc.M114.603118

Chamberlin, Adam; Qiu, Feng; Wang, Yibo; Noskov, Sergei Y.; Larsson, H. Peter
Mapping the Gating and Permeation Pathways in the Voltage-Gated Proton Channel Hv1
JOURNAL OF MOLECULAR BIOLOGY, 427:131-145, JAN 16 2015
abstract, full text, DOI:10.1016/j.jmb.2014.11.018

Barragan, Angela M.; Crofts, Antony R.; Schulten, Klaus; Solov'yov, Ilia A.
Identification of Ubiquinol Binding Motifs at the Q(o)-Site of the Cytochrome bc(1) Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 119:433-447, JAN 15 2015
abstract, full text, TCBG publications, DOI:10.1021/jp510022w

Miller, Yifat; Ma, Buyong; Nussinov, Ruth
Polymorphism in Self-Assembly of Peptide-Based beta-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity
JOURNAL OF PHYSICAL CHEMISTRY B, 119:482-490, JAN 15 2015
abstract, full text, DOI:10.1021/jp511485n

Mejri, Alia; Vardanega, Delphine; Tangour, Bahoueddine; Gharbi, Tijani; Picaud, Fabien
Encapsulation into Carbon Nanotubes and Release of Anticancer Cisplatin Drug Molecule
JOURNAL OF PHYSICAL CHEMISTRY B, 119:604-611, JAN 15 2015
abstract, full text, DOI:10.1021/jp5102384

Li, Chunyu; Strachan, Alejandro
Molecular Scale Simulations on Thermoset Polymers: A Review
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 53:103-122, JAN 15 2015
abstract, full text, DOI:10.1002/polb.23489

Tao, Jinhui; Battle, Keith C.; Pan, Haihua; Salter, E. Alan; Chien, Yung-Ching; Wierzbicki, Andrzej; De Yoreo, James J.
Energetic basis for the molecular-scale organization of bone
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:326-331, JAN 13 2015
abstract, full text, DOI:10.1073/pnas.1404481112

He Jia; Feng Xizeng; Shao Xueguang; Cai Wensheng
Adsorption Behavior of Hydrophobin Proteins on Surface of Mica
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 36:110-115, JAN 10 2015
abstract, full text, DOI:10.7503/cjcu20140808

Baul, Upayan; Vemparala, Satyavani
Ion hydration and associated defects in hydrogen bond network of water: Observation of reorientationally slow water molecules beyond first hydration shell in aqueous solutions of MgCl2
PHYSICAL REVIEW E, 91 Art. No. 012114, JAN 8 2015
abstract, full text, DOI:10.1103/PhysRevE.91.012114

Cui, Di; Ou, Shu-Ching; Patel, Sandeep
Protein Denaturants at Aqueous-Hydrophobic Interfaces: Self-Consistent Correlation between Induced Interfacial Fluctuations and Denaturant Stability at the Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 119:164-178, JAN 8 2015
abstract, full text, DOI:10.1021/jp507203g

Polak, Andraz; Velikonja, Aljaz; Kramar, Peter; Tarek, Mounir; Miklavcic, Damijan
Electroporation Threshold of POPC Lipid Bilayers with Incorporated Polyoxyethylene Glycol (C12E8)
JOURNAL OF PHYSICAL CHEMISTRY B, 119:192-200, JAN 8 2015
abstract, full text, DOI:10.1021/jp509789m

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 015101, JAN 7 2015
abstract, full text, DOI:10.1063/1.4904896

Kim, Hanseong; Zou, Taisong; Modi, Chintan; Doerner, Katerina; Grunkemeyer, Timothy J.; Chen, Liqing; Fromme, Raimund; Matz, Mikhail V.; Ozkan, S. Banu; Wachter, Rebekka M.
A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins
STRUCTURE, 23:34-43, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.11.011

Baker, Joseph L.; Courtemanche, Naomi; Parton, Daniel L.; McCullagh, Martin; Pollard, Thomas D.; Voth, Gregory A.
Electrostatic Interactions between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation
STRUCTURE, 23:68-79, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.10.014

Dai, Jian; Zhou, Huan-Xiang
Reduced Curvature of Ligand-Binding Domain Free-Energy Surface Underlies Partial Agonism at NMDA Receptors
STRUCTURE, 23:228-236, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.11.012

Kasimova, Marina A.; Zaydman, Mark A.; Cui, Jianmin; Tarek, Mounir
PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6
SCIENTIFIC REPORTS, 5 Art. No. 7474, JAN 6 2015
abstract, full text, DOI:10.1038/srep07474

Huang, Wei; Ravikumar, Krishnakumar M.; Chance, Mark R.; Yang, Sichun
Quantitative Mapping of Protein Structure by Hydroxyl Radical Footprinting-Mediated Structural Mass Spectrometry: A Protection Factor Analysis
BIOPHYSICAL JOURNAL, 108:107-115, JAN 6 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.013

Xu, Ji; Li, Xiaoxia; Hou, Chaofeng; Wang, Limin; Zhou, Guangzheng; Ge, Wei; Li, Jinghai
Engineering molecular dynamics simulation in chemical engineering
CHEMICAL ENGINEERING SCIENCE, 121:200-216, JAN 6 2015
abstract, full text, DOI:10.1016/j.ces.2014.09.051

Rovigatti, Lorenzo; Sulc, Petr; Reguly, Istvan Z.; Romano, Flavio
A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1-8, JAN 5 2015
abstract, full text, DOI:10.1002/jcc.23763

Zomot, Elia; Gur, Mert; Bahar, Ivet
Microseconds Simulations Reveal a New Sodium-binding Site and the Mechanism of Sodium-coupled Substrate Uptake by LeuT
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:544-555, JAN 2 2015
abstract, full text, DOI:10.1074/jbc.M114.617555

Bujalowski, Paul J.; Nicholls, Paul; Barral, Jose M.; Oberhauser, Andres F.
Thermally-induced structural changes in an armadillo repeat protein suggest a novel thermosensor mechanism in a molecular chaperone
FEBS LETTERS, 589:123-130, JAN 2 2015
abstract, full text, DOI:10.1016/j.febslet.2014.11.034

Sellers, Michael S.; Lisal, Martin; Brennan, John K.
Exponential-six potential scaling for the calculation of free energies in molecular simulations
MOLECULAR PHYSICS, 113:45-54, JAN 2 2015
abstract, full text, DOI:10.1080/00268976.2014.942405

Ma, Cheng-Wei; Xiu, Zhi-Long; Zeng, An-Ping
Exploring signal transduction in heteromultimeric protein based on energy dissipation model
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:134-146, JAN 2 2015
abstract, full text, DOI:10.1080/07391102.2013.855145

Kelly, Catherine M.; Muzard, Julien; Brooks, Bernard R.; Lee, Gil U.; Buchete, Nicolae-Viorel
Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:9634-9643, 2015
abstract, full text, DOI:10.1039/c4cp05307a

Vitiello, Giuseppe; Falanga, Annarita; Alcides Petruk, Ariel; Merlino, Antonello; Fragneto, Giovanna; Paduano, Luigi; Galdiero, Stefania; D'Errico, Gerardino
Fusion of raft-like lipid bilayers operated by a membranotropic domain of the HSV-type I glycoprotein gH occurs through a cholesterol-dependent mechanism
SOFT MATTER, 11:3003-3016, 2015
abstract, full text, DOI:10.1039/c4sm02769h

Pradeepkiran, Jangampalli Adi; Kumar, Konidala Kranthi; Kumar, Yellapu Nanda; Bhaskar, Matcha
Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M
DRUG DESIGN DEVELOPMENT AND THERAPY, 9:1897-1912, 2015
abstract, full text, DOI:10.2147/DDDT.S77020

Mintzer, Mary Rose; Troxler, Thomas; Gai, Feng
p-Cyanophenylalanine and selenomethionine constitute a useful fluorophore-quencher pair for short distance measurements: application to polyproline peptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:7881-7887, 2015
abstract, full text, DOI:10.1039/c5cp00050e

Abroshan, Hadi; Kim, Hyung J.
On the structural stability of ionic liquid-IRMOF composites: a computational study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6248-6254, 2015
abstract, full text, DOI:10.1039/c4cp02428a

Kucuk, Sami Emre; Neugebauer, Petr; Prisner, Thomas F.; Sezer, Deniz
Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6618-6628, 2015
abstract, full text, DOI:10.1039/c4cp05832a

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Removal of heavy metals from water through armchair carbon and boron nitride nanotubes: a computer simulation study
RSC ADVANCES, 5:25097-25104, 2015
abstract, full text, DOI:10.1039/c4ra17048b

Basu, Ipsita; Mukhopadhyay, Chaitali
Effect of Temperature on the Phase Behaviour of Fully Saturated DAPC Lipid Bilayer: A Comparative Molecular Dynamics Simulation Study
BIOCHEMICAL ROLES OF EUKARYOTIC CELL SURFACE MACROMOLECULES, 842:263-277, 2015
full text

Li, Hui; Chen, Qi; Schoenbeck, Christian; Han, Bao-Hang
Sugar-functionalized water-soluble pillar[5] arene and its host-guest interaction with fullerene
RSC ADVANCES, 5:19041-19047, 2015
abstract, full text, DOI:10.1039/c4ra07523d

Alishahi, Marzieh; Kamali, Reza; Abouali, Omid
Molecular Dynamics Study of Electric Double Layer in Nanochannel
RUSSIAN JOURNAL OF ELECTROCHEMISTRY, 51:49-55, JAN 2015
abstract, full text, DOI:10.1134/S1023193515010024

Gonnet, Pedro
EFFICIENT AND SCALABLE ALGORITHMS FOR SMOOTHED PARTICLE HYDRODYNAMICS ON HYBRID SHARED/DISTRIBUTED-MEMORY ARCHITECTURES
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 37:C95-C121, 2015
abstract, full text, DOI:10.1137/140964266

Insaidoo, Francis K.; Rauscher, Michael A.; Smithline, Shepard J.; Kaarsholm, Niels C.; Feuston, Bradley P.; Ortigosa, Allison D.; Linden, Thomas O.; Roush, David J.
Targeted Purification Development Enabled by Computational Biophysical Modeling
BIOTECHNOLOGY PROGRESS, 31:154-164, JAN-FEB 2015
abstract, full text, DOI:10.1002/btpr.2023

Duarte Junior, Francisco Ferreira; de Lima Neto, Quirino Alves; Rando, Fabiana dos Santos; Bassalobre de Freitas, Douglas Vinicius; Pattaro Junior, Jose Renato; Polizelli, Lorena Gomes; Ferreira Munhoz, Roxelle Ethienne; Vicente Seixas, Flavio Augusto; Fernandez, Maria Aparecida
Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome
MOLECULAR BIOSYSTEMS, 11:801-808, 2015
abstract, full text, DOI:10.1039/c4mb00595c

Kumar, Amit; Sechi, Leonardo A.; Caboni, Pierluigi; Marrosu, Maria Giovanna; Atzori, Luigi; Pieroni, Enrico
Dynamical insights into the differential characteristics of Mycobacterium avium subsp paratuberculosis peptide binding to HLA-DRB1 proteins associated with multiple sclerosis
NEW JOURNAL OF CHEMISTRY, 39:1355-1366, 2015
abstract, full text, DOI:10.1039/c4nj01903b

Luan, Binquan; Tien Huynh; Zhao, Lin; Zhou, Ruhong
Potential Toxicity of Graphene to Cell Functions via Disrupting Protein-Protein Interactions
ACS NANO, 9:663-669, JAN 2015
abstract, full text, DOI:10.1021/nn506011j

Grimes, Leanne; Young, Mark T.
Purinergic P2X Receptors: Structural and Functional Features Depicted by X-Ray and Molecular Modelling Studies
CURRENT MEDICINAL CHEMISTRY, 22:783-798, 2015
abstract, full text

Dean, Kevin M.; Lubbeck, Jennifer L.; Davis, Lloyd M.; Regmi, Chola K.; Chapagain, Prem P.; Gerstman, Bernard S.; Jimenez, Ralph; Palmer, Amy E.
Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching
INTEGRATIVE BIOLOGY, 7:263-273, 2015
abstract, full text, DOI:10.1039/c4ib00251b

Cheng, Bo; Wu, Shaogui; Liu, Shixin; Rodriguez-Aliaga, Piere; Yu, Jin; Cui, Shuxun
Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases
NANOSCALE, 7:2970-2977, 2015
abstract, full text, DOI:10.1039/c4nr07140a

Rakos, Balazs
Modeling of dipole-dipole-coupled, electric field-driven, protein-based computing architectures
INTERNATIONAL JOURNAL OF CIRCUIT THEORY AND APPLICATIONS, 43:60-72, JAN 2015
abstract, full text, DOI:10.1002/cta.1924

Ferrarotti, Marco Jacopo; Bottaro, Sandro; Perez-Villa, Andrea; Bussi, Giovanni
Accurate Multiple Time Step in Biased Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:139-146, JAN 2015
abstract, full text, DOI:10.1021/ct5007086

Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M.; Singh, Satish K.; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R.; Sek, David; Allen, Martin J.
Rational design of viscosity reducing mutants of a monoclonal antibody: Hydrophobic versus electrostatic inter-molecular interactions
MABS, 7:212-230, JAN-FEB 2015
abstract, full text, DOI:10.4161/19420862.2014.985504

Wessel, Jennifer; Chu, Audrey Y.; Willems, Sara M.; Wang, Shuai; Yaghootkar, Hanieh; Brody, Jennifer A.; Dauriz, Marco; Hivert, Marie-France; Raghavan, Sridharan; Lipovich, Leonard; Hidalgo, Bertha; Fox, Keolu; Huffman, Jennifer E.; An, Ping; Lu, Yingchang; Rasmussen-Torvik, Laura J.; Grarup, Niels; Ehm, Margaret G.; Li, Li; Baldridge, Abigail S.; Stancakova, Alena; Abrol, Ravinder; Besse, Celine; Boland, Anne; Bork-Jensen, Jette; Fornage, Myriam; Freitag, Daniel F.; Garcia, Melissa E.; Guo, Xiuqing; Hara, Kazuo; Isaacs, Aaron; Jakobsdottir, Johanna; Lange, Leslie A.; Layton, Jill C.; Li, Man; Zhao, Jing Hua; Meidtner, Karina; Morrison, Alanna C.; Nalls, Mike A.; Peters, Marjolein J.; Sabater-Lleal, Maria; Schurmann, Claudia; Silveira, Angela; Smith, Albert V.; Southam, Lorraine; Stoiber, Marcus H.; Strawbridge, Rona J.; Taylor, Kent D.; Varga, Tibor V.; Allin, Kristine H.; Amin, Najaf; Aponte, Jennifer L.; Aung, Tin; Barbieri, Caterina; Bihlmeyer, Nathan A.; Boehnke, Michael; Bombieri, Cristina; Bowden, Donald W.; Burns, Sean M.; Chen, Yuning; Chen, Yii-Deri; Cheng, Ching-Yu; Correa, Adolfo; Czajkowski, Jacek; Dehghan, Abbas; Ehret, Georg B.; Eiriksdottir, Gudny; Escher, Stefan A.; Farmaki, Aliki-Eleni; Franberg, Mattias; Gambaro, Giovanni; Giulianini, Franco; Goddard, William A., I.I.I.; Goel, Anuj; Gottesman, Omri; Grove, Megan L.; Gustafsson, Stefan; Hai, Yang; Hallmans, Goeran; Heo, Jiyoung; Hoffmann, Per; Ikram, Mohammad K.; Jensen, Richard A.; Jorgensen, Marit E.; Jorgensen, Torben; Karaleftheri, Maria; Khor, Chiea C.; Kirkpatrick, Andrea; Kraja, Aldi T.; Kuusisto, Johanna; Lange, Ethan M.; Lee, I. T.; Lee, Wen-Jane; Leong, Aaron; Liao, Jiemin; Liu, Chunyu; Liu, Yongmei; Lindgren, Cecilia M.; Linneberg, Allan; Malerba, Giovanni; Mamakou, Vasiliki; Marouli, Eirini; Maruthur, Nisa M.; Matchan, Angela; McKean-Cowdin, Roberta; McLeod, Olga; Metcalf, Ginger A.; Mohlke, Karen L.; Muzny, Donna M.; Ntalla, Ioanna; Palmer, Nicholette D.; Pasko, Dorota; Peter, Andreas; Rayner, Nigel W.; Renstroem, Frida; Rice, Ken; Sala, Cinzia F.; Sennblad, Bengt; Serafetinidis, Ioannis; Smith, Jennifer A.; Soranzo, Nicole; Speliotes, Elizabeth K.; Stahl, Eli A.; Stirrups, Kathleen; Tentolouris, Nikos; Thanopoulou, Anastasia; Torres, Mina; Traglia, Michela; Tsafantakis, Emmanouil; Javad, Sundas; Yanek, Lisa R.; Zengini, Eleni; Becker, Diane M.; Bis, Joshua C.; Brown, James B.; Cupples, L. Adrienne; Hansen, Torben; Ingelsson, Erik; Karter, Andrew J.; Lorenzo, Carlos; Mathias, Rasika A.; Norris, Jill M.; Peloso, Gina M.; Sheu, Wayne H. -H.; Toniolo, Daniela; Vaidya, Dhananjay; Varma, Rohit; Wagenknecht, Lynne E.; Boeing, Heiner; Bottinger, Erwin P.; Dedoussis, George; Deloukas, Panos; Ferrannini, Ele; Franco, Oscar H.; Franks, Paul W.; Gibbs, Richard A.; Gudnason, Vilmundur; Hamsten, Anders; Harris, Tamara B.; Hattersley, Andrew T.; Hayward, Caroline; Hofman, Albert; Jansson, Jan-Hakan; Langenberg, Claudia; Launer, Lenore J.; Levy, Daniel; Oostra, Ben A.; O'Donnell, Christopher J.; O'Rahilly, Stephen; Padmanabhan, Sandosh; Pankow, James S.; Polasek, Ozren; Province, Michael A.; Rich, Stephen S.; Ridker, Paul M.; Rudan, Igor; Schulze, Matthias B.; Smith, Blair H.; Uitterlinden, Andre G.; Walker, Mark; Watkins, Hugh; Wong, Tien Y.; Zeggini, Eleftheria; Laakso, Markku; Borecki, Ingrid B.; Chasman, Daniel I.; Pedersen, Oluf; Psaty, Bruce M.; Tai, E. Shyong; van Duijn, Cornelia M.; Wareham, Nicholas J.; Waterworth, Dawn M.; Boerwinkle, Eric; Kao, W. H. Linda; Florez, Jose C.; Loos, Ruth J. F.; Wilson, James G.; Frayling, Timothy M.; Siscovick, David S.; Dupuis, Josee; Rotter, Jerome I.; Meigs, James B.; Scott, Robert A.; Goodarzi, Mark O.; Sharp, Stephen J.; Forouhi, Nita G.; Kerrison, Nicola D.; Lucarelli, Debora M. E.; Sims, Matt; Barroso, Ines; McCarthy, Mark I.; Arriola, Larraitz; Balkau, Beverley; Barricarte, Aurelio; Gonzalez, Carlos; Grioni, Sara; Kaaks, Rudolf; Key, Timothy J.; Navarro, Carmen; Nilsson, Peter M.; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Quiros, J. Ramon; Rolandsson, Olov; Sacerdote, Carlotta; Sanchez, Maria-Jose; Slimani, Nadia; Tjonneland, Anne; Tumino, Rosario; van der A, Daphne L.; van der Schouw, Yvonne T.; Riboli, Elio
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
NATURE COMMUNICATIONS, 6 Art. No. 5897, JAN 2015
abstract, full text, DOI:10.1038/ncomms6897

Cordova-Mateo, Esther; Bertran, Oscar; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Internal organization of macromonomers and dendronized polymers based on thiophene dendrons
SOFT MATTER, 11:1116-1126, 2015
abstract, full text, DOI:10.1039/c4sm02523g

Gray, Alan; Harlen, Oliver G.; Harris, Sarah A.; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J.; Pearson, Arwen R.; Read, Daniel J.; Richardson, Robin A.
In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71:162-172, JAN 2015
abstract, full text, DOI:10.1107/S1399004714026777

Schulz, Robert; Vargiu, Attilio V.; Ruggerone, Paolo; Kleinekathoefer, Ulrich
Computational Study of Correlated Domain Motions in the AcrB Efflux Transporter
BIOMED RESEARCH INTERNATIONAL, Art. No. 487298, 2015
abstract, full text, DOI:10.1155/2015/487298

Lu Shi-Jing; Zhou Xin
Construction of Coarse-Grained Models by Reproducing Equilibrium Probability Density Function
COMMUNICATIONS IN THEORETICAL PHYSICS, 63:10-18, JAN 2015
abstract, full text

Danishuddin, Mohd; Khan, Asad U.
Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
METHODS, 71:135-145, JAN 1 2015
abstract, full text, DOI:10.1016/j.ymeth.2014.10.019

Rocca, Roberta; Moraca, Federica; Costa, Giosue; Alcaro, Stefano; Distinto, Simona; Maccioni, Elias; Ortuso, Francesco; Artese, Anna; Parrotta, Lucia
Structure-Based Virtual Screening of Novel Natural Alkaloid Derivatives as Potential Binders of h-telo and c-myc DNA G-Quadruplex Conformations
MOLECULES, 20:206-223, JAN 2015
abstract, full text, DOI:10.3390/molecules20010206

Decherchi, Sergio; Berteotti, Anna; Bottegoni, Giovanni; Rocchia, Walter; Cavalli, Andrea
The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning
Nature Communications, 6 Art. No. 6155, JAN 2015
abstract, full text, DOI:10.1038/ncomms7155

Katti, Dinesh R.; Sharma, Anurag; Ambre, Avinash H.; Katti, Kalpana S.
Molecular interactions in biomineralized hydroxyapatite amino acid modified nanoclay: In silico design of bone biomaterials
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 46:207-217, JAN 1 2015
abstract, full text, DOI:10.1016/j.msec.2014.07.057

Wu, Wenyun; Yue, Jingying; Li, Dongqi; Lin, Xiaoyang; Zhu, Fangqiang; Yin, Xue; Zhu, Jun; Dai, Xingcan; Liu, Peng; Wei, Yang; Wang, Jiaping; Yang, Haitao; Zhang, Lina; Li, Qunqing; Fan, Shoushan; Jiang, Kaili
Interface dipole enhancement effect and enhanced Rayleigh scattering
NANO RESEARCH, 8:303-319, JAN 2015
abstract, full text, DOI:10.1007/s12274-014-0687-5

Xu, Lei; Li, Youyong; Li, Dan; Xu, Peng; Tian, Sheng; Sun, Huiyong; Liu, Hui; Hou, Tingjun
Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:3370-3382, 2015
abstract, full text, DOI:10.1039/c4cp05095a

Villarreal, Oscar D.; Chen, Liao Y.; Whetten, Robert L.; Yacaman, Miguel J.
Ligand-modulated interactions between charged monolayer-protected Au-144(SR)(60) gold nanoparticles in physiological saline
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:3680-3688, 2015
abstract, full text, DOI:10.1039/c4cp05137h

Wineman-Fisher, Vered; Atsmon-Raz, Yoav; Miller, Yifat
Orientations of Residues along the beta-Arch of Self-Assembled Amylin Fibril-Like Structures Lead to Polymorphism
BIOMACROMOLECULES, 16:156-165, JAN 2015
abstract, full text, DOI:10.1021/bm501326y

Fraiberg, Milana; Afanzar, Oshri; Cassidy, C. Keith; Gabashvili, Alexandra; Schulten, Klaus; Levin, Yishai; Eisenbach, Michael
CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli
MOLECULAR MICROBIOLOGY, 95:231-244, JAN 2015
abstract, full text, TCBG publications, DOI:10.1111/mmi.12858

Gupta, Kushol; Selinsky, Barry S.
Bacterial and algal orthologs of prostaglandin H-2 synthase: novel insights into the evolution of an integral membrane protein
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:83-94, JAN 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.09.011

Rovira, Xavier; Malhaire, Fanny; Scholler, Pauline; Rodrigo, Jordi; Gonzalez-Bulnes, Patricia; Llebaria, Amadeu; Pin, Jean-Philippe; Giraldo, Jesus; Goudet, Cyril
Overlapping binding sites drive allosteric agonism and positive cooperativity in type 4 metabotropic glutamate receptors
FASEB JOURNAL, 29:116-130, JAN 2015
abstract, full text, DOI:10.1096/fj.14-257287

Gerbier, Romain; Leroux, Vincent; Couvineau, Pierre; Alvear-Perez, Rodrigo; Maigret, Bernard; Llorens-Cortes, Catherine; Iturrioz, Xavier
New structural insights into the apelin receptor: identification of key residues for apelin binding
FASEB JOURNAL, 29:314-322, JAN 2015
abstract, full text, DOI:10.1096/fj.14-256339

Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepulveda, Romina V.; Aguayo, Daniel; Gonzalez-Nilo, Fernando; Gonzalez, Carlos; Latorre, Ramon
Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel
JOURNAL OF GENERAL PHYSIOLOGY, 145:61-74, JAN 2015
abstract, full text, DOI:10.1085/jgp.201411194

Rodriguez-Rodriguez, C.; Telpoukhovskaia, M. A.; Ali-Torres, J.; Rodriguez-Santiago, L.; Manso, Y.; Bailey, G. A.; Hidalgo, J.; Sodupe, M.; Orvig, C.
Thioflavin-based molecular probes for application in Alzheimer's disease: from in silico to in vitro models
METALLOMICS, 7:78-87, 2015
abstract, full text, DOI:10.1039/c4mt00167b

Ruiz, Luis; Wu, Yuanqiao; Keten, Sinan
Tailoring the water structure and transport in nanotubes with tunable interiors
NANOSCALE, 7:121-132, 2015
abstract, full text, DOI:10.1039/c4nr05407e

Sule, Nitesh V.; Ugrinov, Angel; Mallik, Sanku; Srivastava, D. K.
Bridging of a substrate between cyclodextrin and an enzyme's active site pocket triggers a unique mode of inhibition
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:141-149, JAN 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.10.016

Choi, Bumjoon; Yoon, Gwonchan; Lee, Sang Woo; Eom, Kilho
Mechanical deformation mechanisms and properties of amyloid fibrils
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1379-1389, 2015
abstract, full text, DOI:10.1039/c4cp03804e

Nierzwicki, L.; Wieczor, M.; Censi, V.; Baginski, M.; Calucci, L.; Samaritani, S.; Czub, J.; Forte, C.
Interaction of cisplatin and two potential antitumoral platinum(II) complexes with a model lipid membrane: a combined NMR and MD study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1458-1468, 2015
abstract, full text, DOI:10.1039/c4cp04360j

Agosta, Lorenzo; Zollo, Giuseppe; Arcangeli, Caterina; Buonocore, Francesco; Gala, Fabrizio; Celino, Massimo
Water driven adsorption of amino acids on the (101) anatase TiO2 surface: an ab initio study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1556-1561, 2015
abstract, full text, DOI:10.1039/c4cp03056g

Leman, Julia Koehler; Ulmschneider, Martin B.; Gray, Jeffrey J.
Computational modeling of membrane proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1-24, JAN 2015
abstract, full text, DOI:10.1002/prot.24703

Ng, Yao Zong; Kannan, Srinivasaraghavan; Lane, David P.; Fuentes, Gloria; Verma, Chandra S.
mAb806 binding to epidermal growth factor receptor: a computational study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:153-168, JAN 2015
abstract, full text, DOI:10.1002/prot.24714

Culleton, Bridget A.; Lall, Patrick; Kinsella, Gemma K.; Doyle, Sean; McCaffrey, John; Fitzpatrick, David A.; Burnell, Ann M.
A role for the Parkinson's disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus
CELL STRESS & CHAPERONES, 20:121-137, JAN 2015
abstract, full text, DOI:10.1007/s12192-014-0531-6

Wang, Feng; Wan, Hua; Hu, Jian-ping; Chang, Shan
Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C
MOLECULAR BIOSYSTEMS, 11:223-231, JAN 2015
abstract, full text, DOI:10.1039/c4mb00383g

Carmona, Christopher; Langan, Paul; Smith, Jeremy C.; Petridis, Loukas
Why genetic modification of lignin leads to low-recalcitrance biomass
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:358-364, 2015
abstract, full text, DOI:10.1039/c4cp05004e

Sun, Yeping; Liu, Qian
Differential structural dynamics and antigenicity of two similar influenza H5N1 virus HA-specific HLA-A*0201-restricted CLT epitopes
RSC ADVANCES, 5:2318-2327, 2015
abstract, full text, DOI:10.1039/c4ra08874c

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; Ho, Chian-Sing; Khadka, Nawal; Katsaras, John
Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations
SOFT MATTER, 11:130-138, 2015
abstract, full text, DOI:10.1039/c4sm02227k

Jana, Asis K.; Sengupta, Neelanjana
A beta self-association and adsorption on a hydrophobic nanosurface: competitive effects and the detection of small oligomers via electrical response
SOFT MATTER, 11:269-279, 2015
abstract, full text, DOI:10.1039/c4sm01845a

Palese, Luigi Leonardo
Random Matrix Theory in molecular dynamics analysis
BIOPHYSICAL CHEMISTRY, 196:1-9, JAN 2015
abstract, full text, DOI:10.1016/j.bpc.2014.08.007

Kelly, Catherine M.; Northey, Thomas; Ryan, Kate; Brooks, Bernard R.; Kholkin, Andrei L.; Rodriguez, Brian J.; Buchete, Nicolae-Viorel
Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field
BIOPHYSICAL CHEMISTRY, 196:16-24, JAN 2015
abstract, full text, DOI:10.1016/j.bpc.2014.08.009

Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael
On the hydration of subnanometric antifouling organosilane adlayers: A molecular dynamics simulation
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 437:197-204, JAN 1 2015
abstract, full text, DOI:10.1016/j.jcis.2014.09.025

Araujo, Pedro M. M.; da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Theoretical Modelling of Potential Chk1 Inhibitors
LETTERS IN DRUG DESIGN & DISCOVERY, 12:60-65, 2015
abstract, full text

Bal, Naresh C.; Jena, Nivedita; Chakravarty, Harapriya; Kumar, Amit; Chi, Mei; Balaraju, Tuniki; Rawale, Sharad V.; Rawale, Jayashree S.; Sharon, Ashoke; Periasamy, Muthu
The C-Terminal Calcium-Sensitive Disordered Motifs Regulate Isoform-Specific Polymerization Characteristics of Calsequestrin
BIOPOLYMERS, 103:15-22, JAN 2015
abstract, full text, DOI:10.1002/bip.22534

Lindahl, Erik
Molecular Dynamics Simulations
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:3-26, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_1

Biggin, Philip C.; Bond, Peter J.
Molecular Dynamics Simulations of Membrane Proteins
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:91-108, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_5

Gedeon, Patrick C.; Thomas, James R.; Madura, Jeffry D.
Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:253-287, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_12

Sorensen, Jesper; Demir, Oezlem; Swift, Robert V.; Feher, Victoria A.; Amaro, Rommie E.
Molecular Docking to Flexible Targets
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:445-469, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_20

Fossepre, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P.
On the Modularity of the Intrinsic Flexibility of the mu Opioid Receptor: A Computational Study
PLOS ONE, 9 Art. No. e115856, DEC 30 2014
abstract, full text, DOI:10.1371/journal.pone.0115856

Fichna, Jakub Piotr; Karolczak, Justyna; Potulska-Chromik, Anna; Miszta, Przemyslaw; Berdynski, Mariusz; Sikorska, Agata; Filipek, Slawomir; Redowicz, Maria Jolanta; Kaminska, Anna; Zekanowski, Cezary
Two Desmin Gene Mutations Associated with Myofibrillar Myopathies in Polish Families
PLOS ONE, 9 Art. No. UNSP e115470, DEC 26 2014
abstract, full text, DOI:10.1371/journal.pone.0115470

Spata, Vincent A.; Matsika, Spiridoula
Role of Excitonic Coupling and Charge-Transfer States in the Absorption and CD Spectra of Adenine-Based Oligonucleotides Investigated through QM/MM Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 118:12021-12030, DEC 25 2014
abstract, full text, DOI:10.1021/jp507520c

Wang, Nuo; Zhou, Shenggao; Kekenes-Huskey, Peter M.; Li, Bo; McCammon, J. Andrew
Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14827-14832, DEC 25 2014
abstract, full text, DOI:10.1021/jp511702w

Raczynski, Przemyslaw; Gorny, Krzysztof; Samios, Jannis; Gburski, Zygmunt
Interaction Between Silicon-Carbide Nanotube and Cholesterol Domain. A Molecular Dynamics Simulation Study.
JOURNAL OF PHYSICAL CHEMISTRY C, 118:30115-30119, DEC 25 2014
abstract, full text, DOI:10.1021/jp505532f

Basu, Ipsita; Multhopadhyay, Chaitali
Insights into Binding of Cholera Toxin to GM1 Containing Membrane
LANGMUIR, 30:15244-15252, DEC 23 2014
abstract, full text, DOI:10.1021/la5036618

Karatasos, Kostas
Graphene/Hyperbranched Polymer Nanocomposites: Insight from Molecular Dynamics Simulations
MACROMOLECULES, 47:8833-8845, DEC 23 2014
abstract, full text, DOI:10.1021/ma502123a

Re, Suyong; Nishima, Wataru; Tahara, Tahei; Sugita, Yuji
Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:4343-4348, DEC 18 2014
abstract, full text, DOI:10.1021/jz502299m

Marinelli, Fabrizio; Almagor, Lior; Hiller, Reuben; Giladi, Moshe; Khananshvili, Daniel; Faraldo-Gomez, Jose D.
Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E5354-E5362, DEC 16 2014
abstract, full text, DOI:10.1073/pnas.1415751111

Pujato, Mario; Kieken, Fabien; Skiles, Amanda A.; Tapinos, Nikos; Fiser, Andras
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes
NUCLEIC ACIDS RESEARCH, 42:13500-13512, DEC 16 2014
abstract, full text, DOI:10.1093/nar/gku1228

Fuerst, Oliver; Nichols, Colin G.; Lamoureux, Guillaume; D'Avanzo, Nazzareno
Identification of a Cholesterol-Binding Pocket in Inward Rectifier K+ (Kir) Channels
BIOPHYSICAL JOURNAL, 107:2786-2796, DEC 16 2014
abstract, full text, DOI:10.1016/j.bpj.2014.10.066

Sinko, Robert; Keten, Sinan
Effect of moisture on the traction-separation behavior of cellulose nanocrystal interfaces
APPLIED PHYSICS LETTERS, 105 Art. No. 243702, DEC 15 2014
abstract, full text, DOI:10.1063/1.4904708

Lopez-Emparan, Ada; Quezada-Martinez, Daniela; Zuniga-Bustos, Matias; Cifuentes, Victor; Iniguez-Luy, Federico; Laura Federico, Maria
Functional Analysis of the Brassica napus L. Phytoene Synthase (PSY) Gene Family
PLOS ONE, 9 Art. No. e114878, DEC 15 2014
abstract, full text, DOI:10.1371/journal.pone.0114878

Naddaf, Lamis; Sayyed-Ahmad, Abdallah
Intracellular crowding effects on the self-association of the bacterial cell division protein FtsZ
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 564:12-19, DEC 15 2014
abstract, full text, DOI:10.1016/j.abb.2014.08.016

Huang, Zhehao; Yao, Yuan; Han, Lu; Che, Shunai
Control of Chiral Nanostructures by Self-Assembly of Designed Amphiphilic Peptides and Silica Biomineralization
CHEMISTRY-A EUROPEAN JOURNAL, 20:17068-17076, DEC 15 2014
abstract, full text, DOI:10.1002/chem.201403498

Zhou, Yuan-Wu; Liu, Jin-Long; Yu, Zu-Guo; Zhao, Ni Qin; Anh, Vo
Fractal and complex network analyses of protein molecular dynamics
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 416:21-32, DEC 15 2014
abstract, full text, DOI:10.1016/j.physa.2014.08.047

Duboue-Dijon, Elise; Laage, Damien
Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D529, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902822

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery
Multibody correlations in the hydrophobic solvation of glycine peptides
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D525, DEC 14 2014
abstract, full text, DOI:10.1063/1.4901886

Martinez, Anna Victoria; Malolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.
Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides A beta(16-22) and Sup35(7-13) in AOT reverse micelles
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D530, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902550

Sharp, Kim A.
The remarkable hydration of the antifreeze protein Maxi: A computational study
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D510, DEC 14 2014
abstract, full text, DOI:10.1063/1.4896693

Sinha, Sudipta Kumar; Jana, Madhurima; Chakraborty, Kausik; Bandyopadhyay, Sanjoy
In silico studies of the properties of water hydrating a small protein
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D502, DEC 14 2014
abstract, full text, DOI:10.1063/1.4895533

Sode, Olaseni; Voth, Gregory A.
Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D527, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902236

Vaitheeswaran, S.; Thirumalai, D.
Entropy and enthalpy of interaction between amino acid side chains in nanopores
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D523, DEC 14 2014
abstract, full text, DOI:10.1063/1.4901204

Wilson, Michael A.; Thuy Hien Nguyen; Pohorille, Andrew
Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D519, DEC 14 2014
abstract, full text, DOI:10.1063/1.4900879

Morishita, Masayo; Mevius, Damiaan; di Luccio, Eric
In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1 and NSD3/WHSC1L
BMC STRUCTURAL BIOLOGY, 14 Art. No. 25, DEC 12 2014
abstract, full text, DOI:10.1186/s12900-014-0025-x

Migliori, Amy D.; Smith, Douglas E.; Arya, Gaurav
Molecular Interactions and Residues Involved in Force Generation in the T4 Viral DNA Packaging Motor
JOURNAL OF MOLECULAR BIOLOGY, 426:4002-4017, DEC 12 2014
abstract, full text, DOI:10.1016/j.jmb.2014.09.023

Nategholeslam, Mostafa; Gray, C. G.; Tomberli, Bruno
Implementation of the Forward-Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14203-14214, DEC 11 2014
abstract, full text, DOI:10.1021/jp504942t

Weng, Lindong; Elliott, Gloria D.
Polymerization Effect of Electrolytes on Hydrogen-Bonding Cryoprotectants: Ion-Dipole Interactions between Metal Ions and Glycerol
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14546-14554, DEC 11 2014
abstract, full text, DOI:10.1021/jp5105533

Fenley, Andrew T.; Muddana, Hari S.; Gilson, Michael K.
Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
PLOS ONE, 9 Art. No. e113119, DEC 11 2014
abstract, full text, DOI:10.1371/journal.pone.0113119

Dwyer, Patrick J.; Vander Valk, Rory J.; Caltaldo, Vito; Dennanicz, David; Keite, Stephen P.
All-Atom CHARMM Force Field and Bulk Properties of Perfluorozinc Phthalocyanines
JOURNAL OF PHYSICAL CHEMISTRY A, 118:11583-11590, DEC 11 2014
abstract, full text, DOI:10.1021/jp506601e

Segrest, Jere P.; Jones, Martin K.; Shao, Baohai; Heinecke, Jay W.
An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations
BIOCHEMISTRY, 53:7625-7640, DEC 9 2014
abstract, full text, DOI:10.1021/bi501111j

Souza, Caio S.; Amaral, Cristiano; Treptow, Werner
Electric fingerprint of voltage sensor domains
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:17510-17515, DEC 9 2014
abstract, full text, DOI:10.1073/pnas.1413971111

Jayaram, B.; Dhingra, Priyanka; Mishra, Avinash; Kaushik, Rahul; Mukherjee, Goutam; Singh, Ankita; Shekhar, Shashank
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins
BMC BIOINFORMATICS, 15 Art. No. S7, DEC 8 2014
abstract, full text, DOI:10.1186/1471-2105-15-S16-S7

Semino, Rocio; Zaldivar, Gervasio; Calvo, Ernesto J.; Laria, Daniel
Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 214509, DEC 7 2014
abstract, full text, DOI:10.1063/1.4902837

Starzyk, Joanna; Gruszecki, Marcin; Tutaj, Krzysztof; Luchowski, Rafal; Szlazak, Radoslaw; Wasko, Piotr; Grudzinski, Wojciech; Czub, Jacek; Gruszecki, Wieslaw I.
Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13821-13832, DEC 4 2014
abstract, full text, DOI:10.1021/jp510245n

Shi, Wei; Hong, Lei; Damodaran, Krishnan; Nulwala, Hunaid B.; Luebke, David R.
Molecular Simulation and Experimental Study of CO2 Absorption in Ionic Liquid Reverse Micelle
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13870-13881, DEC 4 2014
abstract, full text, DOI:10.1021/jp509282h

Sahillioglu, Ali Can; Sumbul, Fidan; Ozoren, Nesrin; Haliloglu, Turkan
Structural and Dynamics Aspects of ASC Speck Assembly
STRUCTURE, 22:1722-1734, DEC 2 2014
abstract, full text, DOI:10.1016/j.str.2014.09.011

Liu, Ming S.; Wang, Die; Morimoto, Hiroyuki; Yim, Howard C. H.; Irving, Aaron T.; Williams, Bryan R. G.; Sadler, Anthony J.
Molecular dynamics reveal a novel kinase-substrate interface that regulates protein translation
JOURNAL OF MOLECULAR CELL BIOLOGY, 6:473-485, DEC 2014
abstract, full text, DOI:10.1093/jmcb/mju044

Dorn, Marcio; Barbachan e Silva, Mariel; Buriol, Luciana S.; Lamb, Luis C.
Three-dimensional protein structure prediction: Methods and computational strategies
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 53:251-276, DEC 2014
abstract, full text, DOI:10.1016/j.compbiolchem.2014.10.001

Peters, Gunther H.; Werge, Mikkel; Elf-Lind, Maria Northved; Madsen, Jesper J.; Velardez, Gustavo F.; Westh, Peter
Interaction of neurotransmitters with a phospholipid bilayer: A molecular dynamics study
CHEMISTRY AND PHYSICS OF LIPIDS, 184:7-17, DEC 2014
abstract, full text, DOI:10.1016/j.chemphyslip.2014.08.003

du Bourg, Lila Bouessel; Ortiz, Aurelie U.; Boutin, Anne; Coudert, Francois-Xavier
Thermal and mechanical stability of zeolitic imidazolate frameworks polymorphs
APL MATERIALS, 2 Art. No. 124110, DEC 2014
abstract, full text, DOI:10.1063/1.4904818

Schoeler, Constantin; Malinowska, Klara H.; Bernardi, Rafael C.; Milles, Lukas F.; Jobst, Markus A.; Durner, Ellis; Ott, Wolfgang; Fried, Daniel B.; Bayer, Edward A.; Schulten, Klaus; Gaub, Hermann E.; Nash, Michael A.
Ultrastable cellulosome-adhesion complex tightens under load
NATURE COMMUNICATIONS, 5 Art. No. 5635, DEC 2014
abstract, full text, TCBG publications, DOI:10.1038/ncomms6635

Li, Tianxia; Yang, Dejun; Zhong, Shijun; Thomas, Joseph M.; Xue, Fengtian; Liu, Jingnan; Kong, Lingbo; Voulalas, Pamela; Hassan, Hazem E.; Park, Jae-Sung; MacKerell, Alexander D., Jr.; Smith, Wanli W.
Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models
HUMAN MOLECULAR GENETICS, 23:6212-6222, DEC 1 2014
abstract, full text, DOI:10.1093/hmg/ddu341

Mahdavi, Somayeh; Kuyucak, Serdar
Systematic Study of Binding of mu-Conotoxins to the Sodium Channel Na(V)1.4
TOXINS, 6:3454-3470, DEC 2014
abstract, full text, DOI:10.3390/toxins6123454

Ma, Buyong; Kolb, Stephanie; Diprima, Michael; Karna, Molleshree; Tosato, Giovanna; Yang, Qiqi; Huang, Qiang; Nussinov, Ruth
Investigation of the interactions between the EphB2 receptor and SNEW peptide variants
GROWTH FACTORS, 32:236-246, DEC 2014
abstract, full text, DOI:10.3109/08977194.2014.985786

Elward, Jennifer M.; Irudayanathan, Flaviyan Jerome; Nangia, Shikha; Chakraborty, Arindam
Optical Signature of Formation of Protein Corona in the Firefly Luciferase-CdSe Quantum Dot Complex
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5224-5228, DEC 2014
abstract, full text, DOI:10.1021/ct500681m

Comer, Jeffrey; Phillips, James C.; Schulten, Klaus; Chipot, Christophe
Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5276-5285, DEC 2014
abstract, full text, TCBG publications, DOI:10.1021/ct500874p

Sahu, Indra D.; Hustedt, Eric J.; Ghimire, Harishchandra; Inbaraj, Johnson J.; McCarrick, Robert M.; Lorigan, Gary A.
CW dipolar broadening EPR spectroscopy and mechanically aligned bilayers used to measure distance and relative orientation between two TOAC spin labels on an antimicrobial peptide
JOURNAL OF MAGNETIC RESONANCE, 249:72-79, DEC 2014
abstract, full text, DOI:10.1016/j.jmr.2014.09.020

Pietra, Francesco
Molecular Dynamics Simulation of Dioxygen Pathways through Mini Singlet Oxygen Generator (miniSOG), a Genetically Encoded Marker and Killer Protein
CHEMISTRY & BIODIVERSITY, 11:1883-1891, DEC 2014
abstract, full text, DOI:10.1002/cbdv.201400125

Delacour, Herve; Lushchekina, Sofya; Mabboux, Isabelle; Ceppa, Franck; Masson, Patrick; Schopfer, Lawrence M.; Lockridge, Oksana
Characterization of a novel butyrylcholinesterase point mutation (p.Ala34Val), "silent" with mivacurium
BIOCHEMICAL PHARMACOLOGY, 92:476-483, DEC 1 2014
abstract, full text, DOI:10.1016/j.bcp.2014.09.014

Ungvarsky, Jan; Plsikova, Jana; Janovec, Ladislav; Koval, Jan; Mikes, Jaromir; Mikesova, Lucia; Harvanova, Denisa; Fedorocko, Peter; Kristian, Pavol; Kasparkova, Jana; Brabec, Viktor; Vojtickova, Maria; Sabolova, Danica; Stramova, Zuzana; Rosocha, Jan; Imrich, Jan; Kozurkova, Maria
Novel trisubstituted acridines as human telomeric quadruplex binding ligands
BIOORGANIC CHEMISTRY, 57:13-29, DEC 2014
abstract, full text, DOI:10.1016/j.bioorg.2014.07.010

Hundt, Nikolas; Preller, Matthias; Swolski, Olga; Ang, Angella M.; Mannherz, Hans G.; Manstein, Dietmar J.; Mueller, Mirco
Molecular mechanisms of disease-related human beta-actin mutations p.R183W and p.E364K
FEBS JOURNAL, 281:5279-5291, DEC 2014
abstract, full text, DOI:10.1111/febs.13068

Lipovsek, Marcela; Fierro, Angelica; Perez, Edwin G.; Boffi, Juan C.; Millar, Neil S.; Fuchs, Paul A.; Katz, Eleonora; Belen Elgoyhen, Ana
Tracking the Molecular Evolution of Calcium Permeability in a Nicotinic Acetylcholine Receptor
MOLECULAR BIOLOGY AND EVOLUTION, 31:3250-3265, DEC 2014
abstract, full text, DOI:10.1093/molbev/msu258

Li, Qing; Scholl, Zackary N.; Marszalek, Piotr E.
Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled-Coil Probes
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 53:13429-13433, DEC 1 2014
abstract, full text, DOI:10.1002/anie.201407211

Jardon-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.
Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1964-1972, DEC 2014
abstract, full text, DOI:10.1016/j.bbabio2014.09.006

Woelke, Anna Lena; Galstyan, Gegham; Knapp, Ernst-Walter
Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pK(A) and conformation
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1998-2003, DEC 2014
abstract, full text, DOI:10.1016/j.bbabio.2014.08.003

Bagatin, Mariane Cristovao; Suniga Tozatti, Camila Santos; Abiko, Layara Akemi; dos Santos Yamazaki, Diego Alberto; Alves Silva, Priscila Rebeca; Perego, Leonardo Martins; Audi, Elisabeth Aparecida; Vicente Seixas, Flavio Augusto; Basso, Ernani Abicht; Gauze, Gisele de Freitas
Molecular Docking and Panicolytic Effect of 8-Prenylnaringenin in the Elevated T-Maze
CHEMICAL & PHARMACEUTICAL BULLETIN, 62:1231-1237, DEC 2014
abstract, full text

Pinto da Silva, Luis; Esteves da Silva, Joaquim C. G.
A Theoretical Analysis of the Potential Role of pi-pi Stacking Interactions in the Photoprotolytic Cycle of Firefly Luciferin
CHEMPHYSCHEM, 15:3761-3767, DEC 1 2014
abstract, full text, DOI:10.1002/cphc.201402558

Kim, Soo-Kyung; Goddard, William A., I.I.I.
Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1175-1190, DEC 2014
abstract, full text, DOI:10.1007/s10822-014-9793-4

Virginia Saavedra-Velez, Margarita; Correa-Basurto, Jose; Matus, Myrna H.; Gasca-Perez, Eloy; Bello, Martiniano; Cuevas-Hernandez, Roberto; Virginia Garcia-Rodriguez, Rosa; Trujillo-Ferrara, Jose; Rafael Ramos-Morales, Fernando
Seeking potential anticonvulsant agents that target GABA(A) receptors using experimental and theoretical procedures
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1217-1232, DEC 2014
abstract, full text, DOI:10.1007/s10822-014-9798-z

Strohalmova-Bohmova, Karolina; Spiwok, Vojtech; Lepsik, Martin; Hadravova, Romana; Krizova, Ivana; Ulbrich, Pavel; Pichova, Iva; Bednarova, Lucie; Ruml, Tomas; Rumlova, Michaela
Role of Mason-Pfizer Monkey Virus CA-NC Spacer Peptide-Like Domain in Assembly of Immature Particles
JOURNAL OF VIROLOGY, 88:14148-14160, DEC 2014
abstract, full text, DOI:10.1128/JVI.02286-14

Persson, Egon; Madsen, Jesper J.; Olsen, Ole H.
The length of the linker between the epidermal growth factor-like domains in factor VIIa is critical for a productive interaction with tissue factor
PROTEIN SCIENCE, 23:1717-1727, DEC 2014
abstract, full text, DOI:10.1002/pro.2553

Nakano, Shogo; Dadashipour, Mohammad; Asano, Yasuhisa
Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844:2059-2067, DEC 2014
abstract, full text, DOI:10.1016/j.bbapap.2014.09.004

Cui, Di; Ou, Shuching; Patel, Sandeep
Protein-Spanning Water Networks and Implications for Prediction of Protein-Protein Interactions Mediated through Hydrophobic Effects
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:3312-3326, DEC 2014
abstract, full text, DOI:10.1002/prot.24683

Pillai, Jitesh K.; Venkadesh, Sarkarai; Ajees, A. Abdul; Rosen, Barry P.; Bhattacharjee, Hiranmoy
Mutations in the ArsA ATPase that restore interaction with the ArsD metallochaperone
BIOMETALS, 27:1263-1275, DEC 2014
abstract, full text, DOI:10.1007/s10534-014-9788-6

Boynton, P.; Balatsky, A. V.; Schuller, I. K.; Di Ventra, M.
Improving sequencing by tunneling with multiplexing and cross-correlations
JOURNAL OF COMPUTATIONAL ELECTRONICS, 13:794-800, DEC 2014
abstract, full text, DOI:10.1007/s10825-014-0571-2

Belkin, Maxim; Chao, Shu-Han; Giannetti, Gino; Aksimentiev, Aleksei
Modeling thermophoretic effects in solid-state nanopores
JOURNAL OF COMPUTATIONAL ELECTRONICS, 13:826-838, DEC 2014
abstract, full text, DOI:10.1007/s10825-014-0594-8

Polak, Andraz; Tarek, Mounir; Tomsic, Matija; Valant, Janez; Ulrih, Natasa Poklar; Jamnik, Andrej; Kramar, Peter; Miklavcic, Damijan
Electroporation of archaeal lipid membranes using MD simulations
BIOELECTROCHEMISTRY, 100:18-26, DEC 2014
abstract, full text, DOI:10.1016/j.bioelechem.2013.12.006

Grizel, Anastasia; Popinako, Anna; Kasimova, Marina A.; Stevens, Louisa; Karlova, Maria; Moisenovich, Mikhail M.; Sokolova, Olga S.
Domain Structure and Conformational Changes in rat K(V)2.1 ion Channel
JOURNAL OF NEUROIMMUNE PHARMACOLOGY, 9:727-739, DEC 2014
abstract, full text, DOI:10.1007/s11481-014-9565-x

Alberga, Domenico; Nicolotti, Orazio; Lattanzi, Gianluca; Nicchia, Grazia Paola; Frigeri, Antonio; Pisani, Francesco; Benfenati, Valentina; Mangiatordi, Giuseppe Felice
A new gating site in human aquaporin-4: Insights from molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3052-3060, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.015

Vermaas, Josh V.; Tajkhorshid, Emad
Conformational heterogeneity of alpha-synuclein in membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3107-3117, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.012

Deleu, Magali; Crowet, Jean-Marc; Nasir, Mehmet N.; Lins, Laurence
Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3171-3190, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.023

Schillinger, Anne-Sophie; Grauffel, Cedric; Khan, Hanif Muhammad; Halskau, Oyvind; Reuter, Nathalie
Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3191-3202, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.09.003

Benavidez, Tomas E.; Torrente, Daniel; Marucho, Marcelo; Garcia, Carlos D.
Adsorption and catalytic activity of glucose oxidase accumulated on OTCE upon the application of external potential
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 435:164-170, DEC 1 2014
abstract, full text, DOI:10.1016/j.jcis.2014.08.012

Adamczyk, Zbigniew; Jamrozy, Krzysztof; Batys, Piotr; Michna, Aneta
Influence of ionic strength on poly(diallyldimethylammonium chloride) macromolecule conformations in electrolyte solutions
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 435:182-190, DEC 1 2014
abstract, full text, DOI:10.1016/j.jcis.2014.07.037

Abdul-Ridha, Alaa; Lane, J. Robert; Mistry, Shailesh N.; Lopez, Laura; Sexton, Patrick M.; Scammells, Peter J.; Christopoulos, Arthur; Canals, Meritxell
Mechanistic Insights into Allosteric Structure-Function Relationships at the M-1 Muscarinic Acetylcholine Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:33701-33711, NOV 28 2014
abstract, full text, DOI:10.1074/jbc.M114.604967

Chatterjee, Prathit; Bagchi, Sayan; Sengupta, Neelanjana
The non-uniform early structural response of globular proteins to cold denaturing conditions: A case study with Yfh1
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 205103, NOV 28 2014
abstract, full text, DOI:10.1063/1.4901897

Khrenova, Maria G.; Savitsky, Alexander P.; Topol, Igor A.; Nemukhin, Alexander V.
Exploration of the Zinc Finger Motif in Controlling Activity of Matrix Metalloproteinases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13505-13512, NOV 27 2014
abstract, full text, DOI:10.1021/jp5088702

Baker, Michelle K.; Abrams, Cameron F.
Dynamics of Lipids, Cholesterol, and Transmembrane alpha-Helices from Microsecond Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13590-13600, NOV 27 2014
abstract, full text, DOI:10.1021/jp507027t

Budnjo, Adnan; Narawane, Shailesh; Grauffel, Cedric; Schillinger, Anne-Sophie; Fossen, Torgils; Reuter, Nathalie; Haug, Bengt Erik
Reversible Ketomethylene-Based Inhibitors of Human Neutrophil Proteinase 3
JOURNAL OF MEDICINAL CHEMISTRY, 57:9396-9408, NOV 27 2014
abstract, full text, DOI:10.1021/jm500782s

James, Kevin A.; Verkhivker, Gennady M.
Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions
PLOS ONE, 9 Art. No. e113488, NOV 26 2014
abstract, full text, DOI:10.1371/journal.pone.0113488

Laine, Jennifer M.; Amat, Miguel; Morgan, Brittany R.; Royer, William E., Jr.; Massi, Francesca
Insight into the Allosteric Mechanism of Scapharca Dimeric Hemoglobin
BIOCHEMISTRY, 53:7199-7210, NOV 25 2014
abstract, full text, DOI:10.1021/bi500591s

Bera, Manindra; Kotamarthi, Hema Chandra; Dutta, Subarna; Ray, Angana; Ghosh, Saptaparni; Bhattacharyya, Dhananjay; Ainavarapu, Sri Rama Koti; Sengupta, Kaushik
Characterization of Unfolding Mechanism of Human Lamin A Ig Fold by Single-Molecule Force Spectroscopy-Implications in EDMD
BIOCHEMISTRY, 53:7247-7258, NOV 25 2014
abstract, full text, DOI:10.1021/bi500726f

Lim, San Sui; Yang, Wei; Krishnarjuna, Bankala; Sivaraman, Komagal Kannan; Chandrashekaran, Indu R.; Kass, Itamar; MacRaild, Christopher A.; Devine, Shane M.; Debono, Cael O.; Anders, Robin F.; Scanlon, Martin J.; Scammells, Peter J.; Norton, Raymond S.; McGowan, Sheena
Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO
BIOCHEMISTRY, 53:7310-7320, NOV 25 2014
abstract, full text, DOI:10.1021/bi5012089

Zhang, Li; Liu, Zhipei; Ren, Tao; Wu, Pan; Shen, Jia-Wei; Zhang, Wei; Wang, Xinping
Understanding the Structure of Hydrophobic Surfactants at the Air/Water Interface from Molecular Level
LANGMUIR, 30:13815-13822, NOV 25 2014
abstract, full text, DOI:10.1021/la5030586

Yang, J.; Singharoy, A.; Sereda, Yu. V.; Ortoleva, P. J.
Quasiequivalence of multiscale coevolution and ensemble MD simulations: A demonstration with lactoferrin
CHEMICAL PHYSICS LETTERS, 616:154-160, NOV 25 2014
abstract, full text, DOI:10.1016/j.cplett.2014.10.020

Shang, Zhiguo; Zhou, Kaifeng; Xu, Chen; Csencsits, Roseann; Cochran, Jared C.; Sindelar, Charles V.
High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force generation
ELIFE, 3, NOV 21 2014
abstract, full text, DOI:10.7554/eLife.04686

Perlinska, Agata; Grynberg, Marcin
Bacillus anthracis pXO1 plasmid encodes a putative membrane-bound bacteriocin
PEERJ, 2 Art. No. UNSP e679, NOV 20 2014
abstract, full text, DOI:10.7717/peerj.679

Furini, Simone; Domene, Carmen
DNA Recognition Process of the Lactose Repressor Protein Studied via Metadynamics and Umbrella Sampling Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13059-13065, NOV 20 2014
abstract, full text, DOI:10.1021/jp505885j

Aranda, Juan; Zinovjev, Kirill; Roca, Maite; Tunon, Inaki
Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:16227-16239, NOV 19 2014
abstract, full text, DOI:10.1021/ja5077124

Kastner, Kevin W.; Shoue, Douglas A.; Estiu, Guillermina L.; Wolford, Julia; Fuerst, Megan F.; Markley, Lowell D.; Izaguirre, Jesus A.; McDowell, Mary Ann
Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach
MALARIA JOURNAL, 13 Art. No. 434, NOV 18 2014
abstract, full text, DOI:10.1186/1475-2875-13-434

Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni
Smooth DNA Transport through a Narrowed Pore Geometry
BIOPHYSICAL JOURNAL, 107:2381-2393, NOV 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.10.017

Sayer, James R.; Wallden, Karin; Pesnot, Thomas; Campbell, Frederick; Gane, Paul J.; Simone, Michela; Koss, Hans; Buelens, Floris; Boyle, Timothy P.; Selwood, David L.; Waksman, Gabriel; Tabor, Alethea B.
2-and 3-substituted imidazo[1,2-a]pyrazines as inhibitors of bacterial type IV secretion
BIOORGANIC & MEDICINAL CHEMISTRY, 22:6459-6470, NOV 15 2014
abstract, full text, DOI:10.1016/j.bmc.2014.09.036

Padhi, Siladitya; Burri, Raghunadha Reddy; Jameel, Shahid; Priyakumar, U. Deva
Atomistic Detailed Mechanism and Weak Cation-Conducting Activity of HIV-1 Vpu Revealed by Free Energy Calculations
PLOS ONE, 9 Art. No. e112983, NOV 13 2014
abstract, full text, DOI:10.1371/journal.pone.0112983

Wei, Chenyu; Pohorille, Andrew
Flip-Flop of Oleic Acid in a Phospholipid Membrane: Rate and Mechanism
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12919-12926, NOV 13 2014
abstract, full text, DOI:10.1021/jp508163e

Perez-Aguilar, Jose Manuel; Shan, Jufang; LeVine, Michael V.; Khelashvili, George; Weinstein, Harel
A Functional Selectivity Mechanism at the Serotonin-2A GPCR Involves Ligand-Dependent Conformations of Intracellular Loop 2
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:16044-16054, NOV 12 2014
abstract, full text, DOI:10.1021/ja508394x

Asthana, Shailendra; Shukla, Saumya; Ruggerone, Paolo; Vargiu, Attilio V.
Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations
BIOCHEMISTRY, 53:6941-6953, NOV 11 2014
abstract, full text, DOI:10.1021/bi500490z

Andreasen, Maria; Skeby, Katrine Kirkeby; Zhang, Shuai; Nielsen, Erik Holm; Klausen, Lasse Hyldgaard; Frahm, Heidi; Christiansen, Gunna; Skrydstrup, Troels; Dong, Mingdong; Schiott, Birgit; Otzen, Daniel
The Importance of Being Capped: Terminal Capping of an Amyloidogenic Peptide Affects Fibrillation Propensity and Fibril Morphology
BIOCHEMISTRY, 53:6968-6980, NOV 11 2014
abstract, full text, DOI:10.1021/bi500674u

Krishnan, Subramanian; Liu, Fan; Abrol, Ravinder; Hodges, Jacqueline; Goddard, William A., I.I.I.; Prasadarao, Nemani V.
The Interaction of N-Glycans in Fc gamma Receptor I alpha-Chain with Escherichia coli K1 Outer Membrane Protein A for Entry into Macrophages EXPERIMENTAL AND COMPUTATIONAL ANALYSIS
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:30937-30949, NOV 7 2014
abstract, full text, DOI:10.1074/jbc.M114.599407

Panecka, Joanna; Mura, Cameron; Trylska, Joanna
Interplay of the Bacterial Ribosomal A-Site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study
PLOS ONE, 9 Art. No. e111811, NOV 7 2014
abstract, full text, DOI:10.1371/journal.pone.0111811

Sathe, Chaitanya; Girdhar, Anuj; Leburton, Jean-Pierre; Schulten, Klaus
Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores
NANOTECHNOLOGY, 25 Art. No. 445105, NOV 7 2014
abstract, full text, TCBG publications, DOI:10.1088/0957-4484/25/44/445105

Dong, Hao; Fiorin, Giacomo; DeGrado, William F.; Klein, Michael L.
Proton Release from the Histidine-Tetrad in the M2 Channel of the Influenza A Virus
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12644-12651, NOV 6 2014
abstract, full text, DOI:10.1021/jp5102225

Craddock, Travis John Adrian; Friesen, Douglas; Mane, Jonathan; Hameroff, Stuart; Tuszynski, Jack A.
The feasibility of coherent energy transfer in microtubules
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 11 Art. No. UNSP 20140677, NOV 6 2014
abstract, full text, DOI:10.1098/rsif.2014.0677

Chen, Rong; Gryn'ova, Ganna; Wu, Yingliang; Coote, Michelle L.; Chung, Shin-Ho
Mechanisms and Energetics of Potassium Channel Block by Local Anesthetics and Antifungal Agents
BIOCHEMISTRY, 53:6786-6792, NOV 4 2014
abstract, full text, DOI:10.1021/bi5009408

Petukh, Marharyta; Wu, Bohua; Stefl, Shannon; Smith, Nick; Hyde-Volpe, David; Wang, Li; Alexov, Emil
Chronic Beryllium Disease: Revealing the Role of Beryllium Ion and Small Peptides Binding to HLA-DP2
PLOS ONE, 9 Art. No. e111604, NOV 4 2014
abstract, full text, DOI:10.1371/journal.pone.0111604

Arcario, Mark J.; Tajkhorshid, Emad
Membrane-Induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3
BIOPHYSICAL JOURNAL, 107:2059-2069, NOV 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.022

Blanchard, Andrew E.; Arcario, Mark J.; Schulten, Klaus; Tajkhorshid, Emad
A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin
BIOPHYSICAL JOURNAL, 107:2112-2121, NOV 4 2014
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2014.09.013

Woelke, Anna Lena; Wagner, Anke; Galstyan, Gegham; Meyer, Tim; Knapp, Ernst-Walter
Proton Transfer in the K-Channel Analog of B-Type Cytochrome c Oxidase from Thermus thermophilus
BIOPHYSICAL JOURNAL, 107:2177-2184, NOV 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.010

Anwar-Mohamed, Anwar; Barakat, Khaled H.; Bhat, Rakesh; Noskov, Sergei Y.; Tyrrell, D. Lorne; Tuszynski, Jack A.; Houghton, Michael
A human ether-a-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity
TOXICOLOGY LETTERS, 230:382-392, NOV 4 2014
abstract, full text, DOI:10.1016/j.toxlet.2014.08.007

Stewart, Matthew B.; Gray, Stephen R.; Vasiljevic, Todor; Orbell, John D.
The role of poly-M and poly-GM sequences in the metal-mediated assembly of alginate gels
CARBOHYDRATE POLYMERS, 112:486-493, NOV 4 2014
abstract, full text, DOI:10.1016/j.carbpol.2014.06.001

Klose, Daniel; Voskoboynikova, Natalia; Orban-Glass, Ioan; Rickert, Christian; Engelhard, Martin; Klare, Johann P.; Steinhoff, Heinz-Juergen
Light-induced switching of HAMP domain conformation and dynamics revealed by time-resolved EPR spectroscopy
FEBS LETTERS, 588:3970-3976, NOV 3 2014
abstract, full text, DOI:10.1016/j.febslet.2014.09.012

Neuhaeuser, Benjamin; Dynowski, Marek; Ludewig, Uwe
Switching substrate specificity of AMT/MEP/Rh proteins
CHANNELS, 8:496-502, NOV-DEC 2014
abstract, full text, DOI:10.4161/19336950.2014.967618

Carvalho, Alexandra T. P.; Barrozo, Alexandre; Doron, Dvir; Kilshtain, Alexandra Vardi; Major, Dan Thomas; Kamerlin, Shina Caroline Lynn
Challenges in computational studies of enzyme structure, function and dynamics
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 54:62-79, NOV 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.09.003

Cardone, Giovanni; Duda, Robert L.; Cheng, Naiqian; You, Lili; Conway, James F.; Hendrix, Roger W.; Steven, Alasdair C.
Metastable Intermediates as Stepping Stones on the Maturation Pathways of Viral Capsids
MBIO, 5 Art. No. e02067, NOV-DEC 2014
abstract, full text, DOI:10.1128/mBio.02067-14

Matthies, Doreen; Zhou, Wenchang; Klyszejko, Adriana L.; Anselmi, Claudio; Yildiz, Oezkan; Brandt, Karsten; Mueller, Volker; Faraldo-Goemez, Jose D.; Meier, Thomas
High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase
NATURE COMMUNICATIONS, 5 Art. No. 5286, NOV 2014
abstract, full text, DOI:10.1038/ncomms6286

Kalinic, Marko; Zloh, Mire; Eric, Slavica
Structural insights into binding of small molecule inhibitors to Enhancer of Zeste Homolog 2
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1109-1128, NOV 2014
abstract, full text, DOI:10.1007/s10822-014-9788-1

Zhang, Xiaoming; Niu, DongDong; Carbonell, Alberto; Wang, Airong; Lee, Angel; Tun, Vinnary; Wang, Zonghua; Carrington, James C.; Chang, Chia-en A.; Jin, Hailing
ARGONAUTE PIWI domain and microRNA duplex structure regulate small RNA sorting in Arabidopsis
NATURE COMMUNICATIONS, 5 Art. No. 5468, NOV 2014
abstract, full text, DOI:10.1038/ncomms6468

Gillet, Natacha; Levy, Bernard; Moliner, Vicent; Demachy, Isabelle; de la Lande, Aurelien
Electron and Hydrogen Atom Transfers in the Hydride Carrier Protein EmoB
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5036-5046, NOV 2014
abstract, full text, DOI:10.1021/ct500173y

Durrant, Jacob D.; Votapka, Lane; Sorensen, Jesper; Amaro, Rommie E.
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5047-5056, NOV 2014
abstract, full text, DOI:10.1021/ct500381c

Bhattacharya, Supriyo; Lee, Sangbae; Grisshammer, Reinhard; Tate, Christopher G.; Vaidehi, Nagarajan
Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5149-5160, NOV 2014
abstract, full text, DOI:10.1021/ct500616v

Adams, David R.; Yuan, Hongjie; Holyoak, Todd; Arajs, Katrina H.; Hakimi, Parvin; Markello, Thomas C.; Wolfe, Lynne A.; Vilboux, Thierry; Burton, Barbara K.; Fajardo, Karin Fuentes; Grahame, George; Holloman, Conisha; Sincan, Murat; Smith, Ann C. M.; Wells, Gordon A.; Huang, Yan; Vega, Hugo; Snyder, James P.; Golas, Gretchen A.; Tifft, Cynthia J.; Boerkoel, Cornelius F.; Hanson, Richard W.; Traynelis, Stephen F.; Kerr, Douglas S.; Gahl, William A.
Three rare diseases in one Sib pair: RAI1, PCK1, GRIN2B mutations associated with Smith-Magenis Syndrome, cytosolic PEPCK deficiency and NMDA receptor glutamate insensitivity
MOLECULAR GENETICS AND METABOLISM, 113:161-170, NOV 2014
abstract, full text, DOI:10.1016/j.ymgme.2014.04.001

Ho, Junming; Newcomer, Michael B.; Ragain, Christina M.; Gascon, Jose A.; Batista, Enrique R.; Loria, J. Patrick; Batista, Victor S.
MoD-QM/MM Structural Refinement Method: Characterization of Hydrogen Bonding in the Oxytricha nova G-Quadruplex
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5125-5135, NOV 2014
abstract, full text, DOI:10.1021/ct500571k

Cocaign, Angelique; Kubiak, Xavier; Xu, Ximing; Garnier, Guillaume; de la Sierra-Gallay, Ines Li; Linh Chi-Bui; Dairou, Julien; Busi, Florent; Abuhammad, Areej; Haouz, Ahmed; Dupret, Jean-Marie; Herrmann, Jean-Louis; Rodrigues-Lima, Fernando
Structural and functional characterization of an arylamine N-acetyltransferase from the pathogen Mycobacterium abscessus: differences from other mycobacterial isoforms and implications for selective inhibition
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70:3066-3079, NOV 2014
abstract, full text, DOI:10.1107/S1399004714021282

Sathaye, Sameer; Zhang, Huixi; Sonmez, Cem; Schneider, Joel P.; MacDermaid, Christopher M.; Von Bargen, Christopher D.; Saven, Jeffery G.; Pochan, Darrin J.
Engineering Complementary Hydrophobic Interactions to Control beta-Hairpin Peptide Self-Assembly, Network Branching, and Hydrogel Properties
BIOMACROMOLECULES, 15:3891-3900, NOV 2014
abstract, full text, DOI:10.1021/bm500874t

Apellaniz, Beatriz; Rujas, Edurne; Carravilla, Pablo; Requejo-Isidro, Jose; Huarte, Nerea; Domene, Carmen; Nieva, Jose L.
Cholesterol-Dependent Membrane Fusion Induced by the gp41 Membrane-Proximal External Region-Transmembrane Domain Connection Suggests a Mechanism for Broad HIV-1 Neutralization
JOURNAL OF VIROLOGY, 88:13367-13377, NOV 2014
abstract, full text, DOI:10.1128/JVI.02151-14

Arenas-Salinas, Mauricio; Townsend, Philip D.; Brito, Christian; Marquez, Valeria; Marabolli, Vanessa; Gonzalez-Nilo, Fernando; Matias, Cata; Watt, Richard K.; Lopez-Castro, Juan D.; Dominguez-Vera, Jose; Pohl, Ehmke; Yevenes, Alejandro
The crystal structure of ferritin from Chlorobium tepidum reveals a new conformation of the 4-fold channel for this protein family
BIOCHIMIE, 106C:39-47, NOV 2014
abstract, full text, DOI:10.1016/j.biochi.2014.07.019

Badu, S. R.; Melnik, R.; Paliy, M.; Prabhakar, S.; Sebetci, A.; Shapiro, B. A.
Modeling of RNA nanotubes using molecular dynamics simulation
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 43:555-564, NOV 2014
abstract, full text, DOI:10.1007/s00249-014-0985-6

Wu, Sangwook; Lee, Chang Jun; Pedersen, Lee G.
Analysis on long-range residue-residue communication using molecular dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2896-2901, NOV 2014
abstract, full text, DOI:10.1002/prot.24629

Mori, Yoshiharu; Okumura, Hisashi
Molecular dynamics of the structural changes of helical peptides induced by pressure
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2970-2981, NOV 2014
abstract, full text, DOI:10.1002/prot.24654

Faller, Christina E.; Guvench, Olgun
Terminal sialic acids on CD44 N-glycans can block hyaluronan binding by forming competing intramolecular contacts with arginine sidechains
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:3079-3089, NOV 2014
abstract, full text, DOI:10.1002/prot.24668

Xi, Yi-Bo; Zhao, Wei-Jie; Zuo, Xiao-Tong; Tjondro, Harry Christianto; Li, Jing; Dai, An-Bang; Wang, Sha; Yan, Yong-Bin
Cataract-causing mutation R233H affects the stabilities of beta B1-and beta A3/beta B1-crystallins with different pH-dependence
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1842:2216-2229, NOV 2014
abstract, full text, DOI:10.1016/j.bbadis.2014.07.022

ben Bdira, Fredj; Gonzalez, Esperanza; Pluta, Paula; Lain, Ana; Sanz-Parra, Arantza; Manuel Falcon-Perez, Juan; Millet, Oscar
Tuning intracellular homeostasis of human uroporphyrinogen III synthase by enzyme engineering at a single hotspot of congenital erythropoietic porphyria
HUMAN MOLECULAR GENETICS, 23:5805-5813, NOV 1 2014
abstract, full text, DOI:10.1093/hmg/ddu298

Leiva, Angel; Fuentes, Irma; Bossel, Esteban; Urzua, Marcela; Mendez, Maximiliano; Pino, Maximiliano; Radic, Deodato; Marquez, Valeria; Gonzalez-Nilo, Fernando D.
Block Copolymers in the Synthesis of Gold Nanoparticles. Two New Approaches: Copolymer Aggregates as Reductants and Stabilizers and Simultaneous Formation of Copolymer Aggregates and Gold Nanoparticles
JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY, 52:3069-3079, NOV 1 2014
abstract, full text, DOI:10.1002/pola.27354

Liu, Sen; Liu, Song; Wang, Yanlin; Liao, Zhaojiang
The P2/P2 ' sites affect the substrate cleavage of TNF-alpha converting enzyme (TACE)
MOLECULAR IMMUNOLOGY, 62:122-128, NOV 2014
abstract, full text, DOI:10.1016/j.molimm.2014.05.017

Tang, Yu-Hang; Karniadakis, George Em
Accelerating dissipative particle dynamics simulations on GPUs: Algorithms, numerics and applications
COMPUTER PHYSICS COMMUNICATIONS, 185:2809-2822, NOV 2014
abstract, full text, DOI:10.1016/j.cpc.2014.06.015

Pisani, Francesco; Mola, Maria Grazia; Simone, Laura; Rosito, Stefania; Alberga, Domenico; Mangiatordi, Giuseppe Felice; Lattanzi, Gianluca; Nicolotti, Orazio; Frigeri, Antonio; Svelto, Maria; Nicchia, Grazia Paola
Identification of a Point Mutation Impairing the Binding between Aquaporin-4 and Neuromyelitis Optica Autoantibodies
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:30578-30589, OCT 31 2014
abstract, full text, DOI:10.1074/jbc.M114.582221

Wang, Connie Y.; Miller, Thomas F., I.I.I.
Allosteric Response and Substrate Sensitivity in Peptide Binding of the Signal Recognition Particle
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:30868-30879, OCT 31 2014
abstract, full text, DOI:10.1074/jbc.M114.584912

Shi, Jipei; Wang, Jianping
Interaction between Metal Cation and Unnatural Peptide Backbone Mediated by Polarized Water Molecules: Study of Infrared Spectroscopy and Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12336-12347, OCT 30 2014
abstract, full text, DOI:10.1021/jp504615f

von Rudorff, Guido Falk; Watermann, Tobias; Sebastiani, Daniel
Perfluoroalkane Force Field for Lipid Membrane Environments
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12531-12540, OCT 30 2014
abstract, full text, DOI:10.1021/jp507464m

Caddeo, Claudia; Fazzi, Daniele; Caironi, Mario; Mattoni, Alessandro
Atomistic Simulations of P(NDI2OD-T2) Morphologies: From Single Chain to Condensed Phases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12556-12565, OCT 30 2014
abstract, full text, DOI:10.1021/jp5085789

Orlando, Marta; Lignani, Gabriele; Maragliano, Luca; Fassio, Anna; Onofri, Franco; Baldelli, Pietro; Giovedi, Silvia; Benfenati, Fabio
Functional Role of ATP Binding to Synapsin I In Synaptic Vesicle Trafficking and Release Dynamics
JOURNAL OF NEUROSCIENCE, 34:14752-14768, OCT 29 2014
abstract, full text, DOI:10.1523/JNEUROSCI.1093-14.2014

Jerabek, Petr; Florian, Jan; Stiborova, Marie; Martinek, Vaclav
Flexible Docking-Based Molecular Dynamics/Steered Molecular Dynamics Calculations of Protein-Protein Contacts in a Complex of Cytochrome P450 1A2 with Cytochronne b(5)
BIOCHEMISTRY, 53:6695-6705, OCT 28 2014
abstract, full text, DOI:10.1021/bi500814t

Li, Junwei; Xie, Xiaoxiao; Liu, Jun; Yu, Hui; Zhang, Suhua; Zhan, Yong; Zhang, Hailin; Logothetis, Diomedes E.; An, Hailong
Lack of Negatively Charged Residues at the External Mouth of Kir2.2 Channels Enable the Voltage-Dependent Block by External Mg2+
PLOS ONE, 9 Art. No. e111372, OCT 28 2014
abstract, full text, DOI:10.1371/journal.pone.0111372

Shi, Guosheng; Shen, Yue; Liu, Jian; Wang, Chunlei; Wang, Ying; Song, Bo; Hu, Jun; Fang, Haiping
Molecular-scale Hydrophilicity Induced by Solute: Molecular-thick Charged Pancakes of Aqueous Salt Solution on Hydrophobic Carbon-based Surfaces
SCIENTIFIC REPORTS, 4 Art. No. 6793, OCT 28 2014
abstract, full text, DOI:10.1038/srep06793

Baxa, Michael C.; Haddadian, Esmael J.; Jumper, John M.; Freed, Karl F.; Sosnick, Tobin R.
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:15396-15401, OCT 28 2014
abstract, full text, DOI:10.1073/pnas.1407768111

Ozcan, Nergiz; Mares, Jiri; Sundholm, Dage; Vaara, Juha
Solvation chemical shifts of perylenic antenna molecules from molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:22309-22320, OCT 28 2014
abstract, full text, DOI:10.1039/c4cp02894e

Dong, Sheng; Wei, Tian-Di; Chen, Xiu-Lan; Li, Chun-Yang; Wang, Peng; Xie, Bin-Bin; Qin, Qi-Long; Zhang, Xi-Ying; Pang, Xiu-Hua; Zhou, Bai-Cheng; Zhang, Yu-Zhong
Molecular Insight into the Role of the N-terminal Extension in the Maturation, Substrate Recognition, and Catalysis of a Bacterial Alginate Lyase from Polysaccharide Lyase Family 18
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:29558-29569, OCT 24 2014
abstract, full text, DOI:10.1074/jbc.M114.584573

Handschuh, Karen; Feenstra, Jennifer; Koss, Matthew; Ferretti, Elisabetta; Risolino, Maurizio; Zewdu, Rediet; Sahai, Michelle A.; Benazet, Jean-Denis; Peng, Xiao P.; Depew, Michael J.; Quintana, Laura; Sharpe, James; Wang, Baolin; Alcorn, Heather; Rivi, Roberta; Butcher, Stephen; Manak, J. Robert; Vaccari, Thomas; Weinstein, Harel; Anderson, Kathryn V.; Lacy, Elizabeth; Selleri, Licia
ESCRT-II/Vps25 Constrains Digit Number by Endosome-Mediated Selective Modulation of FGF-SHH Signaling
CELL REPORTS, 9:674-687, OCT 23 2014
abstract, full text, DOI:10.1016/j.celrep.2014.09.019

Boyken, Scott E.; Chopra, Nikita; Xie, Nan; Joseph, Raji E.; Wales, Thomas E.; Fulton, D. Bruce; Engen, John R.; Jernigan, Robert L.; Andreotti, Amy H.
A Conserved Isoleucine Maintains the Inactive State of Bruton's Tyrosine Kinase
JOURNAL OF MOLECULAR BIOLOGY, 426:3656-3669, OCT 23 2014
abstract, full text, DOI:10.1016/j.jmb.2014.08.018

Arcario, Mark J.; Mayne, Christopher G.; Tajkhorshid, Emad
Atomistic Models of General Anesthetics for Use in in Silico Biological Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12075-12086, OCT 23 2014
abstract, full text, DOI:10.1021/jp502716m

Furlan, Sara; La Penna, Giovanni; Appelhans, Dietmar; Cangiotti, Michela; Ottaviani, Maria Francesca; Danani, Andrea
Combined EPR and Molecular Modeling Study of PPI Dendrimers Interacting with Copper Ions: Effect of Generation and Maltose Decoration
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12098-12111, OCT 23 2014
abstract, full text, DOI:10.1021/jp505420s

Wang, Zunliang; Han, Xiaofeng; He, Nongyue; Chen, Zhan; Brooks, Charles L., I.I.I.
Environmental Effect on Surface Immobilized Biological Molecules
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12176-12185, OCT 23 2014
abstract, full text, DOI:10.1021/jp508550d

Wang, Kaituo; Sitsel, Oleg; Meloni, Gabriele; Autzen, Henriette Elisabeth; Andersson, Magnus; Klymchuk, Tetyana; Nielsen, Anna Marie; Rees, Douglas C.; Nissen, Poul; Gourdon, Pontus
Structure and mechanism of Zn2+-transporting P-type ATPases
NATURE, 514:518-+, OCT 23 2014
abstract, full text, DOI:10.1038/nature13618

Lin, Yen-Lin; Meng, Yilin; Huang, Lei; Roux, Benoit
Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:14753-14762, OCT 22 2014
abstract, full text, DOI:10.1021/ja504146x

Han, Lei; Zhang, Yong-Jun; Zhang, Long; Cui, Xu; Yu, Jinpu; Zhang, Ziding; Liu, Ming S.
Operating Mechanism and Molecular Dynamics of Pheromone-Binding Protein ASP1 as Influenced by pH
PLOS ONE, 9 Art. No. e110565, OCT 22 2014
abstract, full text, DOI:10.1371/journal.pone.0110565

Elghobashi-Meinhardt, Nadia
Niemann-Pick Type C Disease: A QM/MM Study of Conformational Changes in Cholesterol in the NPC1(NTD) and NPC2 Binding Pockets
BIOCHEMISTRY, 53:6603-6614, OCT 21 2014
abstract, full text, DOI:10.1021/bi500548f

Golji, Javad; Mofrad, Mohammad R. K.
The Talin Dimer Structure Orientation Is Mechanically Regulated
BIOPHYSICAL JOURNAL, 107:1802-1809, OCT 21 2014
abstract, full text, DOI:10.1016/j.bpj.2014.08.038

Kern, Nathan R.; Lee, Hui Sun; Wu, Emilia L.; Park, Soohyung; Vanommeslaeghe, Kenno; MacKerell, Alexander D., Jr.; Klauda, Jeffery B.; Jo, Sunhwan; Im, Wonpil
Lipid-Linked Oligosaccharides in Membranes Sample Conformations That Facilitate Binding to Oligosaccharyltransferase
BIOPHYSICAL JOURNAL, 107:1885-1895, OCT 21 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.007

Gkionis, K.; Obodo, J. T.; Cucinotta, C.; Sanvito, S.; Schwingenschloegl, U.
Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions
JOURNAL OF MATERIALS CHEMISTRY A, 2:16498-16506, OCT 21 2014
abstract, full text, DOI:10.1039/c4ta02760d

Tah, Bidisha; Pal, Prabir; Mishra, Sabyashachi; Talapatra, G. B.
Interaction of insulin with anionic phospholipid (DPPG) vesicles
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:21657-21663, OCT 21 2014
abstract, full text, DOI:10.1039/c4cp03028a

Mandal, Manoj; Mukhopadhyay, Chaitali
Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:21706-21716, OCT 21 2014
abstract, full text, DOI:10.1039/c4cp01657b

Ahn, Young O.; Mahinthichaichan, Paween; Lee, Hyun Ju; Ouyang, Hanlin; Kaluka, Daniel; Yeh, Syun-Ru; Arjona, Davinia; Rousseau, Denis L.; Tajkhorshid, Emad; Adelroth, Pia; Gennis, Robert B.
Conformational coupling between the active site and residues within the K-C-channel of the Vibrio cholerae cbb(3)-type (C-family) oxygen reductase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E4419-E4428, OCT 21 2014
abstract, full text, DOI:10.1073/pnas.1411676111

Schmidt, Thomas C.; Welker, Armin; Rieger, Max; Sahu, Prabhat K.; Sotriffer, Christoph A.; Schirmeister, Tanja; Engels, Bernd
Protocol for Rational Design of Covalently Interacting Inhibitors
CHEMPHYSCHEM, 15:3226-3235, OCT 20 2014
abstract, full text, DOI:10.1002/cphc.201402542

Cooper, April M.; Kaestner, Johannes
Averaging Techniques for Reaction Barriers in QM/MM Simulations
CHEMPHYSCHEM, 15:3264-3269, OCT 20 2014
abstract, full text, DOI:10.1002/cphc.201402382

Song, Minseok; Snyder, Mark A.; Mittal, Jeetain
Effect of molecular structure on fluid transport through carbon nanotubes
MOLECULAR PHYSICS, 112:2658-2664, OCT 18 2014
abstract, full text, DOI:10.1080/00268976.2014.903578

Androulaki, Eleni; Vergadou, Niki; Economou, Ioannis G.
Analysis of the heterogeneous dynamics of imidazolium-based [Tf2N-] ionic liquids using molecular simulation
MOLECULAR PHYSICS, 112:2694-2706, OCT 18 2014
abstract, full text, DOI:10.1080/00268976.2014.906670

Kang, Myungshim; Loverde, Sharon M.
Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11965-11972, OCT 16 2014
abstract, full text, DOI:10.1021/jp50476131

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep
Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Trans location into DMPC Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11973-11992, OCT 16 2014
abstract, full text, DOI:10.1021/jp504853t

He, Jia; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Cooperative Recruitment of Amphotericin B Mediated by a Cyclodextrin Dimer
JOURNAL OF PHYSICAL CHEMISTRY C, 118:24173-24180, OCT 16 2014
abstract, full text, DOI:10.1021/jp507325j

Pappalardo, Matteo; Shachaf, Nir; Basile, Livia; Milardi, Danilo; Zeidan, Mouhammed; Raiyn, Jamal; Guccione, Salvatore; Rayan, Anwar
Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH(4)R Antagonism
PLOS ONE, 9 Art. No. e109340, OCT 16 2014
abstract, full text, DOI:10.1371/journal.pone.0109340

Wu, Emilia L.; Cheng, Xi; Jo, Sunhwan; Rui, Huan; Song, Kevin C.; Davila-Contreras, Eder M.; Qi, Yifei; Lee, Jumin; Monje-Galvan, Viviana; Venable, Richard M.; Klauda, Jeffery B.; Im, Wonpil
CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1997-2004, OCT 15 2014
abstract, full text, DOI:10.1002/jcc.23702

Dick, Veronika V.; Klein, Peter
Molecular simulation of the hydrodynamics of water in contact with hydrophilized poly(vinylidene fluoride) surfaces
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 432:70-76, OCT 15 2014
abstract, full text, DOI:10.1016/j.jcis.2014.06.049

Xie, Dexuan
New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecular electrostatics
JOURNAL OF COMPUTATIONAL PHYSICS, 275:294-309, OCT 15 2014
abstract, full text, DOI:10.1016/j.jcp.2014.07.012

Hong, Chunkit; Tieleman, D. Peter; Wang, Yi
Microsecond Molecular Dynamics Simulations of Lipid Mixing
LANGMUIR, 30:11993-12001, OCT 14 2014
abstract, full text, DOI:10.1021/la502363b

Hsu, Hao-jui; Sen, Soumyo; Pearson, Ryan M.; Uddin, Sayam; Kral, Petr; Hong, Seungpyo
Poly(ethylene glycol) Corona Chain Length Controls End-Group-Dependent Cell Interactions of Dendron Micelles
MACROMOLECULES, 47:6911-6918, OCT 14 2014
abstract, full text, DOI:10.1021/ma501258c

Harris, Robert C.; Pettitt, B. Montgomery
Effects of geometry and chemistry on hydrophobic solvation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:14681-14686, OCT 14 2014
abstract, full text, DOI:10.1073/pnas.1406080111

Yao, Qing; Lu, Qiuhe; Wan, Xiaobo; Song, Feng; Xu, Yue; Hu, Mo; Zamyatina, Alla; Liu, Xiaoyun; Huang, Niu; Zhu, Ping; Shao, Feng
A structural mechanism for bacterial autotransporter glycosylation by a dodecameric heptosyltransferase family
ELIFE, 3 Art. No. 03714, OCT 13 2014
abstract, full text, DOI:10.7554/eLife.03714

Pang, Xiaoyun; Fan, Jun; Zhang, Yan; Zhang, Kai; Gao, Bingquan; Ma, Jun; Li, Jian; Deng, Yuchen; Zhou, Qiangjun; Egelman, Edward H.; Hsu, Victor W.; Sun, Fei
A PH Domain in ACAP1 Possesses Key Features of the BAR Domain in Promoting Membrane Curvature
DEVELOPMENTAL CELL, 31:73-86, OCT 13 2014
abstract, full text, DOI:10.1016/j.devcel.2014.08.020

Bellacchio, Emanuele; Palma, Alessia; Corrente, Stefania; Di Girolamo, Francesco; Kemp, E. Helen; Di Matteo, Gigliola; Comelli, Laura; Carsetti, Rita; Cascioli, Simona; Cancrini, Caterina; Fierabracci, Alessandra
The possible implication of the S250C variant of the autoimmune regulator protein in a patient with autoimmunity and immunodeficiency: in silico analysis suggests a molecular pathogenic mechanism for the variant
GENE, 549:286-294, OCT 10 2014
abstract, full text, DOI:10.1016/j.gene.2014.07.064

Jose, Jaya C.; Khatua, Prabir; Bansal, Nupur; Sengupta, Neelanjana; Bandyopadhyay, Sanjoy
Microscopic Hydration Properties of the A beta(1-42) Peptide Monomer and the Globular Protein Ubiquitin: A Comparative Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11591-11604, OCT 9 2014
abstract, full text, DOI:10.1021/jp505629q

Fu, Haohao; Liu, Yingzhe; Adria, Ferran; Shao, Xueguang; Cai, Wensheng; Chipot, Christophe
From Material Science to Avant-Garde Cuisine. The Art of Shaping Liquids into Spheres
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11747-11756, OCT 9 2014
abstract, full text, DOI:10.1021/jp508841p

Morrison, Lindsay J.; Wysocki, Vicki H.
Gas-Phase Helical Peptides Mimic Solution-Phase Behavior
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:14173-14183, OCT 8 2014
abstract, full text, DOI:10.1021/ja507298e

Qiu, Wanzhi; Skafidas, Efstratios
Detection of Protein Conformational Changes with Multilayer Graphene Nanopore Sensors
ACS APPLIED MATERIALS & INTERFACES, 6:16777-16781, OCT 8 2014
abstract, full text, DOI:10.1021/am5040279

Cheng, Yuanhua; Lindert, Steffen; Kekenes-Huskey, Peter; Rao, Vijay S.; Solaro, R. John; Rosevear, Paul R.; Amaro, Rommie; McCulloch, Andrew D.; McCammon, J. Andrew; Regnier, Michael
Computational Studies of the Effect of the S23D/S24D Troponin I Mutation on Cardiac Troponin Structural Dynamics
BIOPHYSICAL JOURNAL, 107:1675-1685, OCT 7 2014
abstract, full text, DOI:10.1016/j.bpj.2014.08.008

Yang, Li-Jun; Zhao, Wen-Hua; Liu, Qian
Detailed conformation dynamics and activation process of wild type c-Abl and T3151 mutant
JOURNAL OF MOLECULAR STRUCTURE, 1075:292-298, OCT 5 2014
abstract, full text, DOI:10.1016/j.molstruc.2014.06.087

Mena-Ulecia, Karel; Vergara-Jaque, Ariela; Poblete, Horacio; Tiznado, William; Caballero, Julio
Study of the Affinity between the Protein Kinase PKA and Peptide Substrates Derived from Kemptide Using Molecular Dynamics Simulations and MM/GBSA
PLOS ONE, 9 Art. No. e109639, OCT 2 2014
abstract, full text, DOI:10.1371/journal.pone.0109639

Church, Philip C.; Goscinski, Andrzej M.
A Survey of Cloud-Based Service Computing Solutions for Mammalian Genomics
IEEE Transactions on Services Computing, 7:726-740, OCT-DEC 2014
abstract, full text, DOI:10.1109/TSC.2014.2353645

Lefoulon, Cecile; Karnik, Rucha; Honsbein, Annegret; Gutla, Paul Vijay; Grefen, Christopher; Riedelsberger, Janin; Poblete, Tomas; Dreyer, Ingo; Gonzalez, Wendy; Blatt, Michael R.
Voltage-Sensor Transitions of the Inward-Rectifying K+ Channel KAT1 Indicate a Latching Mechanism Biased by Hydration within the Voltage Sensor
PLANT PHYSIOLOGY, 166:960-U776, OCT 2014
abstract, full text, DOI:10.1104/pp.114.244319

Vargiu, Attilio V.; Ruggerone, Paolo; Opperman, Timothy J.; Nguyen, Son T.; Nikaido, Hiroshi
Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 58:6224-6234, OCT 2014
abstract, full text, DOI:10.1128/AAC.03283-14

Lin, Ying-Wu; Shu, Xiao-Gang; Du, Ke-Jie; Nie, Chang-Ming; Wen, Ge-Bo
Computational insight into nitration of human myoglobin
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 52:60-65, OCT 2014
abstract, full text, DOI:10.1016/j.compbiolchem.2014.09.004

Shankla, Manish; Aksimentiev, Aleksei
Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene
NATURE COMMUNICATIONS, 5 Art. No. 5171, OCT 2014
abstract, full text, DOI:10.1038/ncomms6171

Cheng, Mary Hongying; Bahar, Ivet
Complete Mapping of Substrate Translocation Highlights the Role of LeuT N-terminal Segment in Regulating Transport Cycle
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003879, OCT 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003879

Gkeka, Paraskevi; Evangelidis, Thomas; Pavlaki, Maria; Lazani, Vasiliki; Christoforidis, Savvas; Agianian, Bogos; Cournia, Zoe
Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003895, OCT 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003895

Geng Yi-Zhao; Ji Qing; Liu Shu-Xia; Yan Shi-Wei
Initial conformation of kinesin's neck linker
CHINESE PHYSICS B, 23 Art. No. 108701, OCT 2014
abstract, full text, DOI:10.1088/1674-1056/23/10/108701

McHarris, Danielle M.; Barr, Daniel A.
Truncated Variants of the GCN4 Transcription Activator Protein Bind DNA with Dramatically Different Dynamical Motifs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2869-2875, OCT 2014
abstract, full text, DOI:10.1021/ci500448e

Abdul-Wahid, Badi'; Feng, Haoyun; Rajan, Dinesh; Costaouec, Ronan; Darve, Eric; Thain, Douglas; Izaguirre, Jesus A.
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:3033-3043, OCT 2014
abstract, full text, DOI:10.1021/ci500321g

Garrido-Arandia, Maria; Gomez-Casado, Cristina; Diaz-Perales, Araceli; Pacios, Luis F.
Molecular Dynamics of Major Allergens from Alternaria, Birch Pollen and Peach
MOLECULAR INFORMATICS, 33:682-694, OCT 2014
abstract, full text, DOI:10.1002/minf.201400057

Kapoor, Abhijeet; Travesset, Alex
Mechanism of the Exchange Reaction in HRAS from Multiscale Modeling
PLOS ONE, 9 Art. No. e108846, OCT 1 2014
abstract, full text, DOI:10.1371/journal.pone.0108846

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Separation of a heavy metal from water through a membrane containing boron nitride nanotubes: molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2468, OCT 2014
abstract, full text, DOI:10.1007/s00894-014-2468-1

Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Ge, Zhongxue; Kang, Ying
Structural characteristics of liquid nitromethane at the nanoscale confinement in carbon nanotubes
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2459, OCT 2014
abstract, full text, DOI:10.1007/s00894-014-2459-2

Wood, Irene; Pickholz, Monica
Triptan partition in model membranes
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2463, OCT 2014
abstract, full text, DOI:10.1007/s00894-014-2463-6

Sugihara, Minoru; Suwa, Makiko; Bondar, Ana-Nicoleta
Dynamics of bovine opsin bound to G-protein fragments
JOURNAL OF STRUCTURAL BIOLOGY, 188:79-86, OCT 2014
abstract, full text, DOI:10.1016/j.jsb.2014.08.001

Wang, Qiuming; Liang, Guizhao; Zhang, Mingzhen; Zhao, Jun; Patel, Kunal; Yu, Xiang; Zhao, Chao; Ding, Binrong; Zhang, Ge; Zhou, Feimeng; Zheng, Jie
De Novo Design of Self-Assembled Hexapeptides as beta-Amyloid (A beta) Peptide Inhibitors
ACS CHEMICAL NEUROSCIENCE, 5:972-981, OCT 2014
abstract, full text, DOI:10.1021/cn500165s

Li, Nan K.; Quiroz, Felipe Garcia; Hall, Carol K.; Chilkoti, Ashutosh; Yingling, Yaroslava G.
Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide
BIOMACROMOLECULES, 15:3522-3530, OCT 2014
abstract, full text, DOI:10.1021/bm500658w

Korb, Oliver; Finn, Paul W.; Jones, Gareth
The cloud and other new computational methods to improve molecular modelling
EXPERT OPINION ON DRUG DISCOVERY, 9:1121-1131, OCT 2014
abstract, full text, DOI:10.1517/17460441.2014941800

Bolintineanu, Dan S.; Volzing, Katherine; Vivcharuk, Victor; Sayyed-Ahmad, Abdallah; Srivastava, Poonam; Kaznessis, Yiannis N.
Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator
JOURNAL OF CHEMICAL AND ENGINEERING DATA, 59:3167-3176, OCT 2014
abstract, full text, DOI:10.1021/je500225x

Anisimov, Victor M.; Bauer, Gregory H.; Chadalavada, Kalyana; Olson, Ryan M.; Glenski, Joseph W.; Krarner, William T. C.; Apra, Edoardo; Kowalski, Karol
Optimization of the Coupled Cluster Implementation in NWChem on Petascale Parallel Architectures
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4307-4316, OCT 2014
abstract, full text, DOI:10.1021/ct500404c

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W.; Hasse, Hans; Vrabec, Jadran; Horsch, Martin
ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4455-4464, OCT 2014
abstract, full text, DOI:10.1021/ct500169q

Orsi, Mario; Ding, Wei; Palaiokostas, Michail
Direct Mixing of Atomistic Solutes and Coarse-Grained Water
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4684-4693, OCT 2014
abstract, full text, DOI:10.1021/ct500065k

Suarez, Dimas; Diaz, Natalia
Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4718-4729, OCT 2014
abstract, full text, DOI:10.1021/ct500700d

Thomas, James R.; Gedeon, Patrick C.; Madura, Jeffry D.
Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2289-2302, OCT 2014
abstract, full text, DOI:10.1002/prot.24588

Krueger, Susan; Shin, Jae-Ho; Curtis, Joseph E.; Rubinson, Kenneth A.; Kelman, Zvi
The solution structure of full-length dodecameric MCM by SANS and molecular modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2364-2374, OCT 2014
abstract, full text, DOI:10.1002/prot.24598

Fang, Liang; Cho, Hyun Ju; Chan, Christina; Feig, Michael
Binding site multiplicity with fatty acid ligands: Implications for the regulation of PKR kinase autophosphorylation with palmitate
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2429-2442, OCT 2014
abstract, full text, DOI:10.1002/prot.24607

Selwa, Edithe; Tru Huynh; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Therese E.
Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2483-2496, OCT 2014
abstract, full text, DOI:10.1002/prot.24612

Barra, Pabla A.; Barraza, Luis F.; Jimenez, Veronica A.; Gavin, Jose A.; Alderete, Joel B.
Drug-dendrimer supramolecular complexation studied from molecular dynamics simulations and NMR spectroscopy
STRUCTURAL CHEMISTRY, 25:1443-1455, OCT 2014
abstract, full text, DOI:10.1007/s11224-014-0424-4

Omidvar, Ramin; Tafazzoli-Shadpour, Mohammad; Rostami, Mostafa; Abolfathi, Nabi
Cancer Mutation Alters Mechanical Stiffness of Epithelial Cadherin Domains: A Molecular Dynamics Study
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:2228-2236, OCT 2014
abstract, full text, DOI:10.1166/jctn.2014.3631

Najor, Matthew S.; Olsen, Kenneth W.; Graham, Daniel J.; de Freitas, Duarte Mota
Contribution of each Trp residue toward the intrinsic fluorescence of the G(i alpha 1) protein
PROTEIN SCIENCE, 23:1392-1402, OCT 2014
abstract, full text, DOI:10.1002/pro.2523

Valenzuela, Claudio; Ramos, Patricio; Carrasco, Cristian; Alejandra Moya-Leon, Maria; Herrera, Raul
Cloning and characterization of a xyloglucan endo-transglycosylase/hydrolase gene expressed in response to inclination in radiata pine seedlings
TREE GENETICS & GENOMES, 10:1305-1315, OCT 2014
abstract, full text, DOI:10.1007/s11295-014-0762-9

Zhuang, Xiaohong; Makover, Judah R.; Im, Wonpil; Klauda, Jeffery B.
A systematic molecular dynamics simulation study of temperature dependent bilayer structural properties
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:2520-2529, OCT 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.06.010

Lockhart, Christopher; Klimov, Dmitri K.
Binding of A beta peptide creates lipid density depression in DMPC bilayer
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:2678-2688, OCT 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.07.010

Breitwieser, Romain; Hu, Yu-Cheng; Chao, Yen Cheng; Li, Ren-Jie; Tzeng, Yi Ren; Li, Lain-Jong; Liou, Sz-Chian; Lin, Keng Ching; Chen, Chih Wei; Pai, Woei Wu
Flipping nanoscale ripples of free-standing graphene using a scanning tunneling microscope tip
CARBON, 77:236-243, OCT 2014
abstract, full text, DOI:10.1016/j.carbon.2014.05.026

Gabrieli, Andrea; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe B.
Fast and efficient optimization of Molecular Dynamics force fields for microporous materials: Bonded interactions via force matching
MICROPOROUS AND MESOPOROUS MATERIALS, 197:339-347, OCT 2014
abstract, full text, DOI:10.1016/j.micromeso.2014.06.023

Ohno, Yousuke; Yokota, Rio; Koyama, Hiroshi; Morimoto, Gentaro; Hasegawa, Aki; Masumoto, Gen; Okimoto, Noriaki; Hirano, Yoshinori; Ibeid, Huda; Narumi, Tetsu; Taiji, Makoto
Petascale molecular dynamics simulation using the fast multipole method on K computer
COMPUTER PHYSICS COMMUNICATIONS, 185:2575-2585, OCT 2014
abstract, full text, DOI:10.1016/j.cpc.2014.06.004

Iacovelli, Federico; Alves, Cassio; Falconi, Mattia; Oteri, Francesco; de Oliveira, Cristiano L. P.; Desideri, Alessandro
Influence of the Single-Strand Linker Composition on the Structural/Dynamical Properties of a Truncated Octahedral DNA Nano-Cage Family
BIOPOLYMERS, 101:992-999, OCT 2014
abstract, full text, DOI:10.1002/bip.22475

Ghosh, Saikat; Ghosh, Dhiman; Ranganathan, Srivastav; Anoop, A.; Kumar, Santosh P.; Jha, Narendra Nath; Padinhateeri, Ranjith; Maji, Samir K.
Investigating the Intrinsic Aggregation Potential of Evolutionarily Conserved Segments in p53
BIOCHEMISTRY, 53:5995-6010, SEP 30 2014
abstract, full text, DOI:10.1021/bi500825d

Zerbetto, Mirco; Piserchia, Andrea; Frezzato, Diego
Looking for Some Free Energy? Call JEFREE (...)
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1865-1881, SEP 30 2014
abstract, full text, DOI:10.1002/jcc.23701

Walavalkar, Ninad M.; Cramer, Jason M.; Buchwald, William A.; Scarsdale, J. Neel; Williams, David C., Jr.
Solution structure and intramolecular exchange of methyl-cytosine binding domain protein 4 (MBD4) on DNA suggests a mechanism to scan for (m)CpG/TpG mismatches
NUCLEIC ACIDS RESEARCH, 42:11218-11232, SEP 29 2014
abstract, full text, DOI:10.1093/nar/gku782

Samson, Andre L.; Knaupp, Anja S.; Kass, Itamar; Kleifeld, Oded; Marijanovic, Emilia M.; Hughes, Victoria A.; Lupton, Chris J.; Buckle, Ashley M.; Bottomley, Stephen P.; Medcalf, Robert L.
Oxidation of an Exposed Methionine Instigates the Aggregation of Glyceraldehyde-3-phosphate Dehydrogenase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:26922-26936, SEP 26 2014
abstract, full text, DOI:10.1074/jbc.M114.570275

Wolff, Philippe; Amal, Ismail; Olieric, Vincent; Chaloin, Olivier; Gygli, Gudrun; Ennifar, Eric; Lorber, Bernard; Guichard, Gilles; Wagner, Jerome; Dejaegere, Annick; Burnouf, Dominique Y.
Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins
JOURNAL OF MEDICINAL CHEMISTRY, 57:7565-7576, SEP 25 2014
abstract, full text, DOI:10.1021/jm500467a

Taranova, Maryna; Hirsh, Andrew D.; Perkins, Noel C.; Andricioaei, Ioan
Role of Microscopic Flexibility in Tightly Curved DNA
JOURNAL OF PHYSICAL CHEMISTRY B, 118:11028-11036, SEP 25 2014
abstract, full text, DOI:10.1021/jp503233u

Fitzpatrick, Jeremy M.; Pellegrini, Maria; Cushing, Patrick R.; Mierke, Dale F.
Small Molecule Inhibition of the Na+/H+ Exchange Regulatory Factor 1 and Parathyroid Hormone 1 Receptor Interaction
BIOCHEMISTRY, 53:5916-5922, SEP 23 2014
abstract, full text, DOI:10.1021/bi500368k

Paasche, Alexander; Zipper, Andreas; Schaefer, Simon; Ziebuhr, John; Schirmeister, Tanja; Engels, Bernd
Evidence for Substrate Binding-Induced Zwitterion Formation in the Catalytic Cys-His Dyad of the SARS-CoV Main Protease
BIOCHEMISTRY, 53:5930-5946, SEP 23 2014
abstract, full text, DOI:10.1021/bi400604t

Sun, Xiaotian; Feng, Zhiwei; Zhang, Liling; Hou, Tingjun; Li, Youyong
The Selective Interaction between Silica Nanoparticles and Enzymes from Molecular Dynamics Simulations
PLOS ONE, 9 Art. No. e107696, SEP 22 2014
abstract, full text, DOI:10.1371/journal.pone.0107696

Caboni, Pierluigi; Liori, Barbara; Kumar, Amit; Santoru, Maria Laura; Asthana, Shailendra; Pieroni, Enrico; Fais, Antonella; Era, Benedetta; Cacace, Enrico; Ruggiero, Valeria; Atzori, Luigi
Metabolomics Analysis and Modeling Suggest a Lysophosphocholines-PAF Receptor Interaction in Fibromyalgia
PLOS ONE, 9 Art. No. e107626, SEP 19 2014
abstract, full text, DOI:10.1371/journal.pone.0107626

Eicher, Thomas; Seeger, Markus A.; Anselmi, Claudio; Zhou, Wenchang; Brandstaetter, Lorenz; Verrey, Francois; Diederichs, Kay; Faraldo-Gomez, Jose D.; Pos, Klaas M.
Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump AcrB
ELIFE, 3 Art. No. UNSP e03145, SEP 19 2014
abstract, full text, DOI:10.7554/eLife.03145

Aghtar, Mortaza; Struempfer, Johan; Olbrich, Carsten; Schulten, Klaus; Kleinekathoefer, Ulrich
Different Types of Vibrations Interacting with Electronic Excitations in Phycoerythrin 545 and Fenna-Matthews-Olson Antenna Systems
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:3131-3137, SEP 18 2014
abstract, full text, TCBG publications, DOI:10.1021/jz501351p

Perisic, Ognjen; Lu, Hui
On the Improvement of Free-Energy Calculation from Steered Molecular Dynamics Simulations Using Adaptive Stochastic Perturbation Protocols
PLOS ONE, 9 Art. No. e101810, SEP 18 2014
abstract, full text, DOI:10.1371/journal.pone.0101810

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald
Exploring Hamiltonian dielectric solvent molecular dynamics
CHEMICAL PHYSICS LETTERS, 612:20-24, SEP 18 2014
abstract, full text, DOI:10.1016/j.cplett.2014.07.070

Yu, Tao; Lee, One-Sun; Schatz, George C.
Molecular Dynamics Simulations and Electronic Excited State Properties of a Self-Assembled Peptide Amphiphile Nanofiber with Metalloporphyrin Arrays
JOURNAL OF PHYSICAL CHEMISTRY A, 118:8553-8562, SEP 18 2014
abstract, full text, DOI:10.1021/jp502459r

Sun, Xianqiang; Agren, Hans; Tu, Yaoquan
Functional Water Molecules in Rhodopsin Activation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10863-10873, SEP 18 2014
abstract, full text, DOI:10.1021/jp505180t

Tidemand, Kasper D.; Schonbeck, Christian; Holm, Rene; Westh, Peter; Peters, Gunther H.
Computational Investigation of Enthalpy-Entropy Compensation in Complexation of Glycoconjugated Bile Salts with beta-Cyclodextrin and Analogs
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10889-10897, SEP 18 2014
abstract, full text, DOI:10.1021/jp506716d

Tang, Zhiye; Zhang, Qiao; Yin, Yadong; Chang, Chia-en A.
Facet Selectivity of Ligands on Silver Nanoplates: Molecular Mechanics Study
JOURNAL OF PHYSICAL CHEMISTRY C, 118:21589-21598, SEP 18 2014
abstract, full text, DOI:10.1021/jp503319s

Chang, Leifu; Zhang, Ziguo; Yang, Jing; McLaughlin, Stephen H.; Barford, David
Molecular architecture and mechanism of the anaphase-promoting complex
NATURE, 513:388-+, SEP 18 2014
abstract, full text, DOI:10.1038/nature13543

Cailliez, Fabien; Mueller, Pavel; Gallois, Michael; de la Lande, Aurelien
ATP Binding and Aspartate Protonation Enhance Photoinduced Electron Transfer in Plant Cryptochrome
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:12974-12986, SEP 17 2014
abstract, full text, DOI:10.1021/ja506084f

McCullagh, Martin; Saunders, Marissa G.; Voth, Gregory A.
Unraveling the Mystery of ATP Hydrolysis in Actin Filaments
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:13053-13058, SEP 17 2014
abstract, full text, DOI:10.1021/ja507169f

Bai, Qifeng; Shao, Yonghua; Pan, Dabo; Zhang, Yang; Liu, Huanxiang; Yao, Xiaojun
Search for beta(2) Adrenergic Receptor Ligands by Virtual Screening via Grid Computing and Investigation of Binding Modes by Docking and Molecular Dynamics Simulations
PLOS ONE, 9 Art. No. e107837, SEP 17 2014
abstract, full text, DOI:10.1371/journal.pone.0107837

Yang, Lee-Wei; Kitao, Akio; Huang, Bang-Chieh; Go, Nobuhiro
Ligand-Induced Protein Responses and Mechanical Signal Propagation Described by Linear Response Theories
BIOPHYSICAL JOURNAL, 107:1415-1425, SEP 16 2014
abstract, full text, DOI:10.1016/j.bpj.2014.07.049

Guan, Xiangying; Lin, Ping; Knoll, Eric; Chakrabarti, Raj
Mechanism of Inhibition of the Human Sirtuin Enzyme SIRT3 by Nicotinamide: Computational and Experimental Studies
PLOS ONE, 9 Art. No. e107729, SEP 15 2014
abstract, full text, DOI:10.1371/journal.pone.0107729

Suresh, Gorle; Priyakumar, U. Deva
DNA-RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18148-18155, SEP 14 2014
abstract, full text, DOI:10.1039/c4cp02478h

Kim, J. I.; Lee, M.; Baek, I.; Yoon, G.; Na, S.
The mechanical response of hIAPP nanowires based on different bending direction simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18493-18500, SEP 14 2014
abstract, full text, DOI:10.1039/c4cp02494j

Jose, Jaya C.; Chatterjee, Prathit; Sengupta, Neelanjana
Cross Dimerization of Amyloid-beta and alpha Synuclein Proteins in Aqueous Environment: A Molecular Dynamics Simulations Study
PLOS ONE, 9 Art. No. e106883, SEP 11 2014
abstract, full text, DOI:10.1371/journal.pone.0106883

Liu, Zizhao; Du, Hongbo; Wickramasinghe, S. Ranil; Qian, Xianghong
Membrane Surface Engineering for Protein Separations: Experiments and Simulations
LANGMUIR, 30:10651-10660, SEP 9 2014
abstract, full text, DOI:10.1021/la5026119

Boiteux, Celine; Vorobyov, Igor; French, Robert J.; French, Christopher; Yarov-Yarovoy, Vladimir; Allen, Toby W.
Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:13057-13062, SEP 9 2014
abstract, full text, DOI:10.1073/pnas.1408710111

Cabello-Aguilar, S.; Abou Chaaya, A.; Picaud, F.; Bechelany, M.; Pochat-Bohatier, C.; Yesylevskyy, S.; Kraszewski, S.; Bechelany, M. C.; Rossignol, F.; Balanzat, E.; Janot, J. M.; Miele, P.; Dejardin, P.; Balme, S.
Experimental and simulation studies of unusual current blockade induced by translocation of small oxidized PEG through a single nanopore
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:17883-17892, SEP 7 2014
abstract, full text, DOI:10.1039/c4cp01954g

Backus, Keriann M.; Dolan, Michael A.; Barry, Conor S.; Joe, Maju; McPhie, Peter; Boshoff, Helena I. M.; Lowary, Todd L.; Davis, Benjamin G.; Barry, Clifton E., I.I.I.
The Three Mycobacterium tuberculosis Antigen 85 Isoforms Have Unique Substrates and Activities Determined by Non-active Site Regions
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:25041-25053, SEP 5 2014
abstract, full text, DOI:10.1074/jbc.M114.581579

Bravo-Rodriguez, Kenny; Ismail-Ali, Ahmed F.; Klopries, Stephan; Kushnir, Susanna; Ismail, Shehab; Fansa, Eyad K.; Wittinghofer, Alfred; Schulz, Frank; Sanchez-Garcia, Elsa
Predicted Incorporation of Non-native Substrates by a Polyketide Synthase Yields Bioactive Natural Product Derivatives
CHEMBIOCHEM, 15:1991-1997, SEP 5 2014
abstract, full text, DOI:10.1002/cbic.201402206

Laghaei, Rozita; Kowallis, William; Evans, Deborah G.; Coalson, Rob D.
Calculation of Iron Transport through Human H-chain Ferritin
JOURNAL OF PHYSICAL CHEMISTRY A, 118:7442-7453, SEP 4 2014
abstract, full text, DOI:10.1021/jp500198u

Chen, Houyang; Ruckenstein, Eli
Nanomembrane Containing a Nanopore in an Electrolyte Solution: A Molecular Dynamics Approach
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:2979-2982, SEP 4 2014
abstract, full text, DOI:10.1021/jz501502y

Han, Wei; Schulten, Klaus
Fibril Elongation by A beta(17-42): Kinetic Network Analysis of Hybrid-Resolution Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:12450-12460, SEP 3 2014
abstract, full text, TCBG publications, DOI:10.1021/ja507002p

Chen, Hong; Zhang, Mingzhen; Yang, Jintao; Zhao, Chao; Hu, Rundong; Chen, Qiang; Chang, Yung; Zheng, Jie
Synthesis and Characterization of Antifouling Poly(N-acryloylaminoethoxyethanol) with Ultralow Protein Adsorption and Cell Attachment
LANGMUIR, 30:10398-10409, SEP 2 2014
abstract, full text, DOI:10.1021/la502136q

Merino, Felipe; Ng, Calista Keow Leng; Veerapandian, Veeramohan; Schoeler, Hans Robert; Jauch, Ralf; Cojocaru, Vlad
Structural Basis for the SOX-Dependent Genomic Redistribution of OCT4 in Stem Cell Differentiation
STRUCTURE, 22:1274-1286, SEP 2 2014
abstract, full text, DOI:10.1016/j.str.2014.06.014

Langan, Paul; Sangha, Amandeep K.; Wymore, Troy; Parks, Jerry M.; Yang, Zamin Koo; Hanson, B. Leif; Fisher, Zoe; Mason, Sax A.; Blakeley, Matthew P.; Forsyth, V. Trevor; Glusker, Jenny P.; Carrell, Horace L.; Smith, Jeremy C.; Keen, David A.; Graham, David E.; Kovalevsky, Andrey
L-Arabinose Binding, Isomerization, and Epimerization by D-Xylose Isomerase: X-Ray/Neutron Crystallographic and Molecular Simulation Study
STRUCTURE, 22:1287-1300, SEP 2 2014
abstract, full text, DOI:10.1016/j.str.2014.07.002

Wu, Zhe; Schulten, Klaus
Synaptotagmin's Role in Neurotransmitter Release Likely Involves Ca2+-induced Conformational Transition
BIOPHYSICAL JOURNAL, 107:1156-1166, SEP 2 2014
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2014.07.041

Amarouch, Mohamed-Yassine; Kasimova, Marina A.; Tarek, Mounir; Abriel, Hugues
Functional interaction between S1 and S4 segments in voltage-gated sodium channels revealed by human channelopathies
CHANNELS, 8:414-420, SEP-OCT 2014
abstract, full text, DOI:10.4161/19336950.2014.958922

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Functionalized graphene as a nanostructured membrane for removal of copper and mercury from aqueous solution: A molecular dynamics simulation study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 53:112-117, SEP 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.07.013

Secrier, Maria; Schneider, Reinhard
Visualizing time-related data in biology, a review
BRIEFINGS IN BIOINFORMATICS, 15:771-782, SEP 2014
abstract, full text, DOI:10.1093/bib/bbt021

Guo, W.; Liu, R.; Bhardwaj, G.; Yang, J. C.; Changou, C.; Ma, A.-.H.; Mazloom, A.; Chintapalli, S.; Xiao, K.; Xiao, W.; Kumaresan, P.; Sanchez, E.; Yeh, C.-.T.; Evans, C. P.; Patterson, R.; Lam, K. S.; Kung, H.-.J.
Targeting Btk/Etk of prostate cancer cells by a novel dual inhibitor
CELL DEATH & DISEASE, 5, SEP 2014
abstract, full text, DOI:10.1038/cddis.2014.343

Gao Wen-Xiu; Wang Hong-Lei; Li Shen-Min
Molecular Dynamics Simulation Study of Structural and Transport Properties of Methanol-Water Mixture in Carbon Nanotubes
ACTA PHYSICO-CHIMICA SINICA, 30:1625-1633, SEP 2014
abstract, full text, DOI:10.3866/PKU.WHXB201407031

Takahashi, Nobuaki; Hamada-Nakahara, Sayaka; Itoh, Yuzuru; Takemura, Kazuhiro; Shimada, Atsushi; Ueda, Yoshifumi; Kitamata, Manabu; Matsuoka, Rei; Hanawa-Suetsugu, Kyoko; Senju, Yosuke; Mori, Masayuki X.; Kiyonaka, Shigeki; Kohda, Daisuke; Kitao, Akio; Mori, Yasuo; Suetsugu, Shiro
TRPV4 channel activity is modulated by direct interaction of the ankyrin domain to PI(4,5)P-2
NATURE COMMUNICATIONS, 5 Art. No. 4994, SEP 2014
abstract, full text, DOI:10.1038/ncomms5994

Yasaei, Poya; Kumar, Bijandra; Hantehzadeh, Reza; Kayyalha, Morteza; Baskin, Artem; Repnin, Nikita; Wang, Canhui; Klie, Robert F.; Chen, Yong P.; Kral, Petr; Salehi-Khojin, Amin
Chemical sensing with switchable transport channels in graphene grain boundaries
NATURE COMMUNICATIONS, 5 Art. No. 4911, SEP 2014
abstract, full text, DOI:10.1038/ncomms5911

Cornejo, Isabel; Andrini, Olga; Isabel Niemeyer, Maria; Maraboli, Vanessa; Danilo Gonzalez-Nilo, F.; Teulon, Jacques; Sepulveda, Francisco V.; Pablo Cid, L.
Identification and Functional Expression of a Glutamate and Avermectin-Gated Chloride Channel from Caligus rogercresseyi, a Southern Hemisphere Sea Louse Affecting Farmed Fish
PLOS PATHOGENS, 10 Art. No. e1004402, SEP 2014
abstract, full text, DOI:10.1371/journal.ppat.1004402

Serra-Vinardell, Jenny; Diaz, Lucia; Guitierrez-de Teran, Hugo; Sanchez-Olle, Gessarni; Bujons, Jordi; Michelakakis, Helen; Mavridou, Irene; Aerts, Johannes M. F. G.; Delgado, Antonio; Grinberg, Daniel; Vilageliu, Lluisa; Casas, Josefina
Selective chaperone effect of aminocyclitol derivatives on G202R and other mutant glucocerebrosidases causing Gaucher disease
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 54:245-254, SEP 2014
abstract, full text, DOI:10.1016/j.biocel.2014.07.017

Daddam, Jayasimha Rayalu; Dowlathabad, Muralidhara Rao; Panthangi, Seshapani; Jasti, Pramodakumari
Molecular Docking and P-glycoprotein Inhibitory Activity of Flavonoids
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 6:167-175, SEP 2014
abstract, full text, DOI:10.1007/s12539-012-0197-7

Feng, Zhiwei; Alqarni, Mohammed Hamed; Yang, Peng; Tong, Qin; Chowdhury, Ananda; Wang, Lirong; Xie, Xiang-Qun
Modeling, Molecular Dynamics Simulation, and Mutation Validation for Structure of Cannabinoid Receptor 2 Based on Known Crystal Structures of GPCRs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2483-2499, SEP 2014
abstract, full text, DOI:10.1021/ci5002718

Guardiani, Carlo; Di Marino, Daniele; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio
Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3589-3597, SEP 2014
abstract, full text, DOI:10.1021/ct500283s

Huggins, David J.
Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3617-3625, SEP 2014
abstract, full text, DOI:10.1021/ct500415g

Dama, James F.; Rotskoff, Grant; Parrinello, Michele; Voth, Gregory A.
Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3626-3633, SEP 2014
abstract, full text, DOI:10.1021/ct500441q

Komuro, Yasuaki; Re, Suyong; Kobayashi, Chigusa; Muneyuki, Eiro; Sugita, Yuji
CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca2+-ATPase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4133-4142, SEP 2014
abstract, full text, DOI:10.1021/ct5004143

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus
xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70:2344-2355, SEP 2014
abstract, full text, TCBG publications, DOI:10.1107/S1399004714013856

Milanovsky, Georgy E.; Ptushenko, Vasily V.; Golbeck, John H.; Semenov, Alexey Yu.; Cherepanov, Dmitry A.
Molecular dynamics study of the primary charge separation reactions in Photosystem I: Effect of the replacement of the axial ligands to the electron acceptor A(0)
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1472-1483, SEP 2014
abstract, full text, DOI:10.1016/j.bbabio.2014.03.001

Chu, Brian K.; Fu, Iris W.; Markegard, Cade B.; Choi, Seong E.; Nguyen, Hung D.
A Tail of Two Peptide Amphiphiles: Effect of Conjugation with Hydrophobic Polymer on Folding of Peptide Sequences
BIOMACROMOLECULES, 15:3313-3320, SEP 2014
abstract, full text, DOI:10.1021/bm500733h

Kanodia, Shivani; Kumar, Gautam; Rizzi, Luca; Pedretti, Alessandro; Hodder, Anthony N.; Romeo, Sergio; Malhotra, Pawan
Synthetic peptides derived from the C-terminal 6 kDa region of Plasmodium falciparum SERA5 inhibit the enzyme activity and malaria parasite development
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:2765-2775, SEP 2014
abstract, full text, DOI:10.1016/j.bbagen.2014.04.013

Friedrichs, Wenke; Langel, Walter
Atomistic modeling of peptide adsorption on rutile (100) in the presence of water and of contamination by low molecular weight alcohols
BIOINTERPHASES, 9 Art. No. 031006, SEP 2014
abstract, full text, DOI:10.1116/1.4883555

Ding, Yun-Qiao; Chen, Cheng-lung; Gu, Qi-Rui; Fu, Li-Hong
Molecular simulation study of the effects of inorganic anions on the properties of chrome-crosslinked collagen
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, 22 Art. No. 065008, SEP 2014
abstract, full text, DOI:10.1088/0965-0393/22/6/065008

Gao, Yi; Olsen, Kenneth W.
Unique Mechanism of Facile Polymorphic Conversion of Acetaminophen in Aqueous Medium
MOLECULAR PHARMACEUTICS, 11:3056-3067, SEP 2014
abstract, full text, DOI:10.1021/mp500251w

Venthur, Herbert; Mutis, Ana; Zhou, Jing-Jiang; Quiroz, Andres
Ligand binding and homology modelling of insect odorant-binding proteins
PHYSIOLOGICAL ENTOMOLOGY, 39:183-198, SEP 2014
abstract, full text, DOI:10.1111/phen.12066

Alberto Batista-Garcia, Ramon; Sanchez-Reyes, Ayixon; Millan-Pacheco, Cesar; Manuel Gonzalez-Zuniga, Victor; Juarez, Soledad; Luis Folch-Mallol, Jorge; Pastor, Nina
A novel TctA citrate transporter from an activated sludge metagenome: Structural and mechanistic predictions for the TTT family
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:1756-1764, SEP 2014
abstract, full text, DOI:10.1002/prot.24529

Varol, Onur; Yuret, Deniz; Erman, Burak; Kabakcioglu, Alkan
Mode coupling points to functionally important residues in myosin II
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:1777-1786, SEP 2014
abstract, full text, DOI:10.1002/prot.24531

Joseph, Dmitri D. A.; Jiao, Wanting; Kessans, Sarah A.; Parker, Emily J.
Substrate-mediated control of the conformation of an ancillary domain delivers a competent catalytic site for N-acetylneuraminic acid synthase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2054-2066, SEP 2014
abstract, full text, DOI:10.1002/prot.24558

Sharp, Kim A.; Kasinath, Vignesh; Wand, A. Joshua
Banding of NMR-derived methyl order parameters: Implications for protein dynamics
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2106-2117, SEP 2014
abstract, full text, DOI:10.1002/prot.24566

Legare, Sebastien; Lagguee, Patrick
The influenza fusion peptide promotes lipid polar head intrusion through hydrogen bonding withphosphates and N-terminal membrane insertion depth
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2118-2127, SEP 2014
abstract, full text, DOI:10.1002/prot.24568

Wang, Beibei; Weng, Jingwei; Wang, Wenning
Multiple conformational states and gate opening of outer membrane protein ToIC revealed by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2169-2179, SEP 2014
abstract, full text, DOI:10.1002/prot.24573

Firouzi, M. A. Mahdjour; Pishkenari, H. Nejat; Mahboobi, H.; Meghdari, A.
Manipulation of biomolecules: A molecular dynamics study
CURRENT APPLIED PHYSICS, 14:1216-1227, SEP 2014
abstract, full text, DOI:10.1016/j.cap.2014.06.014

Sedighi, Mina; Mohebbi, Ali
Investigation of nanoparticle aggregation effect on thermal properties of nanofluid by a combined equilibrium and non-equilibrium molecular dynamics simulation
JOURNAL OF MOLECULAR LIQUIDS, 197:14-22, SEP 2014
abstract, full text, DOI:10.1016/j.molliq.2014.04.019

Huang, Yu-ming M.; Kang, Myungshim; Chang, Chia-en A.
Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics
JOURNAL OF MOLECULAR RECOGNITION, 27:537-548, SEP 2014
abstract, full text, DOI:10.1002/jmr.2377

Baul, Upayan; Kuroda, Kenichi; Vemparala, Satyavani
Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 084902, AUG 28 2014
abstract, full text, DOI:10.1063/1.4893440

Hamulakova, Slavka; Janovec, Ladislav; Hrabinova, Martina; Spilovska, Katarina; Korabecny, Jan; Kristian, Pavol; Kuca, Kamil; Imrich, Jan
Synthesis and Biological Evaluation of Novel Tacrine Derivatives and Tacrine-Coumarin Hybrids as Cholinesterase Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 57:7073-7084, AUG 28 2014
abstract, full text, DOI:10.1021/jm5008648

Mino, German; Barriga, Raul; Gutierrez, Gonzalo
Hydrogen Bonds and Heat Diffusion in alpha-Helices: A Computational Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10025-10034, AUG 28 2014
abstract, full text, DOI:10.1021/jp503420e

Gomez-Castro, Carlos Z.; Vela, Alberto; Quintanar, Liliana; Grande-Aztatzi, Rafael; Mineva, Tzonka; Goursot, Annick
Insights into the Oxygen-Based Ligand of the Low pH Component of the Cu2+-Amyloid-beta Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10052-10064, AUG 28 2014
abstract, full text, DOI:10.1021/jp5047529

Koukos, Panagiotis I.; Glykos, Nicholas M.
Folding Molecular Dynamics Simulations Accurately Predict the Effect of Mutations on the Stability and Structure of a Vammin-Derived Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10076-10084, AUG 28 2014
abstract, full text, DOI:10.1021/jp5046113

Schonbeck, Christian; Westh, Peter; Holm, Rene
Complexation Thermodynamics of Modified Cyclodextrins: Extended Cavities and Distorted Structures
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10120-10129, AUG 28 2014
abstract, full text, DOI:10.1021/jp506001j

Guo, Xiang-Yang; Watermann, Tobias; Sebastiani, Daniel
Local Microphase Separation of a Binary Liquid under Nanoscale Confinement
JOURNAL OF PHYSICAL CHEMISTRY B, 118:10207-10213, AUG 28 2014
abstract, full text, DOI:10.1021/jp505203t

He, Chengzhi; Lamour, Guillaume; Xiao, Adam; Gsponer, Joerg; Li, Hongbin
Mechanically Tightening a Protein Slipknot into a Trefoil Knot
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:11946-11955, AUG 27 2014
abstract, full text, DOI:10.1021/ja503997h

Shi, Mingsong; Zhang, Chunchun; Xie, Yani; Xu, Dingguo
Stereoselective inclusion mechanism of ketoprofen into beta-cyclodextrin: insights from molecular dynamics simulations and free energy calculations
THEORETICAL CHEMISTRY ACCOUNTS, 133 Art. No. 1556, AUG 26 2014
abstract, full text, DOI:10.1007/s00214-014-1556-8

Farimani, A. Barati; Aluru, N. R.; Tajkhorshid, Emad
Thermodynamic insight into spontaneous hydration and rapid water permeation in aquaporins
APPLIED PHYSICS LETTERS, 105 Art. No. 083702, AUG 25 2014
abstract, full text, DOI:10.1063/1.4893782

Teijido, Oscar; Rappaport, Shay M.; Chamberlin, Adam; Noskov, Sergei Y.; Aguilella, Vicente M.; Rostovtseva, Tatiana K.; Bezrukov, Sergey M.
Acidification Asymmetrically Affects Voltage-dependent Anion Channel Implicating the Involvement of Salt Bridges
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:23670-23682, AUG 22 2014
abstract, full text, DOI:10.1074/jbc.M114.576314

Keov, Peter; Lopez, Laura; Devine, Shane M.; Valant, Celine; Lane, J. Robert; Scammells, Peter J.; Sexton, Patrick M.; Christopoulos, Arthur
Molecular Mechanisms of Bitopic Ligand Engagement with the M-1 Muscarinic Acetylcholine Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:23817-23837, AUG 22 2014
abstract, full text, DOI:10.1074/jbc.M114.582874

Bellucci, Michael A.; Trout, Bernhardt L.
Bezier curve string method for the study of rare events in complex chemical systems
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 074110, AUG 21 2014
abstract, full text, DOI:10.1063/1.4893216

Weiser, Brian P.; Salari, Reza; Eckenhoff, Roderic G.; Brannigan, Grace
Computational Investigation of Cholesterol Binding Sites on Mitochondrial VDAC
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9852-9860, AUG 21 2014
abstract, full text, DOI:10.1021/jp504516a

Kubiak-Ossowska, Karina; Mulheran, Paul A.; Nowak, Wieslaw
Fibronectin Module FN(III)9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9900-9908, AUG 21 2014
abstract, full text, DOI:10.1021/jp5020077

Liu, Ying; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Threading or Tumbling? Insight into the Self-Inclusion Mechanism of an altro-alpha-Cyclodextrin Derivative
JOURNAL OF PHYSICAL CHEMISTRY C, 118:19380-19386, AUG 21 2014
abstract, full text, DOI:10.1021/jp503866q

Calandrini, Vania; Arnesano, Fabio; Galliani, Angela; Nguyen, Trung Hai; Lppoliti, Emiliano; Carloni, Paolo; Natile, Giovanni
Platination of the copper transporter ATP7A involved in anticancer drug resistance
DALTON TRANSACTIONS, 43:12085-12094, AUG 21 2014
abstract, full text, DOI:10.1039/c4dt01339e

Bansode, Sneha B.; Jana, Asis K.; Batkulwar, Kedar B.; Warkad, Shrikant D.; Joshi, Rakesh S.; Sengupta, Neelanjana; Kulkarni, Mahesh J.
Molecular Investigations of Protriptyline as a Multi-Target Directed Ligand in Alzheimer's Disease
PLOS ONE, 9 Art. No. e105196, AUG 20 2014
abstract, full text, DOI:10.1371/journal.pone.0105196

Fuller, Jonathan C.; Martinez, Michael; Wade, Rebecca C.
On Calculation of the Electrostatic Potential of a Phosphatidylinositol Phosphate-Containing Phosphatidylcholine Lipid Membrane Accounting for Membrane Dynamics
PLOS ONE, 9 Art. No. e104778, AUG 20 2014
abstract, full text, DOI:10.1371/journal.pone.0104778

Biswas, Mithun; Burghardt, Irene
Azobenzene Photoisomerization-Induced Destabilization of B-DNA
BIOPHYSICAL JOURNAL, 107:932-940, AUG 19 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.044

Agazzi, Federico M.; Mariano Correa, N.; Rodriguez, Javier
Molecular Dynamics Simulation of Water/BHDC Cationic Reverse Micelles. Structural Characterization, Dynamical Properties, and Influence of Solvent on Intermicellar Interactions
LANGMUIR, 30:9643-9653, AUG 19 2014
abstract, full text, DOI:10.1021/la501964q

Mahdavi, Somayeh; Kuyucak, Serdar
Molecular Dynamics Study of Binding of mu-Conotoxin GIIIA to the Voltage-Gated Sodium Channel Na(v)1.4
PLOS ONE, 9 Art. No. e105300, AUG 18 2014
abstract, full text, DOI:10.1371/journal.pone.0105300

Rui, Xianliang; Mehrbod, Mehrdad; Van Agthoven, Johannes F.; Anand, Saurabh; Xiong, Jian-Ping; Mofrad, Mohammad R. K.; Arnaout, M. Amin
The alpha-Subunit Regulates Stability of the Metal Ion at the Ligand-associated Metal Ion-binding Site in beta(3) Integrins
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:23256-23263, AUG 15 2014
abstract, full text, DOI:10.1074/jbc.M114.581470

Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
Multiple branched adaptive steered molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 064101, AUG 14 2014
abstract, full text, DOI:10.1063/1.4891807

Tardia, Piero; Stefanachi, Angela; Niso, Mauro; Stolfa, Diana Antonella; Mangiatordi, Giuseppe Felice; Alberga, Domenico; Nicolotti, Orazio; Lattanzi, Gianluca; Carotti, Angelo; Leonetti, Francesco; Perrone, Roberto; Berardi, Francesco; Azzariti, Amalia; Colabufo, Nicola Antonio; Cellamare, Saverio
Trimethoxybenzanilide-Based P-Glycoprotein Modulators: An Interesting Case of Lipophilicity Tuning by Intramolecular Hydrogen Bonding
JOURNAL OF MEDICINAL CHEMISTRY, 57:6403-6418, AUG 14 2014
abstract, full text, DOI:10.1021/jm500697c

Bernini, Caterina; Arezzini, Elena; Basosi, Riccardo; Sinicropi, Adalgisa
In Silico Spectroscopy of Tryptophan and Tyrosine Radicals Involved in the Long-Range Electron Transfer of Cytochrome c Peroxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9525-9537, AUG 14 2014
abstract, full text, DOI:10.1021/jp5025153

Karandur, Deepti; Wong, Ka-Yiu; Pettitt, B. Montgomery
Solubility and Aggregation of Gly5 in Water
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9565-9572, AUG 14 2014
abstract, full text, DOI:10.1021/jp503358n

Dong, Hao; Klein, Michael L.; Fiorin, Giacomo
Counterion-Assisted Cation Transport in a Biological Calcium Channel
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9668-9676, AUG 14 2014
abstract, full text, DOI:10.1021/jp5059897

Hill, Eric H.; Whitten, David G.; Evans, Deborah G.
Computational Study of Bacterial Membrane Disruption by Cationic Biocides: Structural Basis for Water Pore Formation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:9722-9732, AUG 14 2014
abstract, full text, DOI:10.1021/jp504297s

Tah, Bidisha; Pal, Prabir; Roy, Sourav; Dutta, Debodyuti; Mishra, Sabyashachi; Ghosh, Manash; Talapatra, G. B.
Quantum-mechanical DFT calculation supported Raman spectroscopic study of some amino acids in bovine insulin
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 129:345-351, AUG 14 2014
abstract, full text, DOI:10.1016/j.saa.2014.03.044

Kokhan, Oleksandr; Ponomarenko, Nina; Pokkuluri, P. Raj; Schiffer, Marianne; Tiede, David M.
Multimerization of Solution-State Proteins by Tetrakis(4-sulfonatophenyl)porphyrin
BIOCHEMISTRY, 53:5070-5079, AUG 12 2014
abstract, full text, DOI:10.1021/bi500278g

Shang, Yi; LeRouzic, Valerie; Schneider, Sebastian; Bisignano, Paola; Pasternak, Gavril W.; Filizola, Marta
Mechanistic Insights into the Allosteric Modulation of Opioid Receptors by Sodium Ions
BIOCHEMISTRY, 53:5140-5149, AUG 12 2014
abstract, full text, DOI:10.1021/bi5006915

Kramer, Mitchell; Halleran, Daniel; Rahman, Moazur; Iqbal, Mazhar; Anwar, Muhmad Ikram; Sabet, Salwa; Ackad, Edward; Yousef, Mohammad
Comparative Molecular Dynamics Simulation of Hepatitis C Virus NS3/4A Protease (Genotypes 1b, 3a and 4b) Predicts Conformational Instability of the Catalytic Triad in Drug Resistant Strains
PLOS ONE, 9 Art. No. e104425, AUG 11 2014
abstract, full text, DOI:10.1371/journal.pone.0104425

Masiero, Alessandro; Aufiero, Simona; Minervini, Giovanni; Moro, Stefano; Costa, Rodolfo; Tosatto, Silvio C. E.
Evaluation of the steric impact of flavin adenine dinucleotide in Drosophila melanogaster cryptochrome function
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 450:1606-1611, AUG 8 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.07.038

Wang, Yong; Luan, Bin-Quan; Yang, Zhiyu; Zhang, Xinyue; Ritzo, Brandon; Gates, Kent; Gu, Li-Qun
Single Molecule Investigation of Ag+ Interactions with Single Cytosine-, Methylcytosine- and Hydroxymethylcytosine-Cytosine Mismatches in a Nanopore
SCIENTIFIC REPORTS, 4 Art. No. 5883, AUG 8 2014
abstract, full text, DOI:10.1038/srep05883

Zhu, Yuhong; Chen, Shi-Jie
Many-body effect in ion binding to RNA
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 055101, AUG 7 2014
abstract, full text, DOI:10.1063/1.4890656

Jia, Minyue; Yang, Boyun; Li, Zhongyi; Shen, Huiling; Song, Xiaoxiao; Gu, Wei
Computational Analysis of Functional Single Nucleotide Polymorphisms Associated with the CYP11B2 Gene
PLOS ONE, 9 Art. No. e104311, AUG 7 2014
abstract, full text, DOI:10.1371/journal.pone.0104311

Markosyan, Suren; De Biase, Pablo M.; Czapla, Luke; Samoylova, Olga; Singh, Gurpreet; Cuervo, Javier; Tieleman, D. Peter; Noskov, Sergei Yu.
Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore
NANOSCALE, 6:9006-9016, AUG 7 2014
abstract, full text, DOI:10.1039/c3nr06559f

Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto
MDGRAPE-4: a special-purpose computer system formolecular dynamics simulations
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 372 Art. No. 20130387, AUG 6 2014
abstract, full text, DOI:10.1098/rsta.2013.0387

Araya-Secchi, Raul; Perez-Acle, Tomas; Kang, Seung-gu; Huynh, Tien; Bernardin, Alejandro; Escalona, Yerko; Garate, Jose-Antonio; Martinez, Agustin D.; Garcia, Isaac E.; Saez, Juan C.; Zhou, Ruhong
Characterization of a Novel Water Pocket Inside the Human Cx26 Hemichannel Structure
BIOPHYSICAL JOURNAL, 107:599-612, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.05.037

Orzechowski, Marek; Li, Xiaochuan (Edward); Fischer, Stefan; Lehman, William
An Atomic Model of the Tropomyosin Cable on F-actin
BIOPHYSICAL JOURNAL, 107:694-699, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.034

Shoura, Massa J.; Ranatunga, R. J. K. Udayana; Harris, Sarah A.; Nielsen, Steven O.; Levene, Stephen D.
Contribution of Fluorophore Dynamics and Solvation to Resonant Energy Transfer in Protein-DNA Complexes: A Molecular-Dynamics Study
BIOPHYSICAL JOURNAL, 107:700-710, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.023

Ayoub, Ahmed T.; Craddock, Travis J. A.; Klobukowski, Mariusz; Tuszynski, Jack
Analysis of the Strength of Interfacial Hydrogen Bonds between Tubulin Dimers Using Quantum Theory of Atoms in Molecules
BIOPHYSICAL JOURNAL, 107:740-750, AUG 5 2014
abstract, full text, DOI:10.1016/j.bpj.2014.05.047

Manni, Sandro; Mineev, Konstantin S.; Usmanova, Dinara; Lyukmanova, Ekaterina N.; Shulepko, Mikhail A.; Kirpichnikov, Mikhail P.; Winter, Jonas; Matkovic, Milos; Deupi, Xavier; Arseniev, Alexander S.; Ballmer-Hofer, Kurt
Structural and Functional Characterization of Alternative Transmembrane Domain Conformations in VEGF Receptor 2 Activation
STRUCTURE, 22:1077-1089, AUG 5 2014
abstract, full text, DOI:10.1016/j.str.2014.05.010

Sakuraba, Shun; Matubayasi, Nobuyuki
ERmod: Fast and Versatile Computation Software for Solvation Free Energy with Approximate Theory of Solutions
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1592-1608, AUG 5 2014
abstract, full text, DOI:10.1002/jcc.23651

Harpole, Tyler J.; Grosman, Claudio
Side-chain conformation at the selectivity filter shapes the permeation free-energy landscape of an ion channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E3196-E3205, AUG 5 2014
abstract, full text, DOI:10.1073/pnas.1408950111

Bracke, Nathalie; Wynendaele, Evelien; D'Hondt, Matthias; Haselberg, Rob; Somsen, Govert W.; Pauwels, Ewald; Van de Wiele, Christoph; De Spiegeleer, Bart
Analytical characterization of NOTA-modified somatropins
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 96:1-9, AUG 5 2014
abstract, full text, DOI:10.1016/j.jpba.2014.03.014

Popadic, A.; Walther, J. H.; Koumoutsakos, P.; Praprotnik, M.
Continuum simulations of water flow in carbon nanotube membranes
NEW JOURNAL OF PHYSICS, 16 Art. No. 082001, AUG 4 2014
abstract, full text, DOI:10.1088/1367-2630/16/8/082001

Bairagya, Hridoy R.; Mishra, Deepak K.; Mukhopadhyay, Bishnu P.; Sekar, K.
Conserved water-mediated recognition and dynamics of NAD(+) (carboxamide group) to hIMPDH enzyme: water mimic approach toward the design of isoform-selective inhibitor
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1248-1262, AUG 3 2014
abstract, full text, DOI:10.1080/07391102.2013.812982

Noel, Jeffrey K.; Whitford, Paul Charles
How Simulations Reveal Dynamics, Disorder, and the Energy Landscapes of Biomolecular Function
ISRAEL JOURNAL OF CHEMISTRY, 54:1093-1107, AUG 2014
abstract, full text, DOI:10.1002/ijch.201400018

Leuchter, Jessica D.; Green, Adam T.; Gilyard, Julian; Rambarat, Cecilia G.; Cho, Samuel S.
Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding
ISRAEL JOURNAL OF CHEMISTRY, 54:1152-1164, AUG 2014
abstract, full text, DOI:10.1002/ijch.201400022

Larsson, Per; Pouya, Iman; Lindahl, Erik
From Side Chains Rattling on Picoseconds to Ensemble Simulations of Protein Folding
ISRAEL JOURNAL OF CHEMISTRY, 54:1274-1285, AUG 2014
abstract, full text, DOI:10.1002/ijch.201400020

Reboul, Cyril F.; Whisstock, James C.; Dunstone, Michelle A.
A New Model for Pore Formation by Cholesterol-Dependent Cytolysins
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003791, AUG 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003791

Mateo, Lidia; Ullastres, Anna; Gonzalec, Josefa
A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila
PLOS GENETICS, 10 Art. No. e1004560, AUG 2014
abstract, full text, DOI:10.1371/journal.pgen.1004560

Pietra, Francesco
Binding Pockets and Pathways for Dioxygen through the KijD3 N-Oxygenase in Complex with Flavin Mononucleotide Cofactor and a 3-Aminoglucose Substrate: Predictions from Molecular Dynamics Simulations
CHEMISTRY & BIODIVERSITY, 11:1151-1162, AUG 2014
abstract, full text, DOI:10.1002/cbdv.201400081

Devi, J. Meena
A simulation study on the thermal and wetting behavior of alkane thiol SAM on gold (111) surface
PROGRESS IN NATURAL SCIENCE-MATERIALS INTERNATIONAL, 24:405-411, AUG 2014
abstract, full text, DOI:10.1016/j.pnsc.2014.06.009

Lote, Asawari R.; Kolhatkar, Vidula R.; Insley, Thomas; Kral, Petr; Kolhatkar, Rohit
Oligospermines and Nucleic Acid Interaction: A Structure Property Relationship Study
ACS MACRO LETTERS, 3:829-833, AUG 2014
abstract, full text, DOI:10.1021/mz500358w

Paracha, Rehan Zafar; Ali, Amjad; Ahmad, Jamil; Hussain, Riaz; Niazi, Umar; Muhammad, Syed Aun
Structural evaluation of BTK and PKC delta mediated phosphorylation of MAL at positions Tyr86 and Tyr106
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 51:22-35, AUG 2014
abstract, full text, DOI:10.1016/j.compbiolchem.2014.04.001

Albareda, Marta; Pacios, Luis F.; Manyani, Hamid; Rey, Luis; Brito, Belen; Imperial, Juan; Ruiz-Argueeso, Tomas; Palacios, Jose M.
Maturation of Rhizobium leguminosarum Hydrogenase in the Presence of Oxygen Requires the Interaction of the Chaperone HypC and the Scaffolding Protein HupK
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:21217-21229, AUG 1 2014
abstract, full text, DOI:10.1074/jbc.M114.577403

Lauro, G.; Ferruz, N.; Fulle, S.; Harvey, M. J.; Finn, P. W.; De Fabritiis, G.
Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2185-2189, AUG 2014
abstract, full text, DOI:10.1021/ci500309a

Leonis, Georgios; Avramopoulos, Aggelos; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Yurtsever, Mine; Papadopoulos, Manthos G.
Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human kappa-Opioid Receptor Complexes
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2294-2308, AUG 2014
abstract, full text, DOI:10.1021/ci5002873

Schmidtke, Peter; Ciantar, Marine; Theret, Isabelle; Ducrott, Pierre
Dynamics of hERG Closure Allow Novel Insights into hERG Blocking by Small Molecules
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2320-2333, AUG 2014
abstract, full text, DOI:10.1021/ci5001373

Li, Hui; Fan, Jianfen F.; Li, Rui; Yu, Yi; Yan, Xiliang L.
Molecular dynamics studies on the influences of a gradient electric field on the water chain in a peptide nanotube
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2370, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2370-x

Librando, Vito; Pappalardo, Matteo
Theoretical approach to the innovative mutation of naphthalene 1,2-dioxygenase: a molecular dynamics and docking study
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2354, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2354-x

Tekpinar, Mustafa; Zheng, Wenjun
Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2381, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2381-7

Wang, Yu; Xi, Lei; Yao, Jie; Yang, Jiao; Du, Lin-Fang
Role of pH in structural changes for Pin1 protein: an insight from molecular dynamics study
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2376, AUG 2014
abstract, full text, DOI:10.1007/s00894-014-2376-4

Pavsic, Miha; Guncar, Gregor; Djinovic-Carugo, Kristina; Lenarcic, Brigita
Crystal structure and its bearing towards an understanding of key biological functions of EpCAM
NATURE COMMUNICATIONS, 5 Art. No. 4764, AUG 2014
abstract, full text, DOI:10.1038/ncomms5764

Sixto-Lopez, Yudibeth; Gomez-Vidal, Jose A.; Correa-Basurto, Jose
Exploring the Potential binding Sites of Some Known HDAC Inhibitors on Some HDAC8 Conformers by Docking Studies
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY, 173:1907-1926, AUG 2014
abstract, full text, DOI:10.1007/s12010-014-0976-1

Yang, Jintao; Zhang, Mingzhen; Chen, Hong; Chang, Yung; Chen, Zhan; Zheng, Jie
Probing the Structural Dependence of Carbon Space Lengths of Poly(N-hydroxyalkyl acrylamide)-Based Brushes on Antifouling Performance
BIOMACROMOLECULES, 15:2982-2991, AUG 2014
abstract, full text, DOI:10.1021/bm500598a

Roy, Sourav; Basu, Sankar; Datta, Alok K.; Bhattacharyya, Dhananjay; Banerjee, Rahul; Dasgupta, Dipak
Equilibrium unfolding of cyclophilin from Leishmania donovani: Characterization of intermediate states
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 69:353-360, AUG 2014
abstract, full text, DOI:10.1016/j.ijbiomac.2014.05.063

Maffeo, Christopher; Ngo, Thuy T. M.; Ha, Taekjip; Aksimentiev, Aleksei
A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2891-2896, AUG 2014
abstract, full text, DOI:10.1021/ct500193u

Dixit, Purushottam D.; Dill, Ken A.
Inferring Microscopic Kinetic Rates from Stationary State Distributions
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3002-3005, AUG 2014
abstract, full text, DOI:10.1021/ct5001389

White, Andrew D.; Voth, Gregory A.
Efficient and Minimal Method to Bias Molecular Simulations with Experimental Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:3023-3030, AUG 2014
abstract, full text, DOI:10.1021/ct500320c

Anderson, Janet S.; Mustafi, Sourajit M.; Hernandez, Griselda; LeMaster, David M.
Statistical allosteric coupling to the active site indole ring flip equilibria in the FK506-binding domain
BIOPHYSICAL CHEMISTRY, 192:41-48, AUG 2014
abstract, full text, DOI:10.1016/j.bpc.2014.06.004

Busse-Wicher, Marta; Gomes, Thiago C. F.; Tryfona, Theodora; Nikolovski, Nino; Stott, Katherine; Grantham, Nicholas J.; Bolam, David N.; Skaf, Munir S.; Dupree, Paul
The pattern of xylan acetylation suggests xylan may interact with cellulose microfibrils as a twofold helical screw in the secondary plant cell wall of Arabidopsis thaliana
PLANT JOURNAL, 79:492-506, AUG 2014
abstract, full text, DOI:10.1111/tpj.12575

Amodeo, Giuseppe Federico; Scorciapino, Mariano Andrea; Messina, Angela; De Pinto, Vito; Ceccarelli, Matteo
Charged Residues Distribution Modulates Selectivity of the Open State of Human Isoforms of the Voltage Dependent Anion-Selective Channel
PLOS ONE, 9 Art. No. e103879, AUG 1 2014
abstract, full text, DOI:10.1371/journal.pone.0103879

Yang, Shang; Wang, Xi; Cui, Lei; Ding, Xiang; Niu, Lili; Yang, Fuquan; Wang, Chao; Wang, Chih-chen; Lou, Jizhong
Compact Conformations of Human Protein Disulfide Isomerase
PLOS ONE, 9 Art. No. e103472, AUG 1 2014
abstract, full text, DOI:10.1371/journal.pone.0103472

Collins, Carleton G.; Johnson, Andrew T.; Connell, Richard D.; Nelson, Ruth A.; Murgu, Ivan; Oliver, Allen G.; Smith, Bradley D.
Effect of 1,3-adamantane bridging units within the surrounding macrocycle of squaraine rotaxanes
NEW JOURNAL OF CHEMISTRY, 38:3992-3998, AUG 2014
abstract, full text, DOI:10.1039/c4nj00726c

Manna, Moutusi; Rog, Tomasz; Vattulainen, Ilpo
The challenges of understanding glycolipid functions: An open outlook based on molecular simulations
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 1841:1130-1145, AUG 2014
abstract, full text, DOI:10.1016/j.bbalip.2013.12.016

Sela, Hanan; Spiridon, Laurentiu N.; Ashkenazi, Haim; Bhullar, Navreet K.; Brunner, Susanne; Petrescu, Andrei-Jose; Fahima, Tzion; Keller, Beat; Jordan, Tina
Three-Dimensional Modeling and Diversity Analysis Reveals Distinct AVR Recognition Sites and Evolutionary Pathways in Wild and Domesticated Wheat Pm3 R Genes
MOLECULAR PLANT-MICROBE INTERACTIONS, 27:835-845, AUG 2014
abstract, full text, DOI:10.1094/MPMI-01-14-0009-R

Parasuraman, Ponnusamy; Murugan, Veeramani; Selvin, Jeyasigamani F. A.; Gromiha, M. Michael; Fukui, Kazuhiko; Veluraja, Kasinadar
Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Ac alpha(2-3)Gal: a study by in silico mutations and molecular dynamics simulations
JOURNAL OF MOLECULAR RECOGNITION, 27:482-492, AUG 2014
abstract, full text, DOI:10.1002/jmr.2369

Grosse, Wolfgang; Psakis, Georgios; Mertins, Barbara; Reiss, Philipp; Windisch, Dirk; Brademann, Felix; Buerck, Jochen; Ulrich, Anne; Koert, Ulrich; Essen, Lars-Oliver
Structure-Based Engineering of a Minimal Porin Reveals Loop-Independent Channel Closure
BIOCHEMISTRY, 53:4826-4838, JUL 29 2014
abstract, full text, DOI:10.1021/bi500660q

Zhu, Hong; Xiao, Shiyan; Wang, Lei; Liang, Haojun
Communication: Asymmetrical cation movements through G-quadruplex DNA
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 041103, JUL 28 2014
abstract, full text, DOI:10.1063/1.4891218

Rastaedter, Dominique; Biswas, Mithun; Burghardt, Irene
Molecular Dynamics Study of the Controlled Destabilization of an RNA Hairpin Structure by a Covalently Attached Azobenzene Switch
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8478-8488, JUL 24 2014
abstract, full text, DOI:10.1021/jp501399k

Moritsugu, Kei; Kidera, Akinori; Smith, Jeremy C.
Solvent Friction Effects Propagate over the Entire Protein Molecule through Low-Frequency Collective Modes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8559-8565, JUL 24 2014
abstract, full text, DOI:10.1021/jp503956m

Haverkort, Frank; Stradomska, Anna; Knoester, Jasper
First-Principles Simulations of the Initial Phase of Self-Aggregation of a Cyanine Dye: Structure and Optical Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8877-8890, JUL 24 2014
abstract, full text, DOI:10.1021/jp5049277

Yu, H.; Liu, T.; Zhao, Z.; Chen, Y.; Zeng, J.; Liu, S.; Zhu, F.
Mutations in 3 '-long terminal repeat of HERV-W family in chromosome 7 upregulate syncytin-1 expression in urothelial cell carcinoma of the bladder through interacting with c-Myb
ONCOGENE, 33:3947-3958, JUL 24 2014
abstract, full text, DOI:10.1038/onc.2013.366

Delacour, Herve; Lushchekina, Sofya; Mabboux, Isabelle; Bousquet, Aurore; Ceppa, Franck; Schopfer, Lawrence M.; Lockridge, Oksana; Masson, Patrick
Characterization of a Novel BCHE "Silent'' Allele: Point Mutation (p. Val204Asp) Causes Loss of Activity and Prolonged Apnea with Suxamethonium
PLOS ONE, 9 Art. No. e101552, JUL 23 2014
abstract, full text, DOI:10.1371/journal.pone.0101552

Polak, Andraz; Tarek, Mounir; Tomsic, Matija; Valant, Janez; Ulrih, Natasa Poklar; Jamnik, Andrej; Kramar, Peter; Miklavcic, Damijan
Structural Properties of Archaeal Lipid Bilayers: Small-Angle X-ray Scattering and Molecular Dynamics Simulation Study
LANGMUIR, 30:8308-8315, JUL 22 2014
abstract, full text, DOI:10.1021/la5014208

Rajapaksha, Harinda; Petrovsky, Nikolai
In Silico Structural Homology Modelling and Docking for Assessment of Pandemic Potential of a Novel H7N9 Influenza Virus and Its Ability to Be Neutralized by Existing Anti-Hemagglutinin Antibodies
PLOS ONE, 9 Art. No. e102618, JUL 21 2014
abstract, full text, DOI:10.1371/journal.pone.0102618

Cui, Youtian; Cui, Wenjing; Liu, Zhongmei; Zhou, Li; Kobayashi, Michihiko; Zhou, Zhemin
Improvement of stability of nitrile hydratase via protein fragment swapping
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 450:401-408, JUL 18 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.05.127

Mnpotra, Jagjeet S.; Qiao, Zhuanhong; Cai, Jian; Lynch, Diane L.; Grossfield, Alan; Leioatts, Nicholas; Hurst, Dow P.; Pitman, Michael C.; Song, Zhao-Hui; Reggio, Patricia H.
Structural Basis of G Protein-coupled Receptor-G(i) Protein Interaction FORMATION OF THE CANNABINOID CB2 RECEPTOR-G(i) PROTEIN COMPLEX
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:20259-20272, JUL 18 2014
abstract, full text, DOI:10.1074/jbc.M113.539916

Fogarty, Aoife C.; Laage, Damien
Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7715-7729, JUL 17 2014
abstract, full text, DOI:10.1021/jp409805p

Malolepsza, Edyta; Straub, John E.
Empirical Maps For The Calculation of Amide I Vibrational Spectra of Proteins From Classical Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7848-7855, JUL 17 2014
abstract, full text, DOI:10.1021/jp412827s

Yoon, Jeseong; Lin, Jong-Chin; Hyeon, Changbong; Thirumalai, D.
Dynamical Transition and Heterogeneous Hydration Dynamics in RNA
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7910-7919, JUL 17 2014
abstract, full text, DOI:10.1021/jp500643u

Dinpajooh, Mohammadhasan; Matyushov, Dmitry V.
Non-Gaussian Lineshapes and Dynamics of Time-Resolved Linear and Nonlinear (Correlation) Spectra
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7925-7936, JUL 17 2014
abstract, full text, DOI:10.1021/jp500733s

Chao, Shu-Han; Matthews, Sam S.; Paxman, Ryan; Aksimentiev, Aleksei; Gruebele, Martin; Price, Joshua L.
Two Structural Scenarios for Protein Stabilization by PEG
JOURNAL OF PHYSICAL CHEMISTRY B, 118:8388-8395, JUL 17 2014
abstract, full text, DOI:10.1021/jp502234s

Galan, Jhenny F.; Germany, Edward; Pawlowski, Amanda; Strickland, Lynette; Galinato, Mary Grace I.
Theoretical and Spectroscopic Analysis of N,N '-Diphenylurea and N,N '-Dimethyl-N,N '-diphenylurea Conformations
JOURNAL OF PHYSICAL CHEMISTRY A, 118:5304-5315, JUL 17 2014
abstract, full text, DOI:10.1021/jp503539m

Hilder, Tamsyn A.; Ridone, Pietro; Nakayama, Yoshitaka; Martinac, Boris; Chung, Shin-Ho
Binding of fullerenes and nanotubes to MscL
SCIENTIFIC REPORTS, 4 Art. No. 5609, JUL 17 2014
abstract, full text, DOI:10.1038/srep05609

Schwander, P.; Fung, R.; Ourmazd, A.
Conformations of macromolecules and their complexes from heterogeneous datasets
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 369 Art. No. 20130567, JUL 17 2014
abstract, full text, DOI:10.1098/rstb.2013.0567

Chibani, Siwar; Jacquemin, Denis; Laurent, Adele D.
Modelling solvent effects on the absorption and emission spectra of constrained cyanines with both implicit and explicit QM/EFP models
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1040:321-327, JUL 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.03.033

Goez, Albrecht; Jacob, Christoph R.; Neugebauer, Johannes
Modeling environment effects on pigment site energies: Frozen density embedding with fully quantum-chemical protein densities
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1040:347-359, JUL 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.02.009

Etienne, Thibaud; Gattuso, Hugo; Monari, Antonio; Assfeld, Xavier
QM/MM modeling of Harmane cation fluorescence spectrum in water solution and interacting with DNA
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1040:367-372, JUL 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.03.026

Hamed, Elham; Keten, Sinan
Hierarchical Cascades of Instability Govern the Mechanics of Coiled Coils: Helix Unfolding Precedes Coil Unzipping
BIOPHYSICAL JOURNAL, 107:477-484, JUL 15 2014
abstract, full text, DOI:10.1016/j.bpj.2014.06.009

Dewan, Shalaka; Carnevale, Vincenzo; Bankura, Arindam; Eftekhari-Bafrooei, Ali; Fiorin, Giacomo; Klein, Michael L.; Borguet, Eric
Structure of Water at Charged Interfaces: A Molecular Dynamics Study
LANGMUIR, 30:8056-8065, JUL 15 2014
abstract, full text, DOI:10.1021/la5011055

Bossis, Fabrizio; De Grassi, Anna; Palese, Luigi Leonardo; Pierri, Ciro Leonardo
Prediction of high- and low-affinity quinol-analogue-binding sites in the aa(3) and bo(3) terminal oxidases from Bacillus subtilis and Escherichia coli
BIOCHEMICAL JOURNAL, 461:305-314, JUL 15 2014
abstract, full text, DOI:10.1042/BJ20140082

Raczynski, Przemyslaw; Gorny, Krzysztof; Dawid, Aleksander; Gburski, Zygmunt
Delivery of nitric oxide to the interior of mammalian cell by carbon nanotube: MD simulation
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 554:6-10, JUL 15 2014
abstract, full text, DOI:10.1016/j.abb.2014.04.014

Chang, Hsin-Yang; Chou, Chia-Cheng; Hsu, Min-Feng; Wang, Andrew H. J.
Proposed Carrier Lipid-binding Site of Undecaprenyl Pyrophosphate Phosphatase from Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:18719-18735, JUL 11 2014
abstract, full text, DOI:10.1074/jbc.M114.575076

Bovigny, Christophe; Degiacomi, Matteo Thomas; Lemmin, Thomas; Dal Peraro, Matteo; Stenta, Marco
Reaction Mechanism and Catalytic Fingerprint of Allantoin Racemase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7457-7466, JUL 10 2014
abstract, full text, DOI:10.1021/jp411786z

Noinaj, Nicholas; Kuszak, Adam J.; Balusek, Curtis; Gumbart, James C.; Buchanan, Susan K.
Lateral Opening and Exit Pore Formation Are Required for BamA Function
STRUCTURE, 22:1055-1062, JUL 8 2014
abstract, full text, DOI:10.1016/j.str.2014.05.008

Fu, Iris W.; Markegard, Cade B.; Chu, Brian K.; Nguyen, Hung D.
Role of Hydrophobicity on Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations
LANGMUIR, 30:7745-7754, JUL 8 2014
abstract, full text, DOI:10.1021/la5012988

Korotchenko, Vasiliy N.; Saydmohammed, Manush; Vollmer, Laura L.; Bakan, Ahmet; Sheetz, Kyle; Debiec, Karl T.; Greene, Kristina A.; Agliori, Christine S.; Bahar, Ivet; Day, Billy W.; Vogt, Andreas; Tsang, Michael
In Vivo Structure-Activity Relationship Studies Support Allosteric Targeting of a Dual Specificity Phosphatase
CHEMBIOCHEM, 15:1436-1445, JUL 7 2014
abstract, full text, DOI:10.1002/cbic.201402000

Watly, Joanna; Simonoysky, Eyal; Wieczorek, Robert; Barbosa, Nuno; Miller, Yifat; Kozlowski, Henryk
Insight into the Coordination and the Binding Sites of Cu2+ by the Histidyl-6-Tag using Experimental and Computational Tools
INORGANIC CHEMISTRY, 53:6675-6683, JUL 7 2014
abstract, full text, DOI:10.1021/ic500387u

Bae, Jungeun; Nael, Manal A.; Jiang, Lingzhou; Hwang, Patrick TaeJoon; Mahdi, Fakhri; Jun, Ho-Wook; Elshamy, Wael M.; Zhou, Yu-Dong; Murthy, S. Narasimha; Doerksen, Robert J.; Jo, Seongbong
Quinone Propionic Acid- Based Redox- Triggered Polymer Nanoparticles for Drug Delivery: Computational Analysis and In Vitro Evaluation
JOURNAL OF APPLIED POLYMER SCIENCE, 131 Art. No. 40461, JUL 5 2014
abstract, full text, DOI:10.1002/app.40461

Luan, Binquan; Wang, Chao; Royyuru, Ajay; Stolovitzky, Gustavo
Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages
NANOTECHNOLOGY, 25 Art. No. 265101, JUL 4 2014
abstract, full text, DOI:10.1088/0957-4484/25/26/265101

Zhang, Liqun; Centa, Thomas; Buck, Matthias
Structure and Dynamics Analysis on Plexin-B1 Rho GTPase Binding Domain as a Monomer and Dimer
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7302-7311, JUL 3 2014
abstract, full text, DOI:10.1021/jp503668k

Gillman, Alan L.; Jang, Hyunbum; Lee, Joon; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Arce, Fernando Teran
Activity and Architecture of Pyroglutamate-Modified Amyloid-beta (A beta(pE3-42)) Pores
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7335-7344, JUL 3 2014
abstract, full text, DOI:10.1021/jp5040954

Shi, Wei; Thompson, Robert L.; Albenze, Erik; Steckel, Janice A.; Nulwala, Hunaid B.; Luebke, David R.
Contribution of the Acetate Anion to CO2 Solubility in Ionic Liquids: Theoretical Method Development and Experimental Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7383-7394, JUL 3 2014
abstract, full text, DOI:10.1021/jp502425a

Mukhametov, Azat; Newhouse, E. Irene; Ab Aziz, Nurohaida; Saito, Jennifer A.; Alam, Maqsudul
Allosteric pocket of the dengue virus (serotype 2) NS2B/NS3 protease: In silico ligand screening and molecular dynamics studies of inhibition
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 52:103-113, JUL 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.06.008

Lisse, Thomas S.; Vadivel, Kanagasabai; Bajaj, S. Paul; Zhou, Rui; Chun, Rene F.; Hewison, Martin; Adams, John S.
The heterodimeric structure of heterogeneous nuclear ribonucleoprotein C1/C2 dictates 1,25-dihydroxyvitamin D-directed transcriptional events in osteoblasts
BONE RESEARCH, 2 Art. No. 14011, JUL 1 2014
abstract, full text, DOI:10.1038/boneres.2014.11

Modak, Brenda; Torres, Paulina; Mascayano, Carolina; Torres, Rene; Urzua, Alejandro; Valenzuela, Beatriz
Derivatives of 3H-spiro1-benzofuran-2, 1'-cyclohexanes: immunostimulants for veterinary use
BOLETIN LATINOAMERICANO Y DEL CARIBE DE PLANTAS MEDICINALES Y AROMATICAS, 13:375-380, JUL 2014
abstract, full text

Nevidimov, A. V.
Molecular dynamics simulation of reverse micelles: Standing problems after 25 years of research
RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B, 8:554-558, JUL 2014
abstract, full text, DOI:10.1134/S199079311404023X

Cardone, Giovanni; Moyer, Adam L.; Cheng, Naiqian; Thompson, Cynthia D.; Dvoretzky, Israel; Lowy, Douglas R.; Schiller, John T.; Steven, Alasdair C.; Buck, Christopher B.; Trus, Benes L.
Maturation of the Human Papillomavirus 16 Capsid
MBIO, 5 Art. No. e01104-14, JUL-AUG 2014
abstract, full text, DOI:10.1128/mBio.01104-14

Shen, Ning; Fan, Ye; Pamidighantam, Sudhakar
E-science infrastructures for molecular modeling and parametrization
JOURNAL OF COMPUTATIONAL SCIENCE, 5:576-589, JUL 2014
abstract, full text, DOI:10.1016/j.jocs.2014.01.005

Perez, Camilo; Faust, Belinda; Mehdipour, Ahmad Reza; Francesconi, Kevin A.; Forrest, Lucy R.; Ziegler, Christine
Substrate-bound outward-open state of the betaine transporter BetP provides insights into Na+ coupling
NATURE COMMUNICATIONS, 5 Art. No. 4231, JUL 2014
abstract, full text, DOI:10.1038/ncomms5231

Ricci, Maria; Spijker, Peter; Voitchovsky, Kislon
Water-induced correlation between single ions imaged at the solid-liquid interface
NATURE COMMUNICATIONS, 5 Art. No. 4400, JUL 2014
abstract, full text, DOI:10.1038/ncomms5400

Farelli, Jeremiah D.; Galvin, Brendan D.; Li, Zhiru; Liu, Chunliang; Aono, Miyuki; Garland, Megan; Hallett, Olivia E.; Causey, Thomas B.; Ali-Reynolds, Alana; Saltzberg, Daniel J.; Carlow, Clotilde K. S.; Dunaway-Mariano, Debra; Allen, Karen N.
Structure of the Trehalose-6-phosphate Phosphatase from Brugia malayi Reveals Key Design Principles for Anthelmintic Drugs
PLOS PATHOGENS, 10 Art. No. e1004245, JUL 2014
abstract, full text, DOI:10.1371/journal.ppat.1004245

Kumari, Rashmi; Kumar, Rajendra; Lynn, Andrew
g_mmpbsa-A GROMACS Tool for High-Throughput MM-PBSA Calculations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:1951-1962, JUL 2014
abstract, full text, DOI:10.1021/ci500020m

Campbell, Arthur J.; Lamb, Michelle L.; Joseph-McCarthy, Diane
Ensemble-Based Docking Using Biased Molecular Dynamics
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:2127-2138, JUL 2014
abstract, full text, DOI:10.1021/ci400729j

Mukherjee, Sanchita; Kundu, Sangeeta; Bhattacharyya, Dhananjay
Temperature effect on poly(dA).poly(dT): molecular dynamics simulation studies of polymeric and oligomeric constructs
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:735-749, JUL 2014
abstract, full text, DOI:10.1007/s10822-014-9755-x

Faginas-Lago, Noelia; Alberti, Margarita; Costantini, Alessandro; Lagana, Antonio; Lombardi, Andrea; Pacifici, Leonardo
An innovative synergistic grid approach to the computational study of protein aggregation mechanisms
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2226, JUL 2014
abstract, full text, DOI:10.1007/s00894-014-2226-4

You, Yong; Liu, Fang; Du, Ke-Jie; Wen, Ge-Bo; Lin, Ying-Wu
Structural and functional alterations of myoglobin by glucose-protein interactions
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2358, JUL 2014
abstract, full text, DOI:10.1007/s00894-014-2358-6

Kossmann, Bradley; Ivanov, Ivaylo
Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003704, JUL 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003704

Lonsdale, Richard; Rouse, Sarah L.; Sansom, Mark S. P.; Mulholland, Adrian J.
A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003714, JUL 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003714

Sun, Huiyong; Li, Youyong; Tian, Sheng; Wang, Junmei; Hou, Tingjun
P-loop Conformation Governed Crizotinib Resistance in G2032R-Mutated ROS1 Tyrosine Kinase: Clues from Free Energy Landscape
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003729, JUL 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003729

Chen, Rong; Chung, Shin-Ho
Binding Modes of Two Scorpion Toxins to the Voltage-Gated Potassium Channel Kv1.3 Revealed from Molecular Dynamics
TOXINS, 6:2149-2161, JUL 2014
abstract, full text, DOI:10.3390/toxins6072149

Bucci, Anthony; Abrams, Cameron F.
Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2668-2676, JUL 2014
abstract, full text, DOI:10.1021/ct500088z

Comer, Jeffrey; Schulten, Klaus; Chipot, Christophe
Diffusive Models of Membrane Permeation with Explicit Orientational Freedom
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2710-2718, JUL 2014
abstract, full text, TCBG publications, DOI:10.1021/ct500209j

Ge, Zhenpeng; Li, Quan; Wang, Yi
Free Energy Calculation of Nanodiamond-Membrane Association-The Effect of Shape and Surface Functionalization
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2751-2758, JUL 2014
abstract, full text, DOI:10.1021/ct500194s

Roy, Amitava; Hua, Duy P.; Ward, Joshua M.; Post, Carol Beth
Relative Binding Enthalpies from Molecular Dynamics Simulations Using a Direct Method
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2759-2768, JUL 2014
abstract, full text, DOI:10.1021/ct500200n

Procacci, Piero; Cardelli, Chiara
Fast Switching Alchemical Transformations in Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2813-2823, JUL 2014
abstract, full text, DOI:10.1021/ct500142c

Hazel, Anthony; Chipot, Christophe; Gumbart, James C.
Thermodynamics of Deca-alanine Folding in Water
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2836-2844, JUL 2014
abstract, full text, DOI:10.1021/ct5002076

Ye, Jun; Nadar, S. Venkadesh; Li, Jiaojiao; Rosen, Barry P.
Structure of Escherichia coli Grx2 in complex with glutathione: a dual-function hybrid of glutaredoxin and glutathione S-transferase
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70:1907-1913, JUL 2014
abstract, full text, DOI:10.1107/S1399004714009250

Taxt, Arne M.; Diaz, Yuleima; Bacle, Amelie; Grauffel, Cedric; Reuter, Nathalie; Aasland, Rein; Sommerfelt, Halvor; Puntervoll, Pal
Characterization of Immunological Cross-Reactivity between Enterotoxigenic Escherichia coli Heat-Stable Toxin and Human Guanylin and Uroguanylin
INFECTION AND IMMUNITY, 82:2913-2922, JUL 2014
abstract, full text, DOI:10.1128/IAI.01749-14

Hansen, Freja H.; Skjorringe, Tina; Yasmeen, Saiqa; Arends, Natascha V.; Sahai, Michelle A.; Erreger, Kevin; Andreassen, Thorvald F.; Holy, Marion; Hamilton, Peter J.; Neergheen, Viruna; Karlsborg, Merete; Newman, Amy H.; Pope, Simon; Heales, Simon J. R.; Friberg, Lars; Law, Ian; Pinborg, Lars H.; Sitte, Harald H.; Loland, Claus; Shi, Lei; Weinstein, Harel; Galli, Aurelio; Hjermind, Lena E.; Moller, Lisbeth B.; Gether, Ulrik
Missense dopamine transporter mutations associate with adult parkinsonism and ADHD
JOURNAL OF CLINICAL INVESTIGATION, 124:3107-3120, JUL 2014
abstract, full text, DOI:10.1172/JCI73778

Pessoa, Joao; Fonseca, Fatima; Furini, Simone; Morais-Cabral, Joao H.
Determinants of ligand selectivity in a cyclic nucleotide-regulated potassium channel
JOURNAL OF GENERAL PHYSIOLOGY, 144:39-52, JUL 2014
abstract, full text, DOI:10.1085/jgp.201311145

Salomone, Fabrizio; Breton, Marie; Leray, Isabelle; Cardarelli, Francesco; Boccardi, Claudia; Bonhenry, Daniel; Tarek, Mounir; Mir, Lluis M.; Beltram, Fabio
High-Yield Nontoxic Gene Transfer through Conjugation of the CM18-Tat(11) Chimeric Peptide with Nanosecond Electric Pulses
MOLECULAR PHARMACEUTICS, 11:2466-2474, JUL 2014
abstract, full text, DOI:10.1021/mp500223t

Arenas, F. A.; Leal, C. A.; Pinto, C. A.; Arenas-Salinas, M. A.; Morales, W. A.; Cornejo, F. A.; Diaz-Vasquez, W. A.; Vasquez, C. C.
On the mechanism underlying tellurite reduction by Aeromonas caviae ST dihydrolipoamide dehydrogenase
BIOCHIMIE, 102C:174-182, JUL 2014
abstract, full text, DOI:10.1016/j.biochi.2014.03.008

Bai, Qifeng; Shen, Yulin; Jin, Nengzhi; Liu, Huanxiang; Yao, Xiaojun
Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:2128-2138, JUL 2014
abstract, full text, DOI:10.1016/j.bbagen.2014.03.010

Vogel, Alexander; Scheidt, Holger A.; Feller, Scott E.; Metso, Jari; Badeau, Robert M.; Tikkanen, Matti J.; Wahala, Kristiina; Jauhiainen, Matti; Huster, Daniel
The Orientation and Dynamics of Estradiol and Estradiol Oleate in Lipid Membranes and HDL Disc Models
BIOPHYSICAL JOURNAL, 107:114-125, JUL 1 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.060

Aitha, Mahesh; Richmond, Timothy K.; Hu, Zhenxin; Hetrick, Alyssa; Reese, Raquel; Gunther, Althea; McCarrick, Robert; Bennett, Brian; Crowder, Michael W.
Dilution of dipolar interactions in a spin-labeled, multimeric metalloenzyme for DEER studies
JOURNAL OF INORGANIC BIOCHEMISTRY, 136:40-46, JUL 2014
abstract, full text, DOI:10.1016/j.jinorgbio.2014.03.010

Jennings, Gareth K.; Modi, Anuja; Elenewski, Justin E.; Ritchie, Caroline M.; Thuy Nguyen; Ellis, Keith C.; Hackett, John C.
Spin equilibrium and O-2-binding kinetics of Mycobacterium tuberculosis CYP51 with mutations in the histidine-threonine dyad
JOURNAL OF INORGANIC BIOCHEMISTRY, 136:81-91, JUL 2014
abstract, full text, DOI:10.1016/j.jinorgbio.2014.03.017

Grunzke, Richard; Breuers, Sebastian; Gesing, Sandra; Herres-Pawlis, Sonja; Kruse, Martin; Blunk, Dirk; de la Garza, Luis; Packschies, Lars; Schaefer, Patrick; Schaerfe, Charlotta; Schlemmer, Tobias; Steinke, Thomas; Schuller, Bernd; Mueller-Pfefferkorn, Ralph; Jaekel, Rene; Nagel, Wolfgang E.; Atkinson, Malcolm; Krueger, Jens
Standards-based metadata management for molecular simulations
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 26:1744-1759, JUL 2014
abstract, full text, DOI:10.1002/cpe.3116

Cui, Di; Ou, Shuching; Patel, Sandeep
Free energetics of rigid body association of ubiquitin binding domains: A biochemical model for binding mediated by hydrophobic interaction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:1453-1468, JUL 2014
abstract, full text, DOI:10.1002/prot.24513

Jackson, Colin J.; Coppin, Christopher W.; Carr, Paul D.; Aleksandrov, Alexey; Wilding, Matthew; Sugrue, Elena; Ubels, Joanna; Paks, Michael; Newman, Janet; Peat, Thomas S.; Russell, Robyn J.; Field, Martin; Weik, Martin; Oakeshott, John G.; Scott, Colin
300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme Stabilization
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80:4003-4011, JUL 2014
abstract, full text, DOI:10.1128/AEM.00916-14

Mueller, Gerald; Benkhai, Hicham; Matthes, Rutger; Finke, Birgit; Friedrichs, Wenke; Geist, Norman; Langel, Walter; Kramer, Axel
Poly (hexamethylene biguanide) adsorption on hydrogen peroxide treated Ti-Al-V alloys and effects on wettability, antimicrobial efficacy, and cytotoxicity
BIOMATERIALS, 35:5261-5277, JUL 2014
abstract, full text, DOI:10.1016/j.biometerials.2014.03.033

Moon, Jun Hyuk; Katha, Anki Reddy; Pandian, Shanthi; Kolake, Subramanya Mayya; Han, Sungsoo
Polyamide-POSS hybrid membranes for seawater desalination: Effect of POSS inclusion on membrane properties
JOURNAL OF MEMBRANE SCIENCE, 461:89-95, JUL 1 2014
abstract, full text, DOI:10.1016/j.memsci.2014.03.004

Wise, Olivia; Coskuner, Orkid
New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1278-1289, JUN 30 2014
abstract, full text, DOI:10.1002/jcc.23622

Panshenskov, Mikhail; Solov'yov, Ilia A.; Solov'yov, Andrey V.
Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1317-1329, JUN 30 2014
abstract, full text, DOI:10.1002/jcc.23613

Xia, Bo; Liu, Yinling; Li, Wei; Brice, Allyn R.; Dominy, Brian N.; Cao, Weiguo
Specificity and Catalytic Mechanism in Family 5 Uracil DNA Glycosylase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:18413-18426, JUN 27 2014
abstract, full text, DOI:10.1074/jbc.M114.567354

Zhang, Mingzhen; Hu, Rundong; Liang, Guizhao; Chang, Yung; Sun, Yan; Peng, Zhenmeng; Zheng, Jie
Structural and Energetic Insight into the Cross-Seeding Amyloid Assemblies of Human IAPP and Rat IAPP
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7026-7036, JUN 26 2014
abstract, full text, DOI:10.1021/jp5022246

Bagai, Sampada; Sun, Chongbo; Tang, Tian
Lipid-Modified Polyethylenimine-Mediated DNA Attraction Evaluated by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:7070-7076, JUN 26 2014
abstract, full text, DOI:10.1021/jp503381r

Kamath, Ganesh; Cutler, Richard W.; Deshmukh, Sanket A.; Shakourian-Fard, Mehdi; Parrish, Riley; Huether, Joshua; Butt, Darryl P.; Xiong, H.; Sankaranarayanan, Subramanian K. R. S.
In Silico Based Rank-Order Determination and Experiments on Nonaqueous Electrolytes for Sodium Ion Battery Applications
JOURNAL OF PHYSICAL CHEMISTRY C, 118:13406-13416, JUN 26 2014
abstract, full text, DOI:10.1021/jp502319p

Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Svedas, Vytas
Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions
PLOS ONE, 9 Art. No. e100643, JUN 24 2014
abstract, full text, DOI:10.1371/journal.pone.0100643

Tossavainen, Helena; Kukkurainen, Sampo; Maatta, Juha A. E.; Kahkonen, Niklas; Pihlajamaa, Tero; Hytonen, Vesa P.; Kulomaa, Markku S.; Permi, Perttu
Chimeric Avidin - NMR Structure and Dynamics of a 56 kDa Homotetrameric Thermostable Protein
PLOS ONE, 9 Art. No. e100564, JUN 24 2014
abstract, full text, DOI:10.1371/journal.pone.0100564

Vitorovic-Todorovic, Maja D.; Koukoulitsa, Catherine; Juranic, Ivan O.; Mandic, Ljuba M.; Drakulic, Branko J.
Structural modifications of 4-aryl-4-oxo-2-aminylbutanamides and their acetyl- and butyrylcholinesterase inhibitory activity. Investigation of AChE-ligand interactions by docking calculations and molecular dynamics simulations
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 81:158-175, JUN 23 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.05.008

Yakubovich, Alexander V.; Solov'yov, Andrey V.
Quantitative thermodynamic model for globular protein folding
EUROPEAN PHYSICAL JOURNAL D, 68 Art. No. 145, JUN 23 2014
abstract, full text, DOI:10.1140/epjd/e2014-50097-3

Moore, Stan G.; Crozier, Paul S.
Extension and evaluation of the multilevel summation method for fast long-range electrostatics calculations
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 234112, JUN 21 2014
abstract, full text, DOI:10.1063/1.4883695

Scopelliti, Amanda J.; Heinzelmann, Germano; Kuyucak, Serdar; Ryan, Renae M.; Vandenberg, Robert J.
Na+ Interactions with the Neutral Amino Acid Transporter ASCT1
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:17468-17479, JUN 20 2014
abstract, full text, DOI:10.1074/jbc.M114.565242

Pandolfi, Ronald J.; Edwards, Lauren; Johnston, David; Becich, Peter; Hirst, Linda S.
Designing highly tunable semiflexible filament networks
PHYSICAL REVIEW E, 89 Art. No. 062602, JUN 20 2014
abstract, full text, DOI:10.1103/PhysRevE.89.062602

Goodman, J. S.; Chao, S. -H.; Pogorelov, T. V.; Gruebele, M.
Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding
JOURNAL OF PHYSICAL CHEMISTRY B, 118:6511-6518, JUN 19 2014
abstract, full text, DOI:10.1021/jp412459z

Savelyev, Alexey; MacKerell, Alexander D., Jr.
Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field
JOURNAL OF PHYSICAL CHEMISTRY B, 118:6742-6757, JUN 19 2014
abstract, full text, DOI:10.1021/jp503469s

Vukovic, Lela; Vokac, Elizabeth; Kral, Petr
Molecular Friction-Induced Electroosmotic Phenomena in Thin Neutral Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:2131-2137, JUN 19 2014
abstract, full text, DOI:10.1021/jz500761s

Rajeshwar, Rajitha T.; Smith, Jeremy C.; Krishnan, Marimuthu
Hidden Regularity and Universal Classification of Fast Side Chain Motions in Proteins
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:8590-8605, JUN 18 2014
abstract, full text, DOI:10.1021/ja5024783

Knott, Brandon C.; Crowley, Michael F.; Himmel, Michael E.; Stahlberg, Jerry; Beckham, Gregg T.
Carbohydrate-Protein Interactions That Drive Processive Polysaccharide Translocation in Enzymes Revealed from a Computational Study of Cellobiohydrolase Processivity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:8810-8819, JUN 18 2014
abstract, full text, DOI:10.1021/ja504074g

Sikdar, Samapan; Ghosh, Mahua; De Raychaudhury, Molly; Chakrabarti, J.
Quantum chemical studies on the role of residues in calcium ion binding to Calmodulin
CHEMICAL PHYSICS LETTERS, 605:103-107, JUN 17 2014
abstract, full text, DOI:10.1016/j.cplett.2014.05.017

Mielke, Clinton; Lefort, Natalie; McLean, Carrie G.; Cordova, Jeanine M.; Langlais, Paul R.; Bordner, Andrew J.; Te, Jerez A.; Ozkan, S. Banu; Willis, Wayne T.; Mandarino, Lawrence J.
Adenine Nucleotide Translocase Is Acetylated in Vivo in Human Muscle: Modeling Predicts a Decreased ADP Affinity and Altered Control of Oxidative Phosphorylation
BIOCHEMISTRY, 53:3817-3829, JUN 17 2014
abstract, full text, DOI:10.1021/bi401651e

Heinzelmann, Germano; Kuyucak, Serdar
Molecular Dynamics Simulations Elucidate the Mechanism of Proton Transport in the Glutamate Transporter EAAT3
BIOPHYSICAL JOURNAL, 106:2675-2683, JUN 17 2014
abstract, full text, DOI:10.1016/j.bpj.2014.05.010

Clingman, Carina C.; Deveau, Laura M.; Hay, Samantha A.; Genga, Ryan M.; Shandilya, Shivender M. D.; Massi, Francesca; Ryder, Sean P.
Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite
ELIFE, 3, JUN 16 2014
abstract, full text, DOI:10.7554/eLife.02848

Sinha, Sudipta K.; Saiz, Leonor
Determinants of protein-ligand complex formation in the thyroid hormone receptor alpha: A molecular dynamics simulation study
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1038:57-66, JUN 15 2014
abstract, full text, DOI:10.1016/j.comptc.2014.03.034

Savelyev, Alexey; MacKerell, Alexander D., Jr.
All- Atom Polarizable Force Field for DNA Based on the Classical Drude Oscillator Model
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1219-1239, JUN 15 2014
abstract, full text, DOI:10.1002/jcc.23611

Anoop, Arunagiri; Ranganathan, Srivastav; Das Dhaked, Bhagwan; Jha, Narendra Nath; Pratihar, Supriya; Ghosh, Saikat; Sahay, Shruti; Kumar, Santosh; Das, Subhadeep; Kombrabail, Mamata; Agarwal, Kumud; Jacob, Reeba S.; Singru, Praful; Bhaumik, Prasenjit; Padinhateeri, Ranjith; Kumar, Ashutosh; Maji, Samir K.
Elucidating the Role of Disulfide Bond on Amyloid Formation and Fibril Reversibility of Somatostatin-14 RELEVANCE TO ITS STORAGE AND SECRETION
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:16884-16903, JUN 13 2014
abstract, full text, DOI:10.1074/jbc.M114.548354

Mieda, Shunsuke; Ikeda, Atsushi; Shigeri, Yasushi; Shinoda, Wataru
Thermodynamic Stability of [60]Fullerene and gamma-Cyclodextrin Complex in Aqueous Solution: Free Energy Simulation
JOURNAL OF PHYSICAL CHEMISTRY C, 118:12555-12561, JUN 12 2014
abstract, full text, DOI:10.1021/jp5029905

Liu, Peng; Chipot, Christophe; Cai, Wensheng; Shao, Xueguang
Unveiling the Underlying Mechanism for Compression and Decompression Strokes of a Molecular Engine
JOURNAL OF PHYSICAL CHEMISTRY C, 118:12562-12567, JUN 12 2014
abstract, full text, DOI:10.1021/jp503241p

Belorusova, Anna Y.; Eberhardt, Jerome; Potier, Noelle; Stote, Roland H.; Dejaegere, Annick; Rochel, Natacha
Structural Insights into the Molecular Mechanism of Vitamin D Receptor Activation by Lithocholic Acid Involving a New Mode of Ligand Recognition
JOURNAL OF MEDICINAL CHEMISTRY, 57:4710-4719, JUN 12 2014
abstract, full text, DOI:10.1021/jm5002524

Lasso, Gorka; Yu, Linda P. C.; Gil, David; Lazaro, Melisa; Tong, Liang; Valle, Mikel
Functional Conformations for Pyruvate Carboxylase during Catalysis Explored by Cryoelectron Microscopy
STRUCTURE, 22:911-922, JUN 10 2014
abstract, full text, DOI:10.1016/j.str.2014.04.011

Chen, Qu; Wang, Qi; Liu, Ying-Chun; Wu, Tao
The effect of hydrogen bonds on diffusion mechanism of water inside single-walled carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 214507, JUN 7 2014
abstract, full text, DOI:10.1063/1.4879796

Bernardi, Rafael C.; Cann, Isaac; Schulten, Klaus
Molecular dynamics study of enhanced Man5B enzymatic activity
BIOTECHNOLOGY FOR BIOFUELS, 7 Art. No. 83, JUN 5 2014
abstract, full text, TCBG publications, DOI:10.1186/1754-6834-7-83

Mahmood, Mohammed Arif I.; Ali, Waqas; Adnan, Ashfaq; Iqbal, Samir M.
3D Structural Integrity and Interactions of Single-Stranded Protein-Binding DNA in a Functionalized Nanopore
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5799-5806, JUN 5 2014
abstract, full text, DOI:10.1021/jp411820w

Suresh, Gorle; Priyakumar, U. Deva
Atomistic Investigation of the Effect of Incremental Modification of Deoxyribose Sugars by Locked Nucleic Acid (beta-D-LNA and alpha-L-LNA) Moieties on the Structures and Thermodynamics of DNA-RNA Hybrid Duplexes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5853-5863, JUN 5 2014
abstract, full text, DOI:10.1021/jp5014779

Subramanian, Deepa; Klauda, Jeffery B.; Collings, Peter J.; Anisimov, Mikhail A.
Mesoscale Phenomena in Ternary Solutions of Tertiary Butyl Alcohol, Water, and Propylene Oxide
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5994-6006, JUN 5 2014
abstract, full text, DOI:10.1021/jp4125183

Heldenbrand, Hugh; Janowski, Pawel A.; Giambasu, George; Giese, Timothy J.; Wedekind, Joseph E.; York, Darrin M.
Evidence for the Role of Active Site Residues in the Hairpin Ribozyme from Molecular Simulations along the Reaction Path
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:7789-7792, JUN 4 2014
abstract, full text, DOI:10.1021/ja500180q

Barrios, David A.; D'Antonio, Jennifer; McCombs, Nikolette L.; Zhao, Jing; Franzen, Stefan; Schmidt, Andreas C.; Sombers, Leslie A.; Ghiladi, Reza A.
Peroxygenase and Oxidase Activities of Dehaloperoxidase-Hemoglobin from Amphitrite ornata
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:7914-7925, JUN 4 2014
abstract, full text, DOI:10.1021/ja500293c

Watson, Max C.; Curtis, Joseph E.
Probing the Average Local Structure of Biomolecules Using Small-Angle Scattering and Scaling Laws
BIOPHYSICAL JOURNAL, 106:2474-2482, JUN 3 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.050

Sharma, Monika; Predeus, Alexander V.; Kovacs, Nicholas; Feig, Michael
Differential Mismatch Recognition Specificities of Eukaryotic MutS Homologs, MutS alpha and MutS beta
BIOPHYSICAL JOURNAL, 106:2483-2492, JUN 3 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.026

Wu, Emilia L.; Fleming, Patrick J.; Yeom, Min Sun; Widmalm, Goran; Klauda, Jeffery B.; Fleming, Karen G.; Im, Wonpil
E. coli Outer Membrane and Interactions with OmpLA
BIOPHYSICAL JOURNAL, 106:2493-2502, JUN 3 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.024

Chandler, Danielle E.; Struempfer, Johan; Sener, Melih; Scheuring, Simon; Schulten, Klaus
Light Harvesting by Lamellar Chromatophores in Rhodospirillum photometricum
BIOPHYSICAL JOURNAL, 106:2503-2510, JUN 3 2014
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2014.04.030

Emileh, Ali; Duffy, Caitlin; Holmes, Andrew P.; Bastian, Arangassery Rosemary; Aneja, Rachna; Tuzer, Ferit; Rajagopal, Srivats; Li, Huiyuan; Abrams, Cameron F.; Chaiken, Irwin M.
Covalent Conjugation of a Peptide Triazole to HIV-1 gp120 Enables Intramolecular Binding Site Occupancy
BIOCHEMISTRY, 53:3403-3414, JUN 3 2014
abstract, full text, DOI:10.1021/bi500136f

Vukovic, Lela; Koh, Hye Ran; Myong, Sua; Schulten, Klaus
Substrate Recognition and Specificity of Double-Stranded RNA Binding Proteins
BIOCHEMISTRY, 53:3457-3466, JUN 3 2014
abstract, full text, TCBG publications, DOI:10.1021/bi500352s

Rimmert, Bradley; Sabet, Salwa; Ackad, Edward; Yousef, Mohammad S.
A 3D structural model and dynamics of hepatitis C virus NS3/4A protease (genotype 4a, strain ED43) suggest conformational instability of the catalytic triad: implications in catalysis and drug resistivity
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:950-958, JUN 3 2014
abstract, full text, DOI:10.1080/07391102.2013.800001

Negureanu, Lacramioara; Salsbury, Freddie R., Jr.
Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutS alpha-DNA recognition complex
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:969-992, JUN 3 2014
abstract, full text, DOI:10.1080/07391102.2013.799437

Wang, Beibei; Weng, Jingwei; Wang, Wenning
Free energy profiles of ion permeation and doxorubicin translocation in TolC
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 13 Art. No. 1450031, JUN 2014
abstract, full text, DOI:10.1142/S021963361450031X

Blacklock, Kristin; Verkhivker, Gennady M.
Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003679, JUN 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003679

Khrenova, Maria G.; Nemukhin, Alexander V.; Grigorenko, Bella L.; Wang, Peng; Zhang, Jian-Ping
All-atom structures and calcium binding sites of the bacterial photosynthetic LH1-RC core complex from Thermochromatium tepidum
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2287, JUN 2014
abstract, full text, DOI:10.1007/s00894-014-2287-4

Kucukkal, Tugba G.; Yang, Ye; Chapman, Susan C.; Cao, Weiguo; Alexov, Emil
Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 15:9670-9717, JUN 2014
abstract, full text, DOI:10.3390/ijms15069670

Gentili, D.; Bolognesi, G.; Giacomello, A.; Chinappi, M.; Casciola, C. M.
Pressure effects on water slippage over silane-coated rough surfaces: pillars and holes
MICROFLUIDICS AND NANOFLUIDICS, 16:1009-1018, JUN 2014
abstract, full text, DOI:10.1007/s10404-014-1376-0

Oliveira, Denilson F.; dos Santos Junior, Helvecio M.; Nunes, Alexandro S.; Campos, Vicente P.; de Pinho, Renata S. C.; Gajo, Giovanna C.
Purification and identification of metabolites produced by Bacillus cereus and B. subtilis active against Meloidogyne exigua, and their in silico interaction with a putative phosphoribosyltransferase from M. incognita
ANAIS DA ACADEMIA BRASILEIRA DE CIENCIAS, 86:525-538, JUN 2014
abstract, full text, DOI:10.1590/0001-3765201402412

Ding, Jin-Hong; Li, Ning; Wang, Man-Liu; Zhang, Yan; Lu, Shou-Qin; Long, Mian
The impact of N-terminal phosphorylation on LHCII conformation in state transition
ACTA MECHANICA SINICA, 30:447-456, JUN 2014
abstract, full text, DOI:10.1007/s10409-014-0044-7

Clark, Richard; Takeda, Kyozaburo
Multistage conformational transition in peptide nanotube induced by temperature and/or external electric field
JAPANESE JOURNAL OF APPLIED PHYSICS, 53 Art. No. 065201, JUN 2014
abstract, full text, DOI:10.7567/JJAP.53.065201

Ling, Zhenmin; Kang, Zhen; Liu, Yi; Liu, Song; Chen, Jian; Du, Guocheng
Improvement of catalytic efficiency and thermostability of recombinant Streptomyces griseus trypsin by introducing artificial peptide
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, 30:1819-1827, JUN 2014
abstract, full text, DOI:10.1007/s11274-014-1608-1

Pietra, Francesco
Binding Pockets and Permeation Channels for Dioxygen through Cofactorless 3-Hydroxy-2-methylquinolin-4-one 2,4-Dioxygenase in Association with Its Natural Substrate, 3-Hydroxy-2-methylquinolin-4(1H)-one. A Perspective from Molecular Dynamics Simulations
CHEMISTRY & BIODIVERSITY, 11:861-871, JUN 2014
abstract, full text, DOI:10.1002/cbdv.201400054

de Buyl, Pierre; Colberg, Peter H.; Hoefling, Felix
H5MD: A structured, efficient, and portable file format for molecular data
COMPUTER PHYSICS COMMUNICATIONS, 185:1546-1553, JUN 2014
abstract, full text, DOI:10.1016/j.cpc.2014.01.018

Thibault, Julien C.; Cheatham, Thomas E., I.I.I.; Facelli, Julio C.
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:1810-1819, JUN 2014
abstract, full text, DOI:10.1021/ci500173w

Yu Tao; Guo Xu; Zou Xian-Wu; Sang Jian-Ping
Ion Binding Energies Determining Functional Transport of ClC Proteins
CHINESE PHYSICS LETTERS, 31 Art. No. 068701, JUN 2014
abstract, full text, DOI:10.1088/0256-307X/31/6/068701

Martinez-Olivan, Juan; Rozado-Aguirre, Zurine; Arias-Moreno, Xabier; Angarica, Vladimir E.; Velazquez-Campoy, Adrian; Sancho, Javier
Low-density lipoprotein receptor is a calcium/magnesium sensor-role of LR4 and LR5 ion interaction kinetics in low-density lipoprotein release in the endosome
FEBS JOURNAL, 281:2638-2658, JUN 2014
abstract, full text, DOI:10.1111/febs.12811

Krueger, Jens; Grunzke, Richard; Gesing, Sandra; Breuers, Sebastian; Brinkmann, Andre; de la Garza, Luis; Kohlbacher, Oliver; Kruse, Martin; Nagel, Wolfgang E.; Packschies, Lars; Mueller-Pfefferkorn, Ralph; Schaefer, Patrick; Schaerfe, Charlotta; Steinke, Thomas; Schlemmer, Tobias; Warzecha, Klaus Dieter; Zink, Andreas; Herres-Pawlis, Sonja
The MoSGrid Science Gateway - A Complete Solution for Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2232-2245, JUN 2014
abstract, full text, DOI:10.1021/ct500159h

Jiang, Jianfei; Bakan, Ahmet; Kapralov, Alexandr A.; Silva, K. Ishara; Huang, Zhentai; Amoscato, Andrew A.; Peterson, James; Garapati, Venkata Krishna; Saxena, Sunil; Bayir, Huelya; Atkinson, Jeffrey; Bahar, Ivet; Kagan, Valerian E.
Designing inhibitors of cytochrome c/cardiolipin peroxidase complexes: mitochondria-targeted imidazole-substituted fatty acids
FREE RADICAL BIOLOGY AND MEDICINE, 71:221-230, JUN 2014
abstract, full text, DOI:10.1016/j.freeradbiomed.2014.02.029

Azamat, Jafar; Sardroodi, Jaber Jahanbin
The permeation of potassium and chloride ions through nanotubes: a molecular simulation study
MONATSHEFTE FUR CHEMIE, 145:881-890, JUN 2014
abstract, full text, DOI:10.1007/s00706-013-1136-y

Yennamalli, Ragothaman; Arangarasan, Raj; Bryden, Aaron; Gleicher, Michael; Phillips, George N., Jr.
Using a commodity high-definition television for collaborative structural biology
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 47:1153-1157, JUN 2014
abstract, full text, DOI:10.1107/S160057671400939X

Imtong, Chompounoot; Kanchanawarin, Chalermpol; Katzenmeier, Gerd; Angsuthanasombat, Chanan
Bacillus thuringiensis Cry4Aa insecticidal protein: Functional importance of the intrinsic stability of the unique alpha 4-alpha 5 loop comprising the Pro-rich sequence
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844:1111-1118, JUN 2014
abstract, full text, DOI:10.1016/j.bbapap.2014.03.003

Abriata, Luciano A.; Vila, Alejandro J.; Dal Peraro, Matteo
Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 19:565-575, JUN 2014
abstract, full text, DOI:10.1007/s00775-014-1108-7

Ortiz, Ernesto; Rendon-Anaya, Martha; Rego, Solange Cristina; Schwartz, Elisabeth Ferroni; Domingos Possani, Lourival
Antarease-like Zn-metalloproteases are ubiquitous in the venom of different scorpion genera
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:1738-1746, JUN 2014
abstract, full text, DOI:10.1016/j.bbagen.2013.12.012

Morrison, Ann Michelle Stanley; Goldstone, Jared V.; Lamb, David C.; Kubota, Akira; Lemaire, Benjamin; Stegeman, John J.
Identification, modeling and ligand affinity of early deuterostome CYP51s, and functional characterization of recombinant zebrafish sterol 14 alpha-demethylase
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1840:1825-1836, JUN 2014
abstract, full text, DOI:10.1016/j.bbagen.2013.12.009

Mutis, A.; Palma, R.; Venthur, H.; Iturriaga-Vasquez, P.; Faundez-Parraguez, M.; Mella-Herrera, R.; Kontodimas, D.; Lobos, C.; Quiroz, A.
Molecular Characterization and In Silico Analysis of the Pheromone-Binding Protein of the European Grapevine Moth Lobesia botrana (Denis & Schiffermuller) (Lepidoptera, Tortricidae)
NEOTROPICAL ENTOMOLOGY, 43:266-275, JUN 2014
abstract, full text, DOI:10.1007/s13744-014-0212-2

Tsai, Hui-Hsu Gavin; Chang, Che-Ming; Lee, Jian-Bin
Multi-step formation of a hemifusion diaphragm for vesicle fusion revealed by all-atom molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1529-1535, JUN 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.01.018

Fujita, Takatoshi; Huh, Joonsuk; Saikin, Semion K.; Brookes, Jennifer C.; Aspuru-Guzik, Alan
Theoretical characterization of excitation energy transfer in chlorosome light-harvesting antennae from green sulfur bacteria
PHOTOSYNTHESIS RESEARCH, 120:273-289, JUN 2014
abstract, full text, DOI:10.1007/s11120-014-9978-7

Sencanski, Milan; Dosen-Micovic, Ljiljana
In Silico Study of the Structurally Similar ORL1 Receptor Agonist and Antagonist Pairs Reveal Possible Mechanism of Receptor Activation
PROTEIN JOURNAL, 33:231-242, JUN 2014
abstract, full text, DOI:10.1007/s10930-014-9555-0

Jung, Jaewoon; Mori, Takaharu; Sugita, Yuji
Midpoint Cell Method for Hybrid ( MPI1OpenMP) Parallelization of Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:1064-1072, MAY 30 2014
abstract, full text, DOI:10.1002/jcc.23591

Wang, Zunliang; Han, Xiaofeng; He, Nongyue; Chen, Zhan; Brooks, Charles L., I.I.I.
Molecular Structures of C- and N-Terminus Cysteine Modified Cecropin P1 Chemically Immobilized onto Maleimide-Terminated Self-Assembled Mono layers Investigated by Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5670-5680, MAY 29 2014
abstract, full text, DOI:10.1021/jp5023482

Lee, Cheng-Kuang; Pao, Chun-Wei
Nanomorphology Evolution of P3HT/PCBM Blends during Solution-Processing from Coarse-Grained Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY C, 118:11224-11233, MAY 29 2014
abstract, full text, DOI:10.1021/jp501323p

Huang, Yu-ming M.; Chang, Chia-en A.
Achieving Peptide Binding Specificity and Promiscuity by Loops: Case of the Forkhead-Associated Domain
PLOS ONE, 9 Art. No. e98291, MAY 28 2014
abstract, full text, DOI:10.1371/journal.pone.0098291

Sun, Xiaotian; Feng, Zhiwei; Hou, Tingjun; Li, Youyong
Mechanism of Graphene Oxide as an Enzyme Inhibitor from Molecular Dynamics Simulations
ACS APPLIED MATERIALS & INTERFACES, 6:7153-7163, MAY 28 2014
abstract, full text, DOI:10.1021/am500167c

Mazack, Michael J. M.; Gao, Jiali
Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 204501, MAY 28 2014
abstract, full text, DOI:10.1063/1.4875922

Zorba, Adelajda; Buosi, Vanessa; Kutter, Steffen; Kern, Nadja; Pontiggia, Francesco; Cho, Young-Jin; Kern, Dorothee
Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2
ELIFE, 3 Art. No. e02667, MAY 27 2014
abstract, full text, DOI:10.7554/eLife.02667

Spiga, Enrico; Abriata, Luciano A.; Piazza, Francesco; Dal Peraro, Matteo
Dissecting the Effects of Concentrated Carbohydrate Solutions on Protein Diffusion, Hydration, and Internal Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5310-5321, MAY 22 2014
abstract, full text, DOI:10.1021/jp4126705

Kumazaki, Kaoru; Chiba, Shinobu; Takemoto, Mizuki; Furukawa, Arata; Nishiyama, Ken-ichi; Sugano, Yasunori; Mori, Takaharu; Dohmae, Naoshi; Hirata, Kunio; Nakada-Nakura, Yoshiko; Maturana, Andres D.; Tanaka, Yoshiki; Mori, Hiroyuki; Sugita, Yuji; Arisaka, Fumio; Ito, Koreaki; Ishitani, Ryuichiro; Tsukazaki, Tomoya; Nureki, Osamu
Structural basis of Sec-independent membrane protein insertion by YidC
NATURE, 509:516-+, MAY 22 2014
abstract, full text, DOI:10.1038/nature13167

Kuttel, Michelle; Gordon, Marc; Ravenscroft, Neil
Comparative simulation of pneumococcal serogroup 19 polysaccharide repeating units with two carbohydrate force fields
CARBOHYDRATE RESEARCH, 390:20-27, MAY 22 2014
abstract, full text, DOI:10.1016/j.carres.2014.02.026

Furini, Simone; Barbini, Paolo; Domene, Carmen
Effects of the Protonation State of the EEEE Motif of a Bacterial Na+-channel on Conduction and Pore Structure
BIOPHYSICAL JOURNAL, 106:2175-2183, MAY 20 2014
abstract, full text, DOI:10.1016/j.bpj.2014.04.005

Olivier, Yoann; Muccioli, Luca; Zannoni, Claudio
Quinquephenyl: The Simplest Rigid-Rod-Like Nematic Liquid Crystal, or is it? An Atomistic Simulation
CHEMPHYSCHEM, 15:1345-1355, MAY 19 2014
abstract, full text, DOI:10.1002/cphc.201301126

Pizzirusso, Antonio; Di Pietro, Maria Enrica; De Luca, Giuseppina; Celebre, Giorgio; Longeri, Marcello; Muccioli, Luca; Zannoni, Claudio
Order and Conformation of Biphenyl in Cyanobiphenyl Liquid Crystals: A Combined Atomistic Molecular Dynamics and H-1 NMR Study
CHEMPHYSCHEM, 15:1356-1367, MAY 19 2014
abstract, full text, DOI:10.1002/cphc.201400082

Abad, Enrique; Rommel, Judith B.; Kaestner, Johannes
Reaction Mechanism of the Bicopper Enzyme Peptidylglycine alpha-Hydroxylating Monooxygenase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:13726-13738, MAY 16 2014
abstract, full text, DOI:10.1074/jbc.M114.558494

Mahalingam, Bhuvaneshwari; Van Agthoven, Johannes F.; Xiong, Jian-Ping; Alonso, Jose Luis; Adair, Brian D.; Rui, Xianliang; Anand, Saurabh; Mehrbod, Mehrdad; Mofrad, Mohammad R. K.; Burger, Christa; Goodman, Simon L.; Arnaout, M. Amin
Atomic Basis for the Species-specific Inhibition of alpha V Integrins by Monoclonal Antibody 17E6 Is Revealed by the Crystal Structure of alpha V beta 3 Ectodomain-17E6 Fab Complex
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:13801-13809, MAY 16 2014
abstract, full text, DOI:10.1074/jbc.M113.546929

Korneeva, Vera A.; Trubetskov, Mikhail M.; Korshunova, Alena V.; Lushchekina, Sofya V.; Kolyadko, Vladimir N.; Sergienko, Olga V.; Lunin, Vladimir G.; Panteleev, Mikhail A.; Ataullakhanov, Fazoil I.
Interactions Outside the Proteinase-binding Loop Contribute Significantly to the Inhibition of Activated Coagulation Factor XII by Its Canonical Inhibitor from Corn
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:14109-14120, MAY 16 2014
abstract, full text, DOI:10.1074/jbc.M114.553735

Casanovas, J.; Revilla-Lopez, G.; Bertran, O.; del Valle, L. J.; Turon, P.; Puiggali, J.; Aleman, C.
Restricted Puckering of Mineralized RNA-Like Riboses
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5075-5081, MAY 15 2014
abstract, full text, DOI:10.1021/jp501714q

Gc, Jeevan B.; Bhandari, Yuba R.; Gerstman, Bernard S.; Chapagain, Prem P.
Molecular Dynamics Investigations of the alpha-Helix to beta-Barrel Conformational Transformation in the RfaH Transcription Factor
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5101-5108, MAY 15 2014
abstract, full text, DOI:10.1021/jp502193v

Hansen, Sara K.; Vestergaard, Mikkel; Thogersen, Lea; Schiott, Birgit; Nielsen, Niels Chr.; Vosegaard, Thomas
Lipid Dynamics Studied by Calculation of P-31 Solid-State NMR Spectra Using Ensembles from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:5119-5129, MAY 15 2014
abstract, full text, DOI:10.1021/jp5000304

Wang, Kefeng; Leng, Yang; Lu, Xiong; Ren, Fuzeng
Molecular dynamics simulation of protein effects on interfacial energy between HA surfaces and solutions
MATERIALS LETTERS, 123:191-194, MAY 15 2014
abstract, full text, DOI:10.1016/j.matlet.2014.02.089

Zhang, Cunzheng; Wang, Li; Tu, Zhui; Sun, Xing; He, Qinghua; Lei, Zhaojing; Xu, Chongxin; Liu, Yuan; Zhang, Xiao; Yang, Jingyi; Liu, Xianjin; Xu, Yang
Organophosphorus pesticides detection using broad-specific single-stranded DNA based fluorescence polarization aptamer assay
BIOSENSORS & BIOELECTRONICS, 55:216-219, MAY 15 2014
abstract, full text, DOI:10.1016/j.bios.2013.12.020

Tempkin, Jeremy O. B.; Qi, Bo; Saunders, Marissa G.; Roux, Benoit; Dinner, Aaron R.; Weare, Jonathan
Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 184114, MAY 14 2014
abstract, full text, DOI:10.1063/1.4872021

Hu, Rundong; Zhang, Mingzhen; Patel, Kunal; Wang, Qiuming; Chang, Yung; Gong, Xiong; Zhang, Ge; Zheng, Jie
Cross-Sequence Interactions between Human and Rat Islet Amyloid Polypeptides
LANGMUIR, 30:5193-5201, MAY 13 2014
abstract, full text, DOI:10.1021/la500632d

Kaila, Ville R. I.; Wikstrom, Marten; Hummer, Gerhard
Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:6988-6993, MAY 13 2014
abstract, full text, DOI:10.1073/pnas.1319156111

Cheng, Dong-Qiang; Li, Ying; Huang, Jing-Fei
Molecular Evolution of the Primate alpha-/theta-Defensin Multigene Family
PLOS ONE, 9 Art. No. e97425, MAY 12 2014
abstract, full text, DOI:10.1371/journal.pone.0097425

Zeytuni, Natalie; Uebe, Rene; Maes, Michal; Davidov, Geula; Baram, Michal; Raschdorf, Oliver; Friedler, Assaf; Miller, Yifat; Schueler, Dirk; Zarivach, Raz
Bacterial Magnetosome Biomineralization - A Novel Platform to Study Molecular Mechanisms of Human CDF-Related Type-II Diabetes
PLOS ONE, 9 Art. No. e97154, MAY 12 2014
abstract, full text, DOI:10.1371/journal.pone.0097154

Nibali, Valeria Conti; D'Angelo, Giovanna; Tarek, Mounir
Molecular dynamics simulation of short-wavelength collective dynamics of phospholipid membranes
PHYSICAL REVIEW E, 89 Art. No. 050301, MAY 12 2014
abstract, full text, DOI:10.1103/PhysRevE.89.050301

Gamble, Trevor; Decker, Karl; Plett, Timothy S.; Pevarnik, Matthew; Pietschmann, Jan-Frederik; Vlassiouk, Ivan; Aksimentiev, Aleksei; Siwy, Zuzanna S.
Rectification of Ion Current in Nanopores Depends on the Type of Monovalent Cations: Experiments and Modeling
JOURNAL OF PHYSICAL CHEMISTRY C, 118:9809-9819, MAY 8 2014
abstract, full text, DOI:10.1021/jp501492g

Midya, Uday Sankar; Bandyopadhyay, Sanjoy
Hydration Behavior at the Ice-Binding Surface of the Tenebrio molitor Antifreeze Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4743-4752, MAY 8 2014
abstract, full text, DOI:10.1021/jp412528b

Harrach, Michael F.; Drossel, Barbara
Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 174501, MAY 7 2014
abstract, full text, DOI:10.1063/1.4872239

Ovchinnikov, Victor; Karplus, Martin
Investigations of alpha-helix <->beta-sheet transition pathways in a miniprotein using the finite-temperature string method
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 175103, MAY 7 2014
abstract, full text, DOI:10.1063/1.4871685

Nocek, Boguslaw; Starus, Anna; Makowska-Grzyska, Magdalena; Gutierrez, Blanca; Sanchez, Stephen; Jedrzejczak, Robert; Mack, Jamey C.; Olsen, Kenneth W.; Joachimiak, Andrzej; Holz, Richard C.
The Dimerization Domain in DapE Enzymes Is required for Catalysis
PLOS ONE, 9 Art. No. e93593, MAY 7 2014
abstract, full text, DOI:10.1371/journal.pone.0093593

Henin, Jerome; Salari, Reza; Murlidaran, Sruthi; Brannigan, Grace
A Predicted Binding Site for Cholesterol on the GABA(A) Receptor
BIOPHYSICAL JOURNAL, 106:1938-1949, MAY 6 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.024

Kumar, Raj; Kukreja, Roshan V.; Li, Li; Zhmurov, Artem; Kononova, Olga; Cai, Shuowei; Ahmed, Syed A.; Barsegov, Valeri; Singh, Bal Ram
Botulinum neurotoxin: unique folding of enzyme domain of the most-poisonous poison
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:804-815, MAY 4 2014
abstract, full text, DOI:10.1080/07391102.2013.791878

Bernini, Caterina; Pogni, Rebecca; Basosi, Riccardo; Sinicropi, Adalgisa
Prediction of hydrogen-bonding networks around tyrosyl radical in P. eryngii versatile peroxidase W164Y variants: a QM/MMMD study
MOLECULAR SIMULATION, 40:485-490, MAY 3 2014
abstract, full text, DOI:10.1080/08927022.2013.822967

Chen, Xin; Zhu, Shuyan; Wang, Shoubin; Yang, Dagang; Zhang, Jinglai
Molecular dynamics study on the stability of wild-type and the R220K mutant of human prion protein
MOLECULAR SIMULATION, 40:504-513, MAY 3 2014
abstract, full text, DOI:10.1080/08927022.2013.824572

Kaczmarski, Joe A.; Corry, Ben
Investigating the size and dynamics of voltage-gated sodium channel fenestrations A molecular dynamics study
CHANNELS, 8, MAY-JUN 2014
abstract, full text, DOI:10.4161/chan.28136

Zaraiskaya, Tatiana; Vassiliev, Sergey; Bruce, Doug
Discovering oxygen channel topology in photosystem II using implicit ligand sampling and wavefront propagation
JOURNAL OF COMPUTATIONAL SCIENCE, 5:549-555, MAY 2014
abstract, full text, DOI:10.1016/j.jocs.2013.10.001

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
Modelling and enhanced molecular dynamics to steer structure-based drug discovery
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 114:123-136, MAY 2014
abstract, full text, DOI:10.1016/j.pbiomolbio.2013.06.004

LeVine, Michael V.; Weinstein, Harel
NbIT - A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003603, MAY 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003603

Randjelovic, Jelena; Eric, Slavica; Savic, Vladimir
In silico design of small molecule inhibitors of CDK9/cyclin T1 interaction
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 50:100-112, MAY 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.04.002

Asciutto, Eliana K.; Gaborek, Timothy; Madura, Jeffry D.
Sodium versus potassium effects on the glutamic acid side-chains interaction on a heptapeptide
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 13 Art. No. 1440004, MAY 2014
abstract, full text, DOI:10.1142/S0219633614400045

Chen, Xinyu; Wehle, Sarah; Kuzmanovic, Natascha; Merget, Benjamin; Holzgrabe, Ulrike; Koenig, Burkhard; Sotriffer, Christoph A.; Decker, Michael
Acetylcholinesterase Inhibitors with Photoswitchable Inhibition of beta-Amyloid Aggregation
ACS CHEMICAL NEUROSCIENCE, 5:377-389, MAY 2014
abstract, full text, DOI:10.1021/cn500016p

Nguyen, Phuong T. V.; Yu, Haibo; Keller, Paul A.
Discovery of in silico hits targeting the nsP3 macro domain of chikungunya virus
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2216, MAY 2014
abstract, full text, DOI:10.1007/s00894-014-2216-6

Strom, Alexander M.; Fehling, Samuel C.; Bhattacharyya, Sudeep; Hati, Sanchita
Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations
JOURNAL OF MOLECULAR MODELING, 20, MAY 2014
abstract, full text, DOI:10.1007/s00894-014-2245-1

Lei Dongsheng; Tong Huimin; Zhang Lei; Zhang Xing; Zhang Shengli; Ren Gang
Structure and Function of Cholesteryl Ester Transfer Protein in Transferring Cholesteryl Ester
PROGRESS IN CHEMISTRY, 26:879-888, MAY 2014
abstract, full text, DOI:10.7536/PC131028

Li, Jie; Yang, Lixin; Gaur, Shikha; Zhang, Keqiang; Wu, Xiwei; Yuan, Yate-Ching; Li, Hongzhi; Hu, Shuya; Weng, Yaguang; Yen, Yun
Mutants TP53 p.R273H and p.R273C but not p.R273G Enhance Cancer Cell Malignancy
HUMAN MUTATION, 35:575-584, MAY 2014
abstract, full text, DOI:10.1002/humu.22528

Hall, Benjamin A.; Abd Halim, Khairul Bariyyah; Buyan, Amanda; Emmanouil, Beatrice; Sansom, Mark S. P.
Sidekick for Membrane Simulations: Automated Ensemble Molecular Dynamics Simulations of Transmembrane Helices
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:2165-2175, MAY 2014
abstract, full text, DOI:10.1021/ct500003g

Yang, Lin; da Rocha, Sandro R. P.
PEGylated, NH2-Terminated PAMAM Dendrimers: A Microscopic View from Atomistic Computer Simulations
MOLECULAR PHARMACEUTICS, 11:1459-1470, MAY 2014
abstract, full text, DOI:10.1021/mp400630z

Nevidimov, A. V.; Razumov, V. F.
The monoatomic solvent model in molecular dynamics study of reverse micelles
HIGH ENERGY CHEMISTRY, 48:202-205, MAY 2014
abstract, full text, DOI:10.1134/S0018143914030084

Dasari, Surendra; Theis, Jason D.; Vrana, Julie A.; Zenka, Roman M.; Zimmermann, Michael T.; Kocher, Jean-Pierre A.; Highsmith, W. Edward, Jr.; Kurtin, Paul J.; Dogan, Ahmet
Clinical Proteome Informatics Workbench Detects Pathogenic Mutations in Hereditary Amyloidoses
JOURNAL OF PROTEOME RESEARCH, 13:2352-2358, MAY 2014
abstract, full text, DOI:10.1021/pr4011475

Geng, Hong-Li; Bian, Mei-Ru; Liu, Yang; Cao, Jiang; Chen, Chong; Wang, Zhi-Yuan; Li, Zhen-Yu; Zeng, Ling-Yu; Wang, Xiao-Yun; Wu, Qing-Yun; Xu, Kai-Lin
The D14 and R138 ion pair is involved in dimeric arginine kinase activity, structural stability and folding
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 66:302-310, MAY 2014
abstract, full text, DOI:10.1016/j.ijbiomac.2014.02.039

Brice, Allyn R.; Lazaridis, Themis
Structure and Dynamics of a Fusion Peptide Helical Hairpin on the Membrane Surface: Comparison of Molecular Simulations and NMR
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4461-4470, MAY 1 2014
abstract, full text, DOI:10.1021/jp409412g

Cui, Di; Ou, Shuching; Peters, Eric; Patel, Sandeep
Ion-Specific Induced Fluctuations and Free Energetics of Aqueous Protein Hydrophobic Interfaces: Toward Connecting to Specific-Ion Behaviors at Aqueous Liquid-Vapor Interfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4490-4504, MAY 1 2014
abstract, full text, DOI:10.1021/jp4105294

Aleksandrov, Alexey; Zvereva, Elena; Field, Martin
The Mechanism of Citryl-Coenzyme A Formation Catalyzed by Citrate Synthase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4505-4513, MAY 1 2014
abstract, full text, DOI:10.1021/jp412346g

Liu, Lan; Jalili, Nobar; Baergen, Alyson; Ng, Simon; Bailey, Justin; Derda, Ratmir; Klassen, John S.
Fluorine Bonding Enhances the Energetics of Protein-Lipid Binding in the Gas Phase
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 25:751-757, MAY 2014
abstract, full text, DOI:10.1007/s13361-014-0837-8

Qu, Tao; Tomar, Vikas
An analysis of the effects of temperature and structural arrangements on the thermal conductivity and thermal diffusivity of tropocollagen-hydroxyapatite interfaces
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 38:28-38, MAY 1 2014
abstract, full text, DOI:10.1016/j.msec.2014.01.039

Yang, Zhixiu; Guo, Qiang; Goto, Simon; Chen, Yuling; Li, Ningning; Yan, Kaige; Zhang, Yixiao; Muto, Akira; Deng, Haiteng; Himeno, Hyouta; Lei, Jianlin; Gao, Ning
Structural insights into the assembly of the 30S ribosomal subunit in vivo: functional role of S5 and location of the 17S rRNA precursor sequence
PROTEIN & CELL, 5:394-407, MAY 2014
abstract, full text, DOI:10.1007/s13238-014-0044-1

Kasimova, Marina A.; Tarek, Mounir; Shaytan, Alexey K.; Shaitan, Konstantin V.; Delemotte, Lucie
Voltage-gated ion channel modulation by lipids: Insights from molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1322-1331, MAY 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.01.024

Baker, Michelle K.; Gangupomu, Vamshi K.; Abrams, Cameron F.
Characterization of the water defect at the HIV-1 gp41 membrane spanning domain in bilayers with and without cholesterol using molecular simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1396-1405, MAY 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.01.009

Kiani, F.; Khosravi, T.; Moradi, F.; Rahbari, P.; Aghaei, M. J.; Arabi, M.; Tajik, H.; Kalantarinejad, R.
Computational Investigation of Carbon Nanotubes-Enhanced Membrane for Water Desalination Based on Flux and Rejection Characteristics
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:1237-1243, MAY 2014
abstract, full text, DOI:10.1166/jctn.2014.3488

Hoshyarmanesh, S.; Bahrami, M.; Kalantarinejad, R.
A Multiscale Approach in the Computational Modeling of Bio-Physical Environment of Micro-Mechanical Biosensor Towards the Prostate Specific Antigen Diagnosis
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:1374-1384, MAY 2014
abstract, full text, DOI:10.1166/jctn.2014.3507

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel
A Principal Component Analysis of the Dynamics of Subdomains and Binding Sites in Human Serum Albumin
BIOPOLYMERS, 101:561-572, MAY 2014
abstract, full text, DOI:10.1002/bip.22418

Lee, Myeongsang; Baek, Inchul; Chang, Hyun Joon; Yoon, Gwonchan; Na, Sungsoo
The bond survival time variation of polymorphic amyloid fibrils in the mechanical insight
CHEMICAL PHYSICS LETTERS, 600:68-72, APR 29 2014
abstract, full text, DOI:10.1016/j.cplett.2014.03.043

Xu, Yingzhi; Li, He; Jin, Ying-Hua; Fan, Jun; Sun, Fei
Dimerization Interface of 3-Hydroxyacyl-CoA Dehydrogenase Tunes the Formation of Its Catalytic Intermediate
PLOS ONE, 9 Art. No. e95965, APR 24 2014
abstract, full text, DOI:10.1371/journal.pone.0095965

Mori, Masahiko; Wichukchinda, Nuanjun; Miyahara, Reiko; Rojanawiwat, Archawin; Pathipvanich, Panita; Maekawa, Tomoyuki; Miura, Toshiyuki; Goulder, Philip; Yasunami, Michio; Ariyoshi, Koya; Sawanpanyalert, Pathom
HLA-B(*)35:05 is a protective allele with a unique structure among HIV-1 CRF01_AE-infected Thais, in whom the B(*)57 frequency is low
AIDS, 28:959-967, APR 24 2014
abstract, full text, DOI:10.1097/QAD.0000000000000206

Wu, Emilia L.; Qi, Yifei; Song, Kevin C.; Klauda, Jeffery B.; Im, Wonpil
Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4315-4325, APR 24 2014
abstract, full text, DOI:10.1021/jp500610t

Khrenova, Maria G.; Nemukhin, Alexander V.; Savitsky, Alexander P.
Computational Characterization of Ketone-Ketal Transformations at the Active Site of Matrix Metalloproteinases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:4345-4350, APR 24 2014
abstract, full text, DOI:10.1021/jp501674b

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Torsi, Luisa; Lattanzi, Gianluca
Effects of Annealing and Residual Solvents on Amorphous P3HT and PBTTT Films
JOURNAL OF PHYSICAL CHEMISTRY C, 118:8641-8655, APR 24 2014
abstract, full text, DOI:10.1021/jp410936t

Espinoza-Fonseca, L. Michel; Autry, Joseph M.; Thomas, David D.
Microsecond Molecular Dynamics Simulations of Mg2+- and K+- Bound E1 Intermediate States of the Calcium Pump
PLOS ONE, 9 Art. No. e95979, APR 23 2014
abstract, full text, DOI:10.1371/journal.pone.0095979

Zhao, Junjie; de Serrano, Vesna; Franzen, Stefan
A Model for the Flexibility of the Distal Histidine in Dehaloperoxidase-Hemoglobin A Based on X-ray Crystal Structures of the Carbon Monoxide Adduct
BIOCHEMISTRY, 53:2474-2482, APR 22 2014
abstract, full text, DOI:10.1021/bi5001905

Elder, Robert M.; Jayaraman, Arthi
Simulation study of the effects of surface chemistry and temperature on the conformations of ssDNA oligomers near hydrophilic and hydrophobic surfaces
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 155103, APR 21 2014
abstract, full text, DOI:10.1063/1.4870776

Gongadze, Ekaterina; Velikonja, Aljaz; Perutkova, Sarka; Kramar, Peter; Macek-Lebar, Alenka; Kralj-Iglic, Veronika; Iglic, Ales
Ions and water molecules in an electrolyte solution in contact with charged and dipolar surfaces
ELECTROCHIMICA ACTA, 126:42-60, APR 20 2014
abstract, full text, DOI:10.1016/j.electacta.2013.07.147

Kannam, Sridhar Kumar; Kim, Sung Cheol; Rogers, Priscilla R.; Gunn, Natalie; Wagner, John; Harrer, Stefan; Downton, Matthew T.
Sensing of protein molecules through nanopores: a molecular dynamics study
NANOTECHNOLOGY, 25 Art. No. 155502, APR 18 2014
abstract, full text, DOI:10.1088/0957-4484/25/15/155502

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji
Origin of subdiffusion of water molecules on cell membrane surfaces
SCIENTIFIC REPORTS, 4 Art. No. 4720, APR 17 2014
abstract, full text, DOI:10.1038/srep04720

Wang, Qianqian; Guo, Jingjing; Jiao, Pingzu; Liu, Huanxiang; Yao, Xiaojun
Exploring the Influence of EGCG on the beta-Sheet-Rich Oligomers of Human Islet Amyloid Polypeptide (hIAPP(1-37)) and Identifying Its Possible Binding Sites from Molecular Dynamics Simulation
PLOS ONE, 9 Art. No. e94796, APR 16 2014
abstract, full text, DOI:10.1371/journal.pone.0094796

Spencer, Ryan K.; Li, Hao; Nowick, James S.
X-ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of a Peptide Derived from A beta(17-36)
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:5595-5598, APR 16 2014
abstract, full text, DOI:10.1021/ja5017409

Masetti, Matteo; Falchi, Federico; Recanatini, Maurizio
Protein Dynamics of the HIF-2 alpha PAS-B Domain upon Heterodimerization and Ligand Binding
PLOS ONE, 9 Art. No. e94986, APR 15 2014
abstract, full text, DOI:10.1371/journal.pone.0094986

Nogueira, Juan J.; Gonzalez, Leticia
Molecular Dynamics Simulations of Binding Modes between Methylene Blue and DNA with Alternating GC and AT Sequences
BIOCHEMISTRY, 53:2391-2412, APR 15 2014
abstract, full text, DOI:10.1021/bi500068z

Smith, Natalie E.; Vrielink, Alice; Attwood, Paul V.; Corry, Ben
Binding and Channeling of Alternative Substrates in the Enzyme DmpFG: a Molecular Dynamics Study
BIOPHYSICAL JOURNAL, 106:1681-1690, APR 15 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.013

Saunders, Marissa G.; Tempkin, Jeremy; Weare, Jonathan; Dinner, Aaron R.; Roux, Benoit; Voth, Gregory A.
Nucleotide Regulation of the Structure and Dynamics of G-Actin
BIOPHYSICAL JOURNAL, 106:1710-1720, APR 15 2014
abstract, full text, DOI:10.1016/j.bpj.2014.03.012

Devi, J. Meena
Aggregation of thiol coated gold nanoparticles: A simulation study on the effect of polymer coverage density and solvent
COMPUTATIONAL MATERIALS SCIENCE, 86:174-179, APR 15 2014
abstract, full text, DOI:10.1016/j.commatsci.2014.01.042

Nakano, Shogo; Okazaki, Seiji; Tokiwa, Hiroaki; Asano, Yasuhisa
Binding of NAD(+) and L-Threonine Induces Stepwise Structural and Flexibility Changes in Cupriavidus necator L-Threonine Dehydrogenase*
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:10445-10454, APR 11 2014
abstract, full text, DOI:10.1074/jbc.M113.540773

Zhao, Charles L.; Mahboobi, Seyed Hanif; Moussavi-Baygi, Ruhollah; Mofrad, Mohammad R. K.
The Interaction of CRM1 and the Nuclear Pore Protein Tpr
PLOS ONE, 9 Art. No. e93709, APR 10 2014
abstract, full text, DOI:10.1371/journal.pone.0093709

Garcia-Beltran, Olimpo; Yanez, Osvaldo; Caballero, Julio; Galdamez, Antonio; Mena, Natalia; Nunez, Marco T.; Cassels, Bruce K.
Synthesis of coumarin derivatives as fluorescent probes for membrane and cell dynamics studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 76:79-86, APR 9 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.02.016

Vestergaard, Anna L.; Coleman, Jonathan A.; Lemmin, Thomas; Mikkelsen, Stine A.; Molday, Laurie L.; Vilsen, Bente; Molday, Robert S.; Dal Peraro, Matteo; Andersen, Jens Peter
Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E1334-E1343, APR 8 2014
abstract, full text, DOI:10.1073/pnas.1321165111

Martin, Hugh S. C.; Jha, Shantenu; Coveney, Peter V.
Comparative Analysis of Nucleotide Translocation through Protein Nanopores Using Steered Molecular Dynamics and an Adaptive Biasing Force
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:692-702, APR 5 2014
abstract, full text, DOI:10.1002/jcc.23525

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei
Microsecond Simulations of DNA and Ion Transport in Nanopores with Novel Ion-Ion and Ion-Nucleotides Effective Potentials
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:711-721, APR 5 2014
abstract, full text, DOI:10.1002/jcc.23544

Heinrich, Frank; Nanda, Hirsh; Goh, Haw Zan; Bachert, Collin; Loesche, Mathias; Linstedt, Adam D.
Myristoylation Restricts Orientation of the GRASP Domain on Membranes and Promotes Membrane Tethering*
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:9683-9691, APR 4 2014
abstract, full text, DOI:10.1074/jbc.M113.543561

Dehez, Francois; Delemotte, Lucie; Kramar, Peter; Miklavcic, Damijan; Tarek, Mounir
Evidence of Conducting Hydrophobic Nanopores Across Membranes in Response to an Electric Field
JOURNAL OF PHYSICAL CHEMISTRY C, 118:6752-6757, APR 3 2014
abstract, full text, DOI:10.1021/jp4114865

Villali, Janice; Pontiggia, Francesco; Clarkson, Michael W.; Hagan, Michael F.; Kern, Dorothee
Evidence Against the "Y-T Coupling" Mechanism of Activation in the Response Regulator NtrC
JOURNAL OF MOLECULAR BIOLOGY, 426:1554-1567, APR 3 2014
abstract, full text, DOI:10.1016/j.jmb.2013.12.027

Nibali, Valeria Conti; D'Angelo, Giovanna; Paciaroni, Alessandro; Tobias, Douglas J.; Tarek, Mounir
On the Coupling between the Collective Dynamics of Proteins and Their Hydration Water
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:1181-1186, APR 3 2014
abstract, full text, DOI:10.1021/jz500023e

Sachdeva, Ruchi; Singh, Balvinder
Phosphorylation of Ser-180 of rat aquaporin-4 shows marginal affect on regulation of water permeability: molecular dynamics study
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:555-566, APR 3 2014
abstract, full text, DOI:10.1080/07391102.2013.780981

Rogacheva, Olga N.; Stefanov, Vasiliy E.; Shchegolev, Boris F.; Vershinina, Elena A.; Savvateeva-Popova, Elena V.
Role of arginine 209 in the conformational transition of the protein kinase A regulatory subunit RI alpha A-domain
JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 12 Art. No. 1441005, APR 2014
abstract, full text, DOI:10.1142/S0219720014410054

Hsiao, Ya-Wen; Soderhjelm, Par
Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:443-454, APR 2014
abstract, full text, DOI:10.1007/s10822-014-9724-4

Guardingo, Mireia; Bellido, Elena; Miralles-Lluma, Rosa; Faraudo, Jordi; Sedo, Josep; Tatay, Sergio; Verdaguer, Albert; Busque, Felix; Ruiz-Molina, Daniel
Bioinspired Catechol-Terminated Self-Assembled Monolayers with Enhanced Adhesion Properties
SMALL, 10:1594-1602, APR 2014
abstract, full text, DOI:10.1002/smll.201302406

Meurillon, Maia; Marton, Zsuzsanna; Hospital, Audrey; Jordheim, Lars Petter; Bejaud, Jerome; Lionne, Corinne; Dumontet, Charles; Perigaud, Christian; Chaloin, Laurent; Peyrottes, Suzanne
Structure activity relationships of beta-hydroxyphosphonate nucleoside analogues as cytosolic 5 '-nucleotidase II potential inhibitors: Synthesis, in vitro evaluation and molecular modeling studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 77:18-37, APR 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.02.055

Vass, Marton; Schmidt, Eva; Horti, Ferenc; Keseru, Gyorgy M.
Virtual fragment screening on GPCRs: A case study on dopamine D3 and histamine H4 receptors
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 77:38-46, APR 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.02.034

Ding, Yun-Qiao; Chen, Cheng-Lung; Gu, Qi-Rui; Liao, Jun-Min; Chuang, Po-Hsiang
Application of molecular simulation to investigate chrome(III)-crosslinked collagen problems
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, 22 Art. No. 035007, APR 2014
abstract, full text, DOI:10.1088/0965-0393/22/3/035007

Wu, Ming; He, Jia; Ren, Xiao; Cai, Wen-Sheng; Fang, Yong-Chun; Feng, Xi-Zeng
Development of functional biointerfaces by surface modification of polydimethylsiloxane with bioactive chlorogenic acid
COLLOIDS AND SURFACES B-BIOINTERFACES, 116:700-706, APR 1 2014
abstract, full text, DOI:10.1016/j.colsurfb.2013.11.010

Jin Zhao; Liu Jian; Wang Li-Li; Cao Feng-Lei; Sun Huai
Development and Validation of an All-Atom Force Field for the Energetic Materials TATB, RDX and HMX
ACTA PHYSICO-CHIMICA SINICA, 30:654-661, APR 2014
abstract, full text, DOI:10.3866/PKU.WHXB201402113

Cilurzo, Francesco; Vistoli, Giulio; Gennari, Chiara G. M.; Selmin, Francesca; Gardoni, Fabrizio; Franze, Silvia; Campisi, Monica; Minghetti, Paola
The Role of the Conformational Profile of Polysaccharides on Skin Penetration: The Case of Hyaluronan and Its Sulfates
CHEMISTRY & BIODIVERSITY, 11:551-561, APR 2014
abstract, full text, DOI:10.1002/cbdv.201300130

Castro-Fernandez, Victor; Bravo-Moraga, Felipe; Herrera-Morande, Alejandra; Guixe, Victoria
Bifunctional ADP-dependent phosphofructokinase/ glucokinase activity in the order Methanococcales biochemical characterization of the mesophilic enzyme from Methanococcus maripaludis
FEBS JOURNAL, 281:2017-2029, APR 2014
abstract, full text, DOI:10.1111/febs.12757

Basile, Livia; Pappalardo, Matteo; Guccione, Salvatore; Milardi, Danilo; Ramsay, Rona R.
Computational Comparison of Imidazoline Association with the 12 Binding Site in Human Monoamine Oxidases
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:1200-1207, APR 2014
abstract, full text, DOI:10.1021/ci400346k

Li, Minghui; Petukh, Marharyta; Alexov, Emil; Panchenko, Anna R.
Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:1770-1780, APR 2014
abstract, full text, DOI:10.1021/ct401022c

Ermakova, Elena; Kurbanov, Rauf
Effect of ligand binding on the dynamics of trypsin. Comparison of different approaches
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 49:99-109, APR 2014
abstract, full text, DOI:10.1016/j.jmgm.2014.02.001

Malac, Kamil; Barvik, Ivan
Recognition of 2 ',5 '-linked oligoadenylates by human ribonuclease L: molecular dynamics study
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2123, APR 2014
abstract, full text, DOI:10.1007/s00894-014-2123-x

Raj, Fredrick Robin Devadoss Victor Paul; Exner, Thomas E.
C-alpha torsion angles as a flexible criterion to extract secrets from a molecular dynamics simulation
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2196, APR 2014
abstract, full text, DOI:10.1007/s00894-014-2196-6

Souza, P. C. T.; Puhl, A. C.; Martinez, L.; Aparicio, R.; Nascimento, A. S.; Figueira, A. C. M.; Nguyen, P.; Webb, P.; Skaf, M. S.; Polikarpov, I.
Identification of a New Hormone-Binding Site on the Surface of Thyroid Hormone Receptor
MOLECULAR ENDOCRINOLOGY, 28:534-545, APR 2014
abstract, full text, DOI:10.1210/me.2013-1359

Roberts, Justine J.; Elder, Robert M.; Neumann, Alexander J.; Jayaraman, Arthi; Bryant, Stephanie J.
Interaction of Hyaluronan Binding Peptides with Glycosaminoglycans in Poly(ethylene glycol) Hydrogels
BIOMACROMOLECULES, 15:1132-1141, APR 2014
abstract, full text, DOI:10.1021/bm401524h

Zhang Xiaoyi; Deng Dongjie; Tan Jianjun; He Yu; Li Chunhua; Wang Cunxin
Pharmacophore and Docking-based 3D-QSAR Studies on HIV-1 Integrase Inhibitors
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 30:297-305, APR 2014
abstract, full text, DOI:10.1007/s40242-014-3395-5

Geng Yi-Zhao; Zhang Hui; Ji Qing; Yan Shi-Wei
Locking Function of a Key Residue in Kinesin's Gating Mechanism
CHINESE PHYSICS LETTERS, 31 Art. No. 048702, APR 2014
abstract, full text, DOI:10.1088/0256-307X/31/4/048702

Holm, Rene; Ostergaard, Jesper; Schonbeck, Christian; Jensen, Henrik; Shi, Wei; Peters, Gunther H.; Westh, Peter
Determination of stability constants of tauro- and glyco-conjugated bile salts with the negatively charged sulfobutylether-beta-cyclodextrin: comparison of affinity capillary electrophoresis and isothermal titration calorimetry and thermodynamic analysis of the interaction
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY, 78:185-194, APR 2014
abstract, full text, DOI:10.1007/s10847-013-0287-0

Schonbeck, Christian; Holm, Rene; Westh, Peter; Peters, Gunther H.
Extending the hydrophobic cavity of beta-cyclodextrin results in more negative heat capacity changes but reduced binding affinities
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY, 78:351-361, APR 2014
abstract, full text, DOI:10.1007/s10847-013-0305-2

Friedt, Jenna; Leavens, Fern M. V.; Mercier, Evan; Wieden, Hans-Joachim; Kothe, Ute
An arginine-aspartate network in the active site of bacterial TruB is critical for catalyzing pseudouridine formation
NUCLEIC ACIDS RESEARCH, 42:3857-3870, APR 2014
abstract, full text, DOI:10.1093/nar/gkt1331

Karachevtsev, Maksym V.; Gladchenko, Galyna O.; Leontiev, Victor S.; Karachevtsev, Victor A.
Hybridization of poly(rI) with poly(rC) adsorbed to the carbon nanotube surface
NANOSCALE RESEARCH LETTERS, 9 Art. No. 157, APR 1 2014
abstract, full text, DOI:10.1186/1556-276X-9-157

Drinkwater, Nyssa; Cossins, Benjamin P.; Keeble, Anthony H.; Wright, Michael; Cain, Katharine; Hailu, Hanna; Oxbrow, Amanda; Delgado, Jean; Shuttleworth, Lindsay K.; Kao, Michael W.-.P.; McDonnell, James M.; Beavil, Andrew J.; Henry, Alistair J.; Sutton, Brian J.
Human immunoglobulin E flexes between acutely bent and extended conformations
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21:397-U142, APR 2014
abstract, full text, DOI:10.1038/nsmb.2795

Politis, Argyris; Stengel, Florian; Hall, Zoe; Hernandez, Helena; Leitner, Alexander; Walzthoeni, Thomas; Robinson, Carol V.; Aebersold, Ruedi
A mass spectrometry-based hybrid method for structural modeling of protein complexes
NATURE METHODS, 11:403-+, APR 2014
abstract, full text, DOI:10.1038/NMETH.2841

Braun, Christian J.; Lachnit, Christine; Becker, Patrick; Henkes, Leonhard M.; Arrigoni, Cristina; Kast, Stefan M.; Moroni, Anna; Thiel, Gerhard; Schroeder, Indra
Viral potassium channels as a robust model system for studies of membrane-protein interaction
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:1096-1103, APR 2014
abstract, full text, DOI:10.1016/j.bbamem.2013.06.010

Alekozai, Emal M.; GhattyVenkataKrishna, Pavan K.; Uberbacher, Edward C.; Crowley, Michael F.; Smith, Jeremy C.; Cheng, Xiaolin
Simulation analysis of the cellulase Cel7A carbohydrate binding module on the surface of the cellulose I beta
CELLULOSE, 21:951-971, APR 2014
abstract, full text, DOI:10.1007/s10570-013-0026-0

Wang, Kun; Luo, Huiying; Tian, Jian; Turunen, Ossi; Huang, Huoqing; Shi, Pengjun; Hua, Huifang; Wang, Caihong; Wang, Shuanghe; Yao, Bin
Thermostability Improvement of a Streptomyces Xylanase by Introducing Proline and Glutamic Acid Residues
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80:2158-2165, APR 2014
abstract, full text, DOI:10.1128/AEM.03458-13

Sencanski, Milan; Sukalovic, Vladimir; Shakib, Kaveh; Soskic, Vukic; Dosen-Micovic, Ljiljana; Kostic-Rajacic, Sladjana
Molecular Modeling of 5HT(2A) Receptor - Arylpiperazine Ligands Interactions
CHEMICAL BIOLOGY & DRUG DESIGN, 83:462-471, APR 2014
abstract, full text, DOI:10.1111/cbdd.12261

Warren, Nicholas; Strom, Alexander; Nicolet, Brianna; Albin, Kristine; Albrecht, Joshua; Bausch, Brenna; Dobbe, Megan; Dudek, Megan; Firgens, Samuel; Fritsche, Chad; Gunderson, Anthony; Heimann, Joseph; Her, Cheng; Hurt, Jordan; Konorev, Dmitri; Lively, Matthew; Meacham, Stephanie; Rodriguez, Valentina; Tadayon, Stephanie; Trcka, David; Yang, Yer; Bhattacharyya, Sudeep; Hati, Sanchita
Comparison of the Intrinsic Dynamics of Aminoacyl-tRNA Synthetases
PROTEIN JOURNAL, 33:184-198, APR 2014
abstract, full text, DOI:10.1007/s10930-014-9548-z

Simard, Jean; Ammi, Mehdi; Mayeur, Anais
Comparative study of the bimanual and collaborative modes for closely coupled manipulations
INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES, 72:408-421, APR 2014
abstract, full text, DOI:10.1016/j.ijhcs.2013.12.002

Mernea, Maria; Calborean, Octavian; Grigore, Oana; Dascalu, Traian; Mihailescu, Dan Florin
Validation of protein structural models using THz spectroscopy: a promising approach to solve three-dimensional structures
OPTICAL AND QUANTUM ELECTRONICS, 46:505-514, APR 2014
abstract, full text, DOI:10.1007/s11082-013-9872-0

Howard, Rebecca J.; Trudell, James R.; Harris, R. Adron
Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics
PHARMACOLOGICAL REVIEWS, 66:396-412, APR 2014
abstract, full text, DOI:10.1124/pr.113.007468

Ma, Jun
A molecular dynamics study on the nucleation of calcium phosphate regulated by collagen
JOURNAL OF MATERIALS SCIENCE, 49:3099-3106, APR 2014
abstract, full text, DOI:10.1007/s10853-013-8011-4

Jacobitz, Alex W.; Wereszczynski, Jeff; Yi, Sung Wook; Amer, Brendan R.; Huang, Grace L.; Nguyen, Angelyn V.; Sawaya, Michael R.; Jung, Michael E.; McCammon, J. Andrew; Clubb, Robert T.
Structural and Computational Studies of the Staphylococcus aureus Sortase B-Substrate Complex Reveal a Substrate-stabilized Oxyanion Hole
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:8891-8902, MAR 28 2014
abstract, full text, DOI:10.1074/jbc.M113.509273

Li, Xiaochuan Edward; Orzechowski, Marek; Lehman, William; Fischer, Stefan
Structure and flexibility of the tropomyosin overlap junction
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 446:304-308, MAR 28 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.02.097

Chen, Rong; Chung, Shin-Ho
Mechanism of tetrodotoxin block and resistance in sodium channels
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 446:370-374, MAR 28 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.02.115

Rashid, M. Harunur; Huq, Redwan; Tanner, Mark R.; Chhabra, Sandeep; Khoo, Keith K.; Estrada, Rosendo; Dhawan, Vikas; Chauhan, Satendra; Pennington, Michael W.; Beeton, Christine; Kuyucak, Serdar; Norton, Raymond S.
A potent and Kv1.3-selective analogue of the scorpion toxin HsTX1 as a potential therapeutic for autoimmune diseases
SCIENTIFIC REPORTS, 4 Art. No. 4509, MAR 28 2014
abstract, full text, DOI:10.1038/srep04509

Yan, Leilei; Yan, Chunli; Qian, Kun; Su, Hairui; Kofsky-Wofford, Stephanie A.; Lee, Wei-Chao; Zhao, Xinyang; Ho, Meng-Chiao; Ivanov, Ivaylo; Zheng, Yujun George
Diamidine Compounds for Selective Inhibition of Protein Arginine Methyltransferase 1
JOURNAL OF MEDICINAL CHEMISTRY, 57:2611-2622, MAR 27 2014
abstract, full text, DOI:10.1021/jm401884z

Chen, Rong; Robinson, Anna; Chung, Shin-Ho
Mechanism of mu-Conotoxin PIIIA Binding to the Voltage-Gated Na+ Channel Na(V)1.4
PLOS ONE, 9 Art. No. e93267, MAR 27 2014
abstract, full text, DOI:10.1371/journal.pone.0093267

Mansoorabadi, Steven O.; Wu, Meilan; Tao, Zhihua; Gao, Peng; Pingali, Sai Venkatesh; Guo, Liang; Liu, Hung-wen
Conformational Activation of Poly(ADP-ribose) Polymerase-1 upon DNA Binding Revealed by Small-Angle X-ray Scattering
BIOCHEMISTRY, 53:1779-1788, MAR 25 2014
abstract, full text, DOI:10.1021/bi401439n

Colzani, Mara; Criscuolo, Angela; De Maddis, Danilo; Garzon, Davide; Yeum, Kyung-Jin; Vistoli, Giulio; Carini, Marina; Aldini, Giancarlo
A novel high resolution MS approach for the screening of 4-hydroxy-trans-2-nonenal sequestering agents
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS, 91:108-118, MAR 25 2014
abstract, full text, DOI:10.1016/j.jpba.2013.12.024

Sethi, Ritika; Seppala, Jonne; Tossavainen, Helena; Ylilauri, Mikko; Ruskamo, Salla; Pentikainen, Olli T.; Pentikainen, Ulla; Permi, Perttu; Ylanne, Jari
A Novel Structural Unit in the N-terminal Region of Filamins
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:8588-8598, MAR 21 2014
abstract, full text, DOI:10.1074/jbc.M113.537456

Lindert, Steffen; Maslennikov, Innokentiy; Chiu, Ellis J. C.; Pierce, Levi C.; McCammon, J. Andrew; Choe, Senyon
Drug screening strategy for human membrane proteins: From NMR protein backbone structure to in silica- and NMR-screened hits
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 445:724-733, MAR 21 2014
abstract, full text, DOI:10.1016/j.bbrc.2014.01.179

Bojovschi, A.; Liu, Ming S.; Sadus, Richard J.
Mg2+ coordinating dynamics in Mg:ATP fueled motor proteins
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 115102, MAR 21 2014
abstract, full text, DOI:10.1063/1.4867898

Tomasic, Tihomir; Hajsek, David; Svajger, Urban; Luzar, Jernej; Obermajer, Natasa; Petit-Haertlein, Isabelle; Fieschi, Franck; Anderluh, Marko
Monovalent mannose-based DC-SIGN antagonists: Targeting the hydrophobic groove of the receptor
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 75:308-326, MAR 21 2014
abstract, full text, DOI:10.1016/j.ejmech.2014.01.047

Fiorillo, Annarita; di Marino, Daniele; Bertuccini, Lucia; Via, Allegra; Pozio, Edoardo; Camerini, Serena; Ilari, Andrea; Lalle, Marco
The Crystal Structure of Giardia duodenalis 14-3-3 in the Apo Form: When Protein Post-Translational Modifications Make the Difference
PLOS ONE, 9 Art. No. e92902, MAR 21 2014
abstract, full text, DOI:10.1371/journal.pone.0092902

Zeytuni, Natalie; Uebe, Rene; Maes, Michal; Davidov, Geula; Baram, Michal; Raschdorf, Oliver; Nadav-Tsubery, Merav; Kolusheva, Sofiya; Bitton, Ronit; Goobes, Gil; Friedler, Assaf; Miller, Yifat; Schueler, Dirk; Zarivach, Raz
Cation Diffusion Facilitators Transport Initiation and Regulation Is Mediated by Cation Induced Conformational Changes of the Cytoplasmic Domain
PLOS ONE, 9 Art. No. e92141, MAR 21 2014
abstract, full text, DOI:10.1371/journal.pone.0092141

Sen, Kakali; Thiel, Walter
Role of Two Alternate Water Networks in Compound I Formation in P450eryF
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2810-2820, MAR 20 2014
abstract, full text, DOI:10.1021/jp411272h

Vidossich, Pietro; Loewen, Peter C.; Carpena, Xavi; Fiorin, Giacomo; Fita, Ignacio; Rovira, Carme
Binding of the Antitubercular Pro-Drug Isoniazid in the Heme Access Channel of Catalase-Peroxidase (KatG). A Combined Structural and Metadynamics Investigation
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2924-2931, MAR 20 2014
abstract, full text, DOI:10.1021/jp4123425

Konold, Patrick; Regmi, Chola K.; Chapagain, Prem P.; Gerstman, Bernard S.; Jimenez, Ralph
Hydrogen Bond Flexibility Correlates with Stokes Shift in mPlum Variants
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2940-2948, MAR 20 2014
abstract, full text, DOI:10.1021/jp412371y

Liu, Yanxin; Prigozhin, Maxim B.; Schulten, Klaus; Gruebele, Martin
Observation of Complete Pressure-Jump Protein Refolding in Molecular Dynamics Simulation and Experiment
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:4265-4272, MAR 19 2014
abstract, full text, TCBG publications, DOI:10.1021/ja412639u

Adelman, Joshua L.; Sheng, Ying; Choe, Seungho; Abramson, Jeff; Wright, Ernest M.; Rosenberg, John M.; Grabe, Michael
Structural Determinants of Water Permeation through the Sodium-Galactose Transporter vSGLT
BIOPHYSICAL JOURNAL, 106:1280-1289, MAR 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.01.006

Scharnagl, Christina; Pester, Oxana; Hornburg, Philipp; Hornburg, Daniel; Goetz, Alexander; Langosch, Dieter
Side-Chain to Main-Chain Hydrogen Bonding Controls the Intrinsic Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix
BIOPHYSICAL JOURNAL, 106:1318-1326, MAR 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.02.013

Heinzelmann, Germano; Kuyucak, Serdar
Molecular Dynamics Simulations of the Mammalian Glutamate Transporter EAAT3
PLOS ONE, 9 Art. No. e92089, MAR 18 2014
abstract, full text, DOI:10.1371/journal.pone.0092089

Yang, J.; Calero, C.; Marti, J.
Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 104901, MAR 14 2014
abstract, full text, DOI:10.1063/1.4867385

Yzeiri, Irena; Patra, Niladri; Kral, Petr
Porous carbon nanotubes: Molecular absorption, transport, and separation
JOURNAL OF CHEMICAL PHYSICS, 140, MAR 14 2014
abstract, full text, DOI:10.1063/1.4867542

Lockhart, Christopher; Klimov, Dmitri K.
Alzheimer's A beta 10-40 Peptide Binds and Penetrates DMPC Bilayer: An Isobaric-Isothermal Replica Exchange Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2638-2648, MAR 13 2014
abstract, full text, DOI:10.1021/jp412153s

Madrona, Yarrow; Hollingsworth, Scott A.; Tripathi, Sarvind; Fields, James B.; Rwigema, Jean-Christophe N.; Tobias, Douglas J.; Poulos, Thomas L.
Crystal Structure of Cindoxin, the P450cin Redox Partner
BIOCHEMISTRY, 53:1435-1446, MAR 11 2014
abstract, full text, DOI:10.1021/bi500010m

Guillotin, Laure; Lafite, Pierre; Daniellou, Richard
Unraveling the Substrate Recognition Mechanism and Specificity of the Unusual Glycosyl Hydrolase Family 29 BT2192 from Bacteroides thetaiotaomicron
BIOCHEMISTRY, 53:1447-1455, MAR 11 2014
abstract, full text, DOI:10.1021/bi400951q

Jiang, Xiaoxu; Villafuerte, Maria Katerina R.; Andersson, Magnus; White, Stephen H.; Kaback, H. Ronald
Galactoside-Binding Site in LacY
BIOCHEMISTRY, 53:1536-1543, MAR 11 2014
abstract, full text, DOI:10.1021/bi401716z

Serrano, Soraya; Araujo, Aitziber; Apellaniz, Beatriz; Bryson, Steve; Carravilla, Pablo; de la Arada, Igor; Huarte, Nerea; Rujas, Edurne; Pai, Emil F.; Arrondo, Jose L. R.; Domene, Carmen; Angeles Jimenez, Maria; Nieva, Jose L.
Structure and Immunogenicity of a Peptide Vaccine, Including the Complete HIV-1 gp41 2F5 Epitope IMPLICATIONS FOR ANTIBODY RECOGNITION MECHANISM AND IMMUNOGEN DESIGN
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:6565-6580, MAR 7 2014
abstract, full text, DOI:10.1074/jbc.M113.527747

Lemmin, Thomas; Dimitrov, Mitko; Fraering, Patrick C.; Dal Peraro, Matteo
Perturbations of the Straight Transmembrane alpha-Helical Structure of the Amyloid Precursor Protein Affect Its Processing by gamma-Secretase
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:6763-6774, MAR 7 2014
abstract, full text, DOI:10.1074/jbc.M113.470781

Pang, Xiaodong; Zhou, Huan-Xiang
Design Rules for Selective Binding of Nuclear Localization Signals to Minor Site of Importin alpha
PLOS ONE, 9 Art. No. e91025, MAR 7 2014
abstract, full text, DOI:10.1371/journal.pone.0091025

Padilla-Sanchez, Victor; Gao, Song; Kim, Hyung Rae; Kihara, Daisuke; Sun, Lei; Rossmann, Michael G.; Rao, Venigalla B.
Structure-Function Analysis of the DNA Translocating Portal of the Bacteriophage T4 Packaging Machine
JOURNAL OF MOLECULAR BIOLOGY, 426:1019-1038, MAR 6 2014
abstract, full text, DOI:10.1016/j.jmb.2013.10.011

Tseng, Wen-Chi; Lin, Chia-Ray; Hung, Xing-Guang; Wei, Tsen-Yun; Chen, Yu-Chun; Fang, Tsuei-Yun
Identification of substrate-binding and selectivity-related residues of maltooligosyltrehalose synthase from the thermophilic archaeon Sulfolobus solfataricus ATCC 35092
ENZYME AND MICROBIAL TECHNOLOGY, 56:53-59, MAR 5 2014
abstract, full text, DOI:10.1016/j.enzmictic.2014.01.003

Li, Yunlang; Freudenthal, Bret D.; Beard, William A.; Wilson, Samuel H.; Schlick, Tamar
Optimal and Variant Metal-Ion Routes in DNA Polymerase beta's Conformational Pathways
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:3630-3639, MAR 5 2014
abstract, full text, DOI:10.1021/ja412701f

Zhang, Fan; Tian, Yi; Gao, Feng; Chen, Shulin; Li, Demao; Zhou, Yuxia
Bacterial community in the intestine of the sea urchin Strongylocentrotus intermedius during digestion of Macrocystis pyrifera
MARINE AND FRESHWATER BEHAVIOUR AND PHYSIOLOGY, 47:117-127, MAR 4 2014
abstract, full text, DOI:10.1080/10236244.2014.906095

Boiteux, Celine; Vorobyov, Igor; Allen, Toby W.
Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:3454-3459, MAR 4 2014
abstract, full text, DOI:10.1073/pnas.1320907111

Colavin, Alexandre; Hsin, Jen; Huang, Kerwyn Casey
Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:3585-3590, MAR 4 2014
abstract, full text, DOI:10.1073/pnas.1317061111

Gorham, Ronald D., Jr.; Rodriguez, Wilson; Morikis, Dimitrios
Molecular Analysis of the Interaction between Staphylococcal Virulence Factor Sbi-IV and Complement C3d
BIOPHYSICAL JOURNAL, 106:1164-1173, MAR 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.01.033

Yang, Li-Quan; Sang, Peng; Tao, Yan; Fu, Yun-Xin; Zhang, Ke-Qin; Xie, Yue-Hui; Liu, Shu-Qun
Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:372-393, MAR 4 2014
abstract, full text, DOI:10.1080/07391102.2013.770372

Yu, Haoran; Huang, He
Engineering proteins for thermostability through rigidifying flexible sites
BIOTECHNOLOGY ADVANCES, 32:308-315, MAR-APR 2014
abstract, full text, DOI:10.1016/j.biotechadv.2013.10.012

Pradhan, S. M.; Katti, K. S.; Katti, D. R.
Multiscale Modeling of Collagen Fibril in Bone at Various Crosslink Densities: An Insight into Its Deformation Mechanisms
CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES, 98:181-201, MAR 2014
abstract, full text

Tu, Qing Song; Lee, Michelle; Zhang, Samuel; Li, Shaofan
Molecular Dynamics Simulations of Ions Diffusion in Carbon Nanotubes Embedded in Cell Membrane
CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES, 98:247-259, MAR 2014
abstract, full text

Gamini, Ramya; Han, Wei; Stone, John E.; Schulten, Klaus
Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating
PLOS COMPUTATIONAL BIOLOGY, 10 Art. No. e1003488, MAR 2014
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1003488

Song, Zhen; Ming, Jie; Yang, Binsheng
The effect of metals on SDS-induced partially folded states of CopC
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 19:359-374, MAR 2014
abstract, full text, DOI:10.1007/s00775-013-1071-8

Adhireksan, Zenita; Davey, Gabriela E.; Campomanes, Pablo; Groessl, Michael; Clavel, Catherine M.; Yu, Haojie; Nazarov, Alexey A.; Yeo, Charmian Hui Fang; Ang, Wee Han; Droege, Peter; Rothlisberger, Ursula; Dyson, Paul J.; Davey, Curt A.
Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity
NATURE COMMUNICATIONS, 5 Art. No. 3462, MAR 2014
abstract, full text, DOI:10.1038/ncomms4462

Zhou, Qiangjun; Li, Jiangmei; Yu, Hang; Zhai, Yujia; Gao, Zhen; Liu, Yanxin; Pang, Xiaoyun; Zhang, Lunfeng; Schulten, Klaus; Sun, Fei; Chen, Chang
Molecular insights into the membrane-associated phosphatidylinositol 4-kinase II alpha
NATURE COMMUNICATIONS, 5 Art. No. 3552, MAR 2014
abstract, full text, TCBG publications, DOI:10.1038/ncomms4552

Kunze, Jens; Todoroff, Nickolay; Schneider, Petra; Rodrigues, Tiago; Geppert, Tim; Reisen, Felix; Schreuder, Herman; Saas, Joachim; Hessler, Gerhard; Baringhaus, Karl-Heinz; Schneider, Gisbert
Targeting Dynamic Pockets of HIV-1 Protease by Structure-Based Computational Screening for Allosteric Inhibitors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:987-991, MAR 2014
abstract, full text, DOI:10.1021/ci400712h

Llatser, Ignacio; Demiray, Deniz; Cabellos-Aparicio, Albert; Altilar, D. Turgay; Alarcon, Eduard
N3Sim: Simulation framework for diffusion-based molecular communication nanonetworks
SIMULATION MODELLING PRACTICE AND THEORY, 42:210-222, MAR 2014
abstract, full text, DOI:10.1016/j.simpat.2013.11.004

Wright, David W.; Hall, Benjamin A.; Kenway, Owain A.; Jha, Shantenu; Coveney, Peter V.
Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:1228-1241, MAR 2014
abstract, full text, DOI:10.1021/ct4007037

Aytenfisu, Asaminew H.; Spasic, Aleksandar; Seetin, Matthew G.; Serafini, John; Mathews, David H.
Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:1292-1301, MAR 2014
abstract, full text, DOI:10.1021/ct400861g

des Georges, Amedee; Hashem, Yaser; Unbehaun, Anett; Grassucci, Robert A.; Taylor, Derek; Hellen, Christopher U. T.; Pestova, Tatyana V.; Frank, Joachim
Structure of the mammalian ribosomal pre-termination complex associated with eRF1 center dot eRF3 center dot GDPNP
NUCLEIC ACIDS RESEARCH, 42:3409-3418, MAR 2014
abstract, full text, DOI:10.1093/nar/gkt1279

Ferrari, Florent; Paris, Cedric; Maigret, Bernard; Bidouil, Christelle; Delaunay, Stephane; Humeau, Catherine; Chevalot, Isabelle
Molecular rules for chemo- and regio-selectivity of Candida antarctica lipase B in peptide acylation reactions
JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 101:122-132, MAR 2014
abstract, full text, DOI:10.1016/j.molcatb.2013.12.007

Huang, Lan; Cao, Yang; Zhou, Jianfang; Qin, Kun; Zhu, Wenfei; Zhu, Yun; Yang, Lei; Wang, Dayan; Wei, Hong; Shu, Yuelong
A Conformational Restriction in the Influenza A Virus Neuraminidase Binding Site by R152 Results in a Combinational Effect of I222T and H274Y on Oseltamivir Resistance
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 58:1639-1645, MAR 2014
abstract, full text, DOI:10.1128/AAC.01848-13

Jiang, Wei; Phillips, James C.; Huang, Lei; Fajer, Mikolai; Meng, Yilin; Gumbart, James C.; Luo, Yun; Schulten, Klaus; Roux, Benoit
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD
COMPUTER PHYSICS COMMUNICATIONS, 185:908-916, MAR 2014
abstract, full text, TCBG publications, DOI:10.1016/j.cpc.2013.12.014

Fibriansah, Guntur; Tan, Joanne L.; Smith, Scott A.; de Alwis, Adamberage R.; Thiam-Seng Ng; Kostyuchenko, Victor A.; Ibarra, Kristie D.; Wang, Jiaqi; Harris, Eva; de Silva, Aravinda; Crowe, James E., Jr.; Lok, Shee-Mei
A potent anti-dengue human antibody preferentially recognizes the conformation of E protein monomers assembled on the virus surface
EMBO MOLECULAR MEDICINE, 6:358-371, MAR 2014
abstract, full text, DOI:10.1002/emmm.201303404

Rusu, Victor H.; Horta, Vitor A. C.; Horta, Bruno A. C.; Lins, Roberto D.; Baron, Riccardo
MDWiZ: A platform for the automated translation of molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 48:80-86, MAR 2014
abstract, full text, DOI:10.1016/j.jmgm.2013.12.006

Ai, Haixin; Zhang, Li; Chang, Alan K.; Wei, Hongyun; Che, Yuchen; Liu, Hongsheng
Virtual screening of potential inhibitors from TCM for the CPSF30 binding site on the NS1A protein of influenza A virus
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2142, MAR 2014
abstract, full text, DOI:10.1007/s00894-014-2142-7

Mikulska, Karolina; Strzelecki, Janusz; Nowak, Wieslaw
Nanomechanics of beta-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2144, MAR 2014
abstract, full text, DOI:10.1007/s00894-014-2144-5

Hirtz, Michael; Kumar, Naresh; Chi, Lifeng
Simulation Modeling of Supported Lipid Membranes - A Review
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 14:617-623, MAR 2014
abstract, full text, DOI:10.2174/1568026614666140118204332

Lushchekina, Sofya V.; Nemukhin, Alexander V.; Varfolomeev, Sergei D.; Masson, Patrick
Molecular Modeling Evidence for His438 Flip in the Mechanism of Butyrylcholinesterase Hysteretic Behavior
JOURNAL OF MOLECULAR NEUROSCIENCE, 52:434-445, MAR 2014
abstract, full text, DOI:10.1007/s12031-013-0178-2

Geng, Yi-Zhao; Li, Tie; Ji, Qing; Yan, Shiwei
Simulation Study of Interactions Between Kinesin's Neck Linker and Motor Domain
CELLULAR AND MOLECULAR BIOENGINEERING, 7:99-105, MAR 2014
abstract, full text, DOI:10.1007/s12195-014-0320-4

Ruiz, Luis; Keten, Sinan
Multiscale Modeling of Elasticity and Fracture in Organic Nanotubes
JOURNAL OF ENGINEERING MECHANICS, 140:431-442, MAR 1 2014
abstract, full text, DOI:10.1061/(ASCE)EM.1943-7889.0000471

Pal, Anirban; Agarwala, Abhishek; Raha, Spumyendu; Bhattacharya, Baidurya
Performance metrics in a hybrid MPI-OpenMP based molecular dynamics simulation with short-range interactions
JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING, 74:2203-2214, MAR 2014
abstract, full text, DOI:10.1016/j.jpdc.2013.12.008

Citlalli Contreras-Romo, M.; Correa-Basurto, Jose; Padilla-Martinez, Itzia; Martinez-Archundia, Marlet; Martinez-Ramos, Federico; Slusarz, Magdalena J.; Lopez-Perez, Gilberto; Quintanar-Stephano, Andres
Theoretical studies, synthesis, and biological activity of 1-[(4-methylphenyl)sulfonyl]-5-oxo-2,3,4,5-tetrahydro-1H-1-benzazepine-4 -carbonitrile (C9) as a non-peptide antagonist of the arginine vasopressin V1a and V2 receptors
MEDICINAL CHEMISTRY RESEARCH, 23:1581-1590, MAR 2014
abstract, full text, DOI:10.1007/s00044-013-0739-5

Walker, Ryan G.; Deng, Xiaodi; Melchior, John T.; Morris, Jamie; Tso, Patrick; Jones, Martin K.; Segrest, Jere P.; Thompson, Thomas B.; Davidson, W. Sean
The Structure of Human Apolipoprotein A-IV as Revealed by Stable Isotope-assisted Cross-linking, Molecular Dynamics, and Small Angle X-ray Scattering
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:5596-5608, FEB 28 2014
abstract, full text, DOI:10.1074/jbc.M113.541037

Abdul-Ridha, Alaa; Lopez, Laura; Keov, Peter; Thal, David M.; Mistry, Shailesh N.; Sexton, Patrick M.; Lane, J. Robert; Canals, Meritxell; Christopoulos, Arthur
Molecular Determinants of Allosteric Modulation at the M-1 Muscarinic Acetylcholine Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:6067-6079, FEB 28 2014
abstract, full text, DOI:10.1074/jbc.M113.539080

Ljubetic, Ajasja; Urbancic, Iztok; Strancar, Janez
Recovering position-dependent diffusion from biased molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 084109, FEB 28 2014
abstract, full text, DOI:10.1063/1.4866448

Meyer, Austin G.; Sawyer, Sara L.; Ellington, Andrew D.; Wilke, Claus O.
Analyzing machupo virus-receptor binding by molecular dynamics simulations
PEERJ, 2 Art. No. e266, FEB 27 2014
abstract, full text, DOI:10.7717/peerj.266

Johnson, Quentin R.; Lindsay, Richard J.; Raval, Sherin R.; Dobbs, Jeremy S.; Nellas, Ricky B.; Shen, Tongye
Effects of Branched O-Glycosylation on a Semiflexible Peptide Linker
JOURNAL OF PHYSICAL CHEMISTRY B, 118:2050-2057, FEB 27 2014
abstract, full text, DOI:10.1021/jp410788r

Strzelecki, Janusz; Peplowski, Lukasz; Lenartowski, Robert; Nowak, Wieslaw; Balter, Aleksander
Mechanical transition in a highly stretched and torsionally constrained DNA
PHYSICAL REVIEW E, 89 Art. No. 020701, FEB 27 2014
abstract, full text, DOI:10.1103/PhysRevE.89.020701

Volpert, Marianna; Mangum, Jonathan E.; Jamsai, Duangporn; D'Sylva, Rebecca; O'Bryan, Moira K.; McIntyre, Peter
Eukaryotic expression, purification and structure/function analysis of native, recombinant CRISP3 from human and mouse
SCIENTIFIC REPORTS, 4 Art. No. 4217, FEB 27 2014
abstract, full text, DOI:10.1038/srep04217

Murciano-Calles, Javier; Corbi-Verge, Carles; Candel, Adela M.; Luque, Irene; Martinez, Jose C.
Post-Translational Modifications Modulate Ligand Recognition by the Third PDZ Domain of the MAGUK Protein PSD-95
PLOS ONE, 9 Art. No. e90030, FEB 26 2014
abstract, full text, DOI:10.1371/journal.pone.0090030

Correa-Basurto, J.; Bello, M.; Rosales-Hernandez, M. C.; Hernandez-Rodriguez, M.; Nicolas-Vazquez, I.; Rojo-Dominguez, A.; Trujillo-Ferrara, J. G.; Miranda, Rene; Flores-Sandoval, C. A.
QSAR, docking, dynamic simulation and quantum mechanics studies to explore the recognition properties of cholinesterase binding sites
CHEMICO-BIOLOGICAL INTERACTIONS, 209:1-13, FEB 25 2014
abstract, full text, DOI:10.1016/j.cbi.2013.12.001

Sheng, Jia; Li, Li; Engelhart, Aaron E.; Gan, Jianhua; Wang, Jiawei; Szostak, Jack W.
Structural insights into the effects of 2 '-5 ' linkages on the RNA duplex
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:3050-3055, FEB 25 2014
abstract, full text, DOI:10.1073/pnas.1317799111

Megow, Joerg; Renger, Thomas; May, Volkhard
Mixed Quantum-Classical Description of Excitation Energy Transfer in Supramolecular Complexes: Screening of the Excitonic Coupling
CHEMPHYSCHEM, 15:478-485, FEB 24 2014
abstract, full text, DOI:10.1002/cphc.201300625

Li, Min; Chang, Shan; Yang, Longjin; Shi, Jingyi; McFarland, Kelli; Yang, Xiao; Moller, Alyssa; Wang, Chunguang; Zou, Xiaoqin; Chi, Chengwu; Cui, Jianmin
Conopeptide Vt3.1 Preferentially Inhibits BK Potassium Channels Containing beta 4 Subunits via Electrostatic Interactions*
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:4735-4742, FEB 21 2014
abstract, full text, DOI:10.1074/jbc.M113.535898

Tanaka, Naoto; Delemotte, Lucie; Klein, Michael L.; Komaromy, Andras M.; Tanaka, Jacqueline C.
A Cyclic Nucleotide-Gated Channel Mutation Associated with Canine Daylight Blindness Provides Insight into a Role for the S2 Segment Tri-Asp motif in Channel Biogenesis
PLOS ONE, 9 Art. No. e88768, FEB 21 2014
abstract, full text, DOI:10.1371/journal.pone.0088768

Temmerman, Koen; de Diego, Inaki; Pogenberg, Vivian; Simon, Bertrand; Jonko, Weronika; Li, Xun; Wilmanns, Matthias
A PEF/Y Substrate Recognition and Signature Motif Plays a Critical Role in DAPK-Related Kinase Activity
CHEMISTRY & BIOLOGY, 21:264-273, FEB 20 2014
abstract, full text, DOI:10.1016/j.chembiol.2013.12.008

Vermaas, Josh V.; Tajkhorshid, Emad
A Microscopic View of Phospholipid Insertion into Biological Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1754-1764, FEB 20 2014
abstract, full text, DOI:10.1021/jp409854w

Heinzelmann, Germano; Chen, Po-Chia; Kuyucak, Serdar
Computation of Standard Binding Free Energies of Polar and Charged Ligands to the Glutamate Receptor GluA2
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1813-1824, FEB 20 2014
abstract, full text, DOI:10.1021/jp412195m

Feil, Susanne C.; Ascher, David B.; Kuiper, Michael J.; Tweten, Rodney K.; Parker, Michael W.
Structural Studies of Streptococcus pyogenes Streptolysin O Provide Insights into the Early Steps of Membrane Penetration
JOURNAL OF MOLECULAR BIOLOGY, 426:785-792, FEB 20 2014
abstract, full text, DOI:10.1016/j.jmb.2013.11.020

Kim, Hajin; Abeysirigunawarden, Sanjaya C.; Chen, Ke; Mayerle, Megan; Ragunathan, Kaushik; Luthey-Schulten, Zaida; Ha, Taekjip; Woodson, Sarah A.
Protein-guided RNA dynamics during early ribosome assembly
NATURE, 506:334-+, FEB 20 2014
abstract, full text, DOI:10.1038/nature13039

Li, Li; Szostak, Jack W.
The Free Energy Landscape of Pseudorotation in 3 '-5 ' and 2 '-5 ' Linked Nucleic Acids
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2858-2865, FEB 19 2014
abstract, full text, DOI:10.1021/ja412079b

Ide, Julien; Mereau, Raphael; Ducasse, Laurent; Castet, Frederic; Bock, Harald; Olivier, Yoann; Cornil, Jerome; Beljonne, David; D'Avino, Gabriele; Roscioni, Otello Maria; Muccioli, Luca; Zannoni, Claudio
Charge Dissociation at Interfaces between Discotic Liquid Crystals: The Surprising Role of Column Mismatch
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2911-2920, FEB 19 2014
abstract, full text, DOI:10.1021/ja4114769

Xiong, Feifei; Xia, Liliang; Wang, Jingfang; Wu, Biao; Wang, Dengyu; Yuan, Longfang; Cheng, Yating; Zhu, Hongying; Che, Xiaoyan; Zhang, Qinghua; Zhao, Guoping; Wang, Ying
A High-Affinity CDR-Grafted Antibody against Influenza A H5N1 Viruses Recognizes a Conserved Epitope of H5 Hemagglutinin
PLOS ONE, 9 Art. No. e88777, FEB 18 2014
abstract, full text, DOI:10.1371/journal.pone.0088777

Giambasu, George M.; Luchko, Tyler; Herschlag, Daniel; York, Darrin M.; Case, David A.
Ion Counting from Explicit-Solvent Simulations and 3D-RISM
BIOPHYSICAL JOURNAL, 106:883-894, FEB 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.01.021

Wang, Yong; Liu, Yanxin; DeBerg, Hannah A.; Nomura, Takeshi; Hoffman, Melinda Tonks; Rohde, Paul R.; Schulten, Klaus; Martinac, Boris; Selvin, Paul R.
Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel
ELIFE, 3 Art. No. e01834, FEB 18 2014
abstract, full text, TCBG publications, DOI:10.7554/eLife.01834

Stewart, Matthew B.; Gray, Stephen R.; Vasiljevic, Todor; Orbell, John D.
Exploring the molecular basis for the metal-mediated assembly of alginate gels
CARBOHYDRATE POLYMERS, 102:246-253, FEB 15 2014
abstract, full text, DOI:10.1016/j.carbpol.2013.11.034

Alizadeh, Ali; Parsafar, GolamAbbas
Temperature dependence and the effect of charge configuration on water permeation through modified carbon nanotubes: A simulation study
FLUID PHASE EQUILIBRIA, 363:282-289, FEB 15 2014
abstract, full text, DOI:10.1016/j.fluid.2013.12.005

Huggins, David J.
Comparing Distance Metrics for Rotation Using the k-Nearest Neighbors Algorithm for Entropy Estimation
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:377-385, FEB 15 2014
abstract, full text, DOI:10.1002/jcc.23504

Hynninen, Antti-Pekka; Crowley, Michael F.
New Faster CHARMM Molecular Dynamics Engine
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:406-413, FEB 15 2014
abstract, full text, DOI:10.1002/jcc.23501

Yoon, Gwonchan; Lee, Myeongsang; Kim, Jae In; Na, Sungsoo; Eom, Kilho
Role of Sequence and Structural Polymorphism on the Mechanical Properties of Amyloid Fibrils
PLOS ONE, 9 Art. No. e88502, FEB 14 2014
abstract, full text, DOI:10.1371/journal.pone.0088502

D'Amore, Claudio; Di Leva, Francesco Saverio; Sepe, Valentina; Renga, Barbara; Del Gaudio, Chiara; D'Auria, Maria Valeria; Zampella, Angela; Fiorucci, Stefano; Limongelli, Vittorio
Design, Synthesis, and Biological Evaluation of Potent Dual Agonists of Nuclear and Membrane Bile Acid Receptors
JOURNAL OF MEDICINAL CHEMISTRY, 57:937-954, FEB 13 2014
abstract, full text, DOI:10.1021/jm401873d

Narawane, Shailesh; Budnjo, Adnan; Grauffel, Cedric; Haug, Bengt Erik; Reuter, Nathalie
In Silico Design, Synthesis, and Assays of Specific Substrates for Proteinase 3: Influence of Fluorogenic and Charged Groups
JOURNAL OF MEDICINAL CHEMISTRY, 57:1111-1115, FEB 13 2014
abstract, full text, DOI:10.1021/jm401559r

Pogorelov, Taras V.; Vermaas, Josh V.; Arcario, Mark J.; Tajkhorshid, Emad
Partitioning of Amino Acids into a Model Membrane: Capturing the Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1481-1492, FEB 13 2014
abstract, full text, DOI:10.1021/jp4089113

Duboue-Dijon, Elise; Fogarty, Aoife C.; Laage, Damien
Temperature Dependence of Hydrophobic Hydration Dynamics: From Retardation to Acceleration
JOURNAL OF PHYSICAL CHEMISTRY B, 118:1574-1583, FEB 13 2014
abstract, full text, DOI:10.1021/jp408603n

Carrasco-Sanchez, Veronica; Vergara-Jaque, Ariela; Zuniga, Matias; Comer, Jeffrey; John, Amalraj; Nachtigall, Fabiane M.; Valdes, Oscar; Duran-Lara, Esteban F.; Sandoval, Claudia; Santos, Leonardo S.
In situ and in silico evaluation of amine- and folate-terminated dendrimers as nanocarriers of anesthetics
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 73:250-257, FEB 12 2014
abstract, full text, DOI:10.1016/j.ejmech.2013.11.040

Campomanes, Pablo; Kellett, Whitney R.; Easthon, Lindsey M.; Ozarowski, Andrew; Allen, Karen N.; Angerhofer, Alexander; Rothlisberger, Ursula; Richards, Nigel G. J.
Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2313-2323, FEB 12 2014
abstract, full text, DOI:10.1021/ja408138f

Lee, Wook; Engels, Bernd
The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate
BIOCHEMISTRY, 53:919-931, FEB 11 2014
abstract, full text, DOI:10.1021/bi401308j

Park, Eunyong; Menetret, Jean-Francois; Gumbart, James C.; Ludtke, Steven J.; Li, Weikai; Whynot, Andrew; Rapoport, Tom A.; Akey, Christopher W.
Structure of the SecY channel during initiation of protein translocation
NATURE, 506:102-+, FEB 6 2014
abstract, full text, DOI:10.1038/nature12720

Huh, Joonsuk; Saikin, Semion K.; Brookes, Jennifer C.; Valleau, Stephanie; Fujita, Takatoshi; Aspuru-Guzik, Alan
Atomistic Study of Energy Funneling in the Light-Harvesting Complex of Green Sulfur Bacteria
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:2048-2057, FEB 5 2014
abstract, full text, DOI:10.1021/ja412035q

Wang, Deqiang; Harrer, Stefan; Luan, Binquan; Stolovitzky, Gustavo; Peng, Hongbo; Afzali-Ardakani, Ali
Regulating the Transport of DNA through Biofriendly Nanochannels in a Thin Solid Membrane
SCIENTIFIC REPORTS, 4 Art. No. 3985, FEB 5 2014
abstract, full text, DOI:10.1038/srep03985

Kyrychenko, Alexander; Freites, J. Alfredo; He, Jing; Tobias, Douglas J.; Wimley, William C.; Ladokhin, Alexey S.
Structural Plasticity in the Topology of the Membrane-Interacting Domain of HIV-1 gp41
BIOPHYSICAL JOURNAL, 106:610-620, FEB 4 2014
abstract, full text, DOI:10.1016/j.bpj.2013.12.032

Kwansa, Albert L.; De Vita, Raffaella; Freeman, Joseph W.
Mechanical recruitment of N- and C-crosslinks in collagen type I
MATRIX BIOLOGY, 34:161-169, FEB 2014
abstract, full text, DOI:10.1016/j.matbio.2013.10.012

Klappenberger, Florian
Two-dimensional functional molecular nanoarchitectures - Complementary investigations with scanning tunneling microscopy and X-ray spectroscopy
PROGRESS IN SURFACE SCIENCE, 89:1-55, FEB 2014
abstract, full text, DOI:10.1016/j.progsurf.2013.10.002

Gumbart, James C.; Beeby, Morgan; Jensen, Grant J.; Roux, Benoit
Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations
PLOS COMPUTATIONAL BIOLOGY, 10, FEB 2014
abstract, full text, DOI:10.1371/journal.pcbi.1003475

Pang, Xue-qin; Liu, Jian-yong
GPCR A(2A)AR Agonist Binding and Induced Conformation Changes of Functional Switches
CHINESE JOURNAL OF CHEMICAL PHYSICS, 27:29-38, FEB 2014
abstract, full text, DOI:10.1063/1674-0068/27/01/29-38

Newcomb, Christina J.; Sur, Shantanu; Ortony, Julia H.; Lee, One-Sun; Matson, John B.; Boekhoven, Job; Yu, Jeong Min; Schatz, George C.; Stupp, Samuel I.
Cell death versus cell survival instructed by supramolecular cohesion of nanostructuresl
NATURE COMMUNICATIONS, 5 Art. No. 3321, FEB 2014
abstract, full text, DOI:10.1038/ncomms4321

Pietra, Francesco
On Dioxygen Permeation through a Dehydrogenase-Pyrroloquinoline Quinone Complex. A Molecular-Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 11:209-216, FEB 2014
abstract, full text, DOI:10.1002/cbdv.201300314

Wu Yun-Long; Xu Xin-Hai; Yang Xue-Jun; Zou Shun; Ren Xiao-Guang
MDSLB: A new static load balancing method for parallel molecular dynamics simulations
CHINESE PHYSICS B, 23 Art. No. 028903, FEB 2014
abstract, full text, DOI:10.1088/1674-1056/23/2/028903

Patel, Jagdish Suresh; Berteotti, Anna; Ronsisvalle, Simone; Rocchia, Walter; Cavalli, Andrea
Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:470-480, FEB 2014
abstract, full text, DOI:10.1021/ci4003574

Ning, Lulu; Guo, Jingjing; Jin, Nengzhi; Liu, Huanxiang; Yao, Xiaojun
The role of Cys179-Cys214 disulfide bond in the stability and folding of prion protein: insights from molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2106, FEB 2014
abstract, full text, DOI:10.1007/s00894-014-2106-y

Barra, Pabla A.; Barraza, Luis; Jimenez, Veronica A.; Gavin, Jose A.; Alderete, Joel B.
Complexation of Mefenamic Acid by Low-Generation PAMAM Dendrimers: Insight from NMR Spectroscopy Studies and Molecular Dynamics Simulations
MACROMOLECULAR CHEMISTRY AND PHYSICS, 215:372-383, FEB 2014
abstract, full text, DOI:10.1002/macp.201300398

Lee, Jooyong; Jeon, Jonggu; Kim, Min-Seok; Lee, Hochan; Cho, Minhaeng
Amide I IR probing of core and shell hydrogen-bond structures in reverse micelles
PURE AND APPLIED CHEMISTRY, 86:135-149, FEB 2014
abstract, full text, DOI:10.1515/pac-2014-5016

Amarasinghe, Priyanthi M.; Anandarajah, A.; Ghosh, Pijush
Molecular dynamic study of capillary forces on clay particles
APPLIED CLAY SCIENCE, 88-89:170-177, FEB 2014
abstract, full text, DOI:10.1016/j.clay.2013.12.022

Ambrosia, Matthew Stanley; Ha, Man Yeong; Balachandar, S.
Dynamic hydrophobicity on flat and pillared graphite surfaces with different pillar surface fractions
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 28:669-677, FEB 2014
abstract, full text, DOI:10.1007/s12206-013-1178-4

Mishra, Panchanand; Dixit, Anshuman; Ray, Mamata; Sabat, Surendra Chandra
Mechanistic study of CuZn-SOD from Ipomoea carnea mutated at dimer interface: Enhancement of peroxidase activity upon monomerization
BIOCHIMIE, 97:181-193, FEB 2014
abstract, full text, DOI:10.1016/j.biochi.2013.10.014

Van Wart, Adam T.; Durrant, Jacob; Votapka, Lane; Amaro, Rommie E.
Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:511-517, FEB 2014
abstract, full text, DOI:10.1021/ct4008603

Mansour, Andrew Abi; Ortoleva, Peter J.
Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:518-523, FEB 2014
abstract, full text, DOI:10.1021/ct400615a

Maragliano, Luca; Roux, Benoit; Vanden-Eijnden, Eric
Comparison between Mean Forces and Swarms-of-Trajectories String Methods
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:524-533, FEB 2014
abstract, full text, DOI:10.1021/ct400606c

Comer, Jeffrey; Schulten, Klaus; Chipot, Christophe
Calculation of Lipid-Bilayer Permeabilities Using an Average Force
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:554-564, FEB 2014
abstract, full text, TCBG publications, DOI:10.1021/ct400925s

Mullen, Ryan Gotchy; Shea, Joan-Emma; Peters, Baron
Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:659-667, FEB 2014
abstract, full text, DOI:10.1021/ct4009798

Xing, Yan-Fei; Yang, Chuan-Lu; Mo, Yong-Fang; Wang, Mei-Shan; Ma, Xiao-Guang
Dynamic Mechanism of Single-Stranded DNA Encapsulated into Single-Wall Carbon Nanotubes: A Molecular Dynamics Simulation Study
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 83 Art. No. 024801, FEB 2014
abstract, full text, DOI:10.7566/JPSJ.83.024801

Contreras-Romo, Martha C.; Martinez-Archundia, Marlet; Deeb, Omar; Slusarz, Magdalena J.; Ramirez-Salinas, Gema; Garduno-Juarez, Ramon; Quintanar-Stephano, Andres; Ramirez-Galicia, Guillermo; Correa-Basurto, Jose
Exploring the Ligand Recognition Properties of the Human Vasopressin V1a Receptor Using QSAR and Molecular Modeling Studies
CHEMICAL BIOLOGY & DRUG DESIGN, 83:207-223, FEB 2014
abstract, full text, DOI:10.1111/cbdd.12229

Chen, Bo; Boel, Gregory; Hashem, Yaser; Ning, Wei; Fei, Jingyi; Wang, Chi; Gonzalez, Ruben L., Jr.; Hunt, John F.; Frank, Joachim
EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21:152-+, FEB 2014
abstract, full text, DOI:10.1038/nsmb.2741

Rothe, Benjamin; Back, Regis; Quinternet, Marc; Bizarro, Jonathan; Robert, Marie-Cecile; Blaud, Magali; Romier, Christophe; Manival, Xavier; Charpentier, Bruno; Bertrand, Edouard; Branlant, Christiane
Characterization of the interaction between protein Snu13p/15.5K and the Rsa1p/NUFIP factor and demonstration of its functional importance for snoRNP assembly
NUCLEIC ACIDS RESEARCH, 42:2015-2036, FEB 2014
abstract, full text, DOI:10.1093/nar/gkt1091

Song, Jianing; Ji, Changge; Zhang, John Z. H.
Insights on Na+ binding and conformational dynamics in multidrug and toxic compound extrusion transporter NorM
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:240-249, FEB 2014
full text

Geng, Yi-Zhao; Liu, Shu-Xia; Ji, Qing; Yan, Shiwei
Mechanical amplification mechanism of kinesin's beta-domain
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 543:10-14, FEB 1 2014
abstract, full text, DOI:10.1016/j.abb.2013.12.017

Kojic, M.; Milosevic, M.; Kojic, N.; Kim, K.; Ferrari, M.; Ziemys, A.
A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, 269:123-138, FEB 1 2014
abstract, full text, DOI:10.1016/j.cma.2013.11.010

Gonzalez, Pablo M.; Lagos, Carlos F.; Ward, Weslyn C.; Polli, James E.
Structural Requirements of the Human Sodium-Dependent Bile Acid Transporter (hASBT): Role of 3-and 7-OH Moieties on Binding and Translocation of Bile Acids
MOLECULAR PHARMACEUTICS, 11:588-598, FEB 2014
abstract, full text, DOI:10.1021/mp400575t

Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni
PLUMED 2: New feathers for an old bird
COMPUTER PHYSICS COMMUNICATIONS, 185:604-613, FEB 2014
abstract, full text, DOI:10.1016/j.cpc.2013.09.018

Chen, Dongping; Totton, Tim S.; Akroyd, Jethro W. J.; Mosbach, Sebastian; Kraft, Markus
Size-dependent melting of polycyclic aromatic hydrocarbon nano-clusters: A molecular dynamics study
CARBON, 67:79-91, FEB 2014
abstract, full text, DOI:10.1016/j.carbon.2013.09.058

Sun, Chongbo; Tang, Tian
Study on the role of polyethylenimine as gene delivery carrier using molecular dynamics simulations
JOURNAL OF ADHESION SCIENCE AND TECHNOLOGY, 28:399-416, FEB 1 2014
abstract, full text, DOI:10.1080/01694243.2012.693830

Bouard, Charlotte; Terreux, Raphael; Hope, Jennifer; Chemelle, Julie Anne; Puisieux, Alain; Ansieau, Stephane; Payen, Lea
Interhelical loops within the bHLH domain are determinant in maintaining TWIST1-DNA complexes
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:226-241, FEB 1 2014
abstract, full text, DOI:10.1080/07391102.2012.762722

Spijker, Peter; Hiasa, Takumi; Musso, Tiziana; Nishioka, Rina; Onishi, Hiroshi; Foster, Adam S.
Understanding the Interface of Liquids with an Organic Crystal Surface from Atonnistic Simulations and AFM Experiments
JOURNAL OF PHYSICAL CHEMISTRY C, 118:2058-2066, JAN 30 2014
abstract, full text, DOI:10.1021/jp4106647

Chien, Michael W.; Johnson, Robert R.; Pillai, Shreekumar R.; Singh, Shree Ram; Johnson, A. T. Charlie, Jr.
Mechanics and Energetics of DNA Hybridization on Single-Walled Carbon Nanotubes Explored Using Adaptive Biasing Force Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 118:2209-2214, JAN 30 2014
abstract, full text, DOI:10.1021/jp4102288

Xiao, Shiyan; Klein, Michael L.; LeBard, David N.; Levine, Benjamin G.; Liang, Haojun; MacDermaid, Christopher M.; Afonso-Prieto, Mercedes
Magnesium-Dependent RNA Binding to the PA Endonuclease Domain of the Avian Influenza Polymerase
JOURNAL OF PHYSICAL CHEMISTRY B, 118:873-889, JAN 30 2014
abstract, full text, DOI:10.1021/jp408383g

Lundborg, Magnus; Apostolov, Rossen; Spangberg, Daniel; Gardenas, Anders; van der Spoel, David; Lindahl, Erik
An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 35:260-269, JAN 30 2014
abstract, full text, DOI:10.1002/jcc.23495

Strauss, Ishai; Chan, Henry; Kral, Petr
Ultralong Polarization Chains Induced by Ions Solvated in Confined Water Monolayers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:1170-1173, JAN 29 2014
abstract, full text, DOI:10.1021/ja4087962

Mullen, Ryan Gotchy; Shea, Joan-Emma; Peters, Baron
Communication: An existence test for dividing surfaces without recrossing
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 041104, JAN 28 2014
abstract, full text, DOI:10.1063/1.4862504

Solov'yov, Ilia A.; Domratcheva, Tatiana; Schulten, Klaus
Separation of photo-induced radical pair in cryptochrome to a functionally critical distance
SCIENTIFIC REPORTS, 4 Art. No. 3845, JAN 24 2014
abstract, full text, TCBG publications, DOI:10.1038/srep03845

Sun, Mei-Hui; Liu, Shuang-Quan; Du, Ke-Jie; Nie, Chang-Ming; Lin, Ying-Wu
A spectroscopic study of uranyl-cytochrome b(5)/cytochrome c interactions
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 118:130-137, JAN 24 2014
abstract, full text, DOI:10.1016/j.saa.2013.08.112

Meng, Yilin; Roux, Benoit
Locking the Active Conformation of c-Src Kinase through the Phosphorylation of the Activation Loop
JOURNAL OF MOLECULAR BIOLOGY, 426:423-435, JAN 23 2014
abstract, full text, DOI:10.1016/j.jmb.2013.10.001

Jean-Francois, Frantz L.; Dai, Jian; Yu, Lu; Myrick, Alissa; Rubin, Eric; Fajer, Piotr G.; Song, Likai; Zhou, Huan-Xiang; Cross, Timothy A.
Binding of MgtR, a Salmonella Transmembrane Regulatory Peptide, to MgtC, a Mycobacterium tuberculosis Virulence Factor: A Structural Study
JOURNAL OF MOLECULAR BIOLOGY, 426:436-446, JAN 23 2014
abstract, full text, DOI:10.1016/j.jmb.2013.10.014

Rashid, M. Harunur; Kuyucak, Serdar
Free Energy Simulations of Binding of HsTx1 Toxin to Kv1 Potassium Channels: the Basis of Kv1.3/Kv1.1 Selectivity
JOURNAL OF PHYSICAL CHEMISTRY B, 118:707-716, JAN 23 2014
abstract, full text, DOI:10.1021/jp410950h

Dolores Elola, M.; Rodriguez, Javier
Solvation of Coumarin 480 within nano-confining environments: Structure and dynamics
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 034702, JAN 21 2014
abstract, full text, DOI:10.1063/1.4861586

Jung, Segun; Schlick, Tamar
Interconversion between Parallel and Antiparallel Conformations of a 4H RNA junction in Domain 3 of Foot-and-Mouth Disease Virus IRES Captured by Dynamics Simulations
BIOPHYSICAL JOURNAL, 106:447-458, JAN 21 2014
abstract, full text, DOI:10.1016/j.bpj.2013.12.008

Li, Chun-Yang; Wei, Tian-Di; Zhang, Sheng-Hui; Chen, Xiu-Lan; Gao, Xiang; Wang, Peng; Xie, Bin-Bin; Su, Hai-Nan; Qin, Qi-Long; Zhang, Xi-Ying; Yu, Juan; Zhang, Hong-Hai; Zhou, Bai-Cheng; Yang, Gui-Peng; Zhang, Yu-Zhong
Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:1026-1031, JAN 21 2014
abstract, full text, DOI:10.1073/pnas.1312354111

Wakai, Nobuhiko; Takemura, Kazuhiro; Morita, Takami; Kitao, Akio
Mechanism of Deep-Sea Fish alpha-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations
PLOS ONE, 9 Art. No. e85852, JAN 20 2014
abstract, full text, DOI:10.1371/journal.pone.0085852

Araujo, Pedro M. M.; da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Comparative theoretical study of the binding of potential cancer-treatment drugs to Checkpoint kinase 1
CHEMICAL PHYSICS LETTERS, 591:273-276, JAN 20 2014
abstract, full text, DOI:10.1016/j.cplett.2013.11.049

Van Ngo; Stefanovski, Darko; Haas, Stephan; Farley, Robert A.
Non-Equilibrium Dynamics Contribute to Ion Selectivity in the KcsA Channel
PLOS ONE, 9 Art. No. e86079, JAN 17 2014
abstract, full text, DOI:10.1371/journal.pone.0086079

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Correlated Dynamical Crossovers of the Hydration Layer of a Single-Stranded DNA Oligomer
JOURNAL OF PHYSICAL CHEMISTRY B, 118:413-422, JAN 16 2014
abstract, full text, DOI:10.1021/jp408234k

Beecher, Consuelo N.; Young, Robert P.; Langeslay, Derek J.; Mueller, Leonard J.; Larive, Cynthia K.
Hydroxyl-Proton Hydrogen Bonding in the Heparin Oligosaccharide Arixtra in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 118:482-491, JAN 16 2014
abstract, full text, DOI:10.1021/jp410540d

Lee, Sarah; Tran, Alan; Allsopp, Matthew; Lim, Joseph B.; Henin, Jerome; Klauda, Jeffery B.
CHARMM36 United Atom Chain Model for Lipids and Surfactants
JOURNAL OF PHYSICAL CHEMISTRY B, 118:547-556, JAN 16 2014
abstract, full text, DOI:10.1021/jp410344g

Megow, Joerg; May, Volkhard
Plasmon enhanced molecular absorption: A mixed quantum-classical description of supramolecular complexes attached to a metal nanoparticle
CHEMICAL PHYSICS, 428:6-13, JAN 15 2014
abstract, full text, DOI:10.1016/j.chemphys.2013.10.023

Escobar, Francisco Velazquez; Hildebrandt, Thomas; Utesch, Tillmann; Schmitt, Franz Josef; Seuffert, Ina; Michael, Norbert; Schulz, Claudia; Mroginski, Maria Andrea; Friedrich, Thomas; Hildebrandt, Peter
Structural Parameters Controlling the Fluorescence Properties of Phytochromes
BIOCHEMISTRY, 53:20-29, JAN 14 2014
abstract, full text, DOI:10.1021/bi401287u

Chamberlin, Adam; Qiu, Feng; Rebolledo, Santiago; Wang, Yibo; Noskov, Sergei Y.; Larsson, H. Peter
Hydrophobic plug functions as a gate in voltage-gated proton channels
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E273-E282, JAN 14 2014
abstract, full text, DOI:10.1073/pnas.1318018111

Zhang, Yanxing; Gao, Puyuan; Zhang, Liuyao; Yang, Zongxian
The search for the good Pd-based catalyst for oxygen reduction reaction: core-shell M4@Pd20 nanowires
JOURNAL OF NANOPARTICLE RESEARCH, 16 Art. No. 2225, JAN 10 2014
abstract, full text, DOI:10.1007/s11051-013-2225-x

Pepin, Robert; Laszlo, Kenneth J.; Peng, Bo; Marek, Ales; Bush, Matthew F.; Turecek, Frantisek
Comprehensive Analysis of Gly-Leu-Gly-Gly-Lys Peptide Dication Structures and Cation-Radical Dissociations Following Electron Transfer: From Electron Attachment to Backbone Cleavage, Ion-Molecule Complexes, and Fragment Separation
JOURNAL OF PHYSICAL CHEMISTRY A, 118:308-324, JAN 9 2014
abstract, full text, DOI:10.1021/jp411100c

Zhao, Juan; Shi, Jipei; Wang, Jianping
Amide-I Characteristics of Helical beta-Peptides by Linear Infrared Measurement and Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:94-106, JAN 9 2014
abstract, full text, DOI:10.1021/jp4095936

Honarparvar, Bahareh; Govender, Thavendran; Maguire, Glenn E. M.; Soliman, Mahmoud E. S.; Kruger, Hendrik G.
Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity
CHEMICAL REVIEWS, 114:493-537, JAN 8 2014
full text, DOI:10.1021/cr300314q

Cisneros, G. Andres; Karttunen, Mikko; Ren, Pengyu; Sagui, Celeste
Classical Electrostatics for Biomolecular Simulations
CHEMICAL REVIEWS, 114:779-814, JAN 8 2014
full text, DOI:10.1021/cr300461d

Petridis, Loukas; Arnbaye, Haile; Jagadamma, Sindhu; Kilbey, S. Michael, I.I.; Lokitz, Bradley S.; Lauter, Valeria; Mayes, Melanie A.
Spatial Arrangement of Organic Compounds on a Model Mineral Surface: Implications for Soil Organic Matter Stabilization
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 48:79-84, JAN 7 2014
abstract, full text, DOI:10.1021/es403430k

Duff, Nathan; Dahal, Yuba Raj; Schmit, Jeremy D.; Peters, Baron
Salting out the polar polymorph: Analysis by alchemical solvent transformation
JOURNAL OF CHEMICAL PHYSICS, 140 Art. No. 014501, JAN 7 2014
abstract, full text, DOI:10.1063/1.4853775

Prieto, Lidia; He, Yi; Lazaridis, Themis
Protein Arcs May Form Stable Pores in Lipid Membranes
BIOPHYSICAL JOURNAL, 106:154-161, JAN 7 2014
abstract, full text, DOI:10.1016/j.bpj.2013.11.4490

Cruz-Chu, Eduardo R.; Malafeev, Alexander; Pajarskas, Tautrimas; Pivkin, Igor V.; Koumoutsakos, Petros
Structure and Response to Flow of the Glycocalyx Layer
BIOPHYSICAL JOURNAL, 106:232-243, JAN 7 2014
abstract, full text, DOI:10.1016/j.bpj.2013.09.060

Cai, Kaicong; Su, Tingting; Lin, Shen; Zheng, Renhui
Molecular mechanics force field-based general map for the solvation effect on amide I probe of peptide in different micro-environments
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 117:548-556, JAN 3 2014
abstract, full text, DOI:10.1016/j.saa.2013.08.058

Comer, Jeffrey; Roux, Benoit; Chipot, Christophe
Achieving ergodic sampling using replica-exchange free-energy calculations
MOLECULAR SIMULATION, 40:218-228, JAN 2 2014
abstract, full text, DOI:10.1080/08927022.2013.841909

Chen, Cong; Zhang, Kun; Wang, Ping; Li, Wei Zhong; Song, Yong Chen; Zhang, Ning
Ion hydration and hydrogen bond structure in NaCl solutions at temperatures and pressures for carbon dioxide sequestration: the effects of solvated CO2 molecules
MOLECULAR PHYSICS, 112:74-84, JAN 2 2014
abstract, full text, DOI:10.1080/00268976.2013.800244

Shamloo, Amir; Nikbin, Ehsan; Mehboudi, Nastaran; Damirchi, Behzad
HOMO-OLIGOMERIZATION OF TRANSMEMBRANE alpha-DOMAIN OF INTEGRIN
2014 36TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC), 1162-1165, 2014
abstract, full text

Macwan, Isaac; Zhao, Zihe; Sobh, Omar; Patra, Prabir
A FLAGELLUM BASED STUDY OF SEMICONDUCTOR NANOFABRICATION THROUGH MAGNETOTAXIS
2014 36TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC), 2777-2780, 2014
abstract, full text

Reeves, Melissa S.; Whitnell, Robert M.
New Computational Physical Chemistry Experiments: Using POGIL Techniques with ab Initio and Molecular Dynamics Calculations
ADDRESSING THE MILLENNIAL STUDENT IN UNDERGRADUATE CHEMISTRY, 1180:71-90, 2014
abstract, full text

Langmead, Christopher James
Generative Models of Conformational Dynamics
PROTEIN CONFORMATIONAL DYNAMICS, 805:87-105, 2014
abstract, full text, DOI:10.1007/978-3-319-02970-2_4

Kuyucak, Serdar; Norton, Raymond S.
Computational approaches for designing potent and selective analogs of peptide toxins as novel therapeutics
FUTURE MEDICINAL CHEMISTRY, 6:1645-1658, 2014
abstract, full text, DOI:10.4155/FMC.14.98

Yim, Keun Soo
Characterization of Impact of Transient Faults and Detection of Data Corruption Errors in Large-Scale N-Body Programs Using Graphics Processing Units
2014 IEEE 28TH INTERNATIONAL PARALLEL AND DISTRIBUTED PROCESSING SYMPOSIUM, DOI:10.1109/IPDPS.2014.55, 2014
abstract, full text, DOI:10.1109/IPDPS.2014.55

Badu, Shyam R.; Melnik, Roderik; Paliy, Maxim; Prabhakar, Sanjay; Sebetci, Ali; Shapiro, Bruce A.
High Performance Computing Studies of RNA Nanotubes
PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2, 601-607, 2014
abstract, full text

LeVine, Michael; Perez-Aguilar, Jose Manuel; Weinstein, Harel
N-body Information Theory (NbIT) Analysis of Rigid-Body Dynamics in Intracellular Loop 2 of the 5-HT2A Receptor
PROCEEDINGS IWBBIO 2014: INTERNATIONAL WORK-CONFERENCE ON BIOINFORMATICS AND BIOMEDICAL ENGINEERING, VOLS 1 AND 2, 1190-1201, 2014
abstract, full text

Katagiri, Satoshi; Hayashi, Takaaki; Akahori, Masakazu; Itabashi, Takeshi; Nishino, Jo; Yoshitake, Kazutoshi; Furuno, Masaaki; Ikeo, Kazuho; Okada, Tetsuji; Tsuneoka, Hiroshi; Iwata, Takeshi
RHO Mutations (p.W126L and p.A346P) in Two Japanese Families with Autosomal Dominant Retinitis Pigmentosa
JOURNAL OF OPHTHALMOLOGY, Art. No. 210947, 2014
abstract, full text, DOI:10.1155/2014/210947

Azamat, J.; Sardroodi, J. J.; Rastkar, A.
Water desalination through armchair carbon nanotubes: a molecular dynamics study
RSC ADVANCES, 4:63712-63718, 2014
abstract, full text, DOI:10.1039/c4ra08249d

Luan, Binquan; Zhou, Bo; Tien Huynh; Zhou, Ruhong
Controlled transport of DNA through a Y-shaped carbon nanotube in a solid membrane
NANOSCALE, 6:11479-11483, 2014
abstract, full text, DOI:10.1039/c4nr02754j

Ou, Shu-Ching; Cui, Di; Patel, Sandeep
Association of alkanes with the aqueous liquid-vapor interface: a reference system for interpreting hydrophobicity generally through interfacial fluctuations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26779-26785, 2014
abstract, full text, DOI:10.1039/c4cp03170a

Saharay, Moumita; Kirkpatrick, R. James
Ab initio and metadynamics studies on the role of essential functional groups in biomineralization of calcium carbonate and environmental situations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26843-26854, 2014
abstract, full text, DOI:10.1039/c4cp03904a

Zhao, Yuan; Chen, Nanhao; Mo, Yirong; Cao, Zexing
A full picture of enzymatic catalysis by hydroxynitrile lyases from Hevea brasiliensis: protonation dependent reaction steps and residue-gated movement of the substrate and the product
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26864-26875, 2014
abstract, full text, DOI:10.1039/c4cp04032e

Meneksedag-Erol, Deniz; Sun, Chongbo; Tang, Tian; Uludag, Hasan
Molecular Dynamics Simulations of Polyplexes and Lipoplexes Employed in Gene Delivery
INTRACELLULAR DELIVERY II: FUNDAMENTALS AND APPLICATIONS, 7:277-311, 2014
abstract, full text, DOI:10.1007/978-94-017-8896-0_15

Kutalkova, Eva; Hrncirik, Josef; Ingr, Marek
Pressure induced structural changes and dimer destabilization of HIV-1 protease studied by molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:25906-25915, 2014
abstract, full text, DOI:10.1039/c4cp03676j

Dutta, Debodyuti; Mishra, Sabyashachi
The structural and energetic aspects of substrate binding and the mechanism of action of the DapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) investigated using a hybrid QM/MM method
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:26348-26358, 2014
abstract, full text, DOI:10.1039/c4cp03986f

Moreau, Pascale; Dezhenkova, Lyubov G.; Anizon, Fabrice; Nauton, Lionel; Thery, Vincent; Liang, Shuguang; Kaluzhny, Dmitry N.; Shtil, Alexander A.
New Potent and Selective Inhibitor of Pim-1/3 Protein Kinases Sensitizes Human Colon Carcinoma Cells to Doxorubicin
ANTI-CANCER AGENTS IN MEDICINAL CHEMISTRY, 14:1228-1236, 2014
abstract, full text

Mielecki, Marcin; Milner-Krawczyk, Malgorzata; Grzelak, Krystyna; Mielecki, Damian; Krzysko, Krystiana A.; Lesyng, Bogdan; Priebe, Waldemar
Analogs of Cinnamic Acid Benzyl Amide As Nonclassical Inhibitors of Activated JAK2 Kinase
CURRENT CANCER DRUG TARGETS, 14:638-651, 2014
abstract, full text

Pontecchiani, Fabio; Simonovsky, Eyal; Wieczorek, Robert; Barbosa, Nuno; Rowinska-Zyrek, Magdalena; Potocki, Slawomir; Remelli, Maurizio; Miller, Yifat; Kozlowski, Henryk
The unusual binding mechanism of Cu(II) ions to the poly-histidyl domain of a peptide found in the venom of an African viper
DALTON TRANSACTIONS, 43:16680-16689, 2014
abstract, full text, DOI:10.1039/c4dt02257b

Hirst, Jonathan D.; Glowacki, David R.; Baaden, Marc
Molecular simulations and visualization: introduction and overview
FARADAY DISCUSSIONS, 169:9-22, 2014
abstract, full text, DOI:10.1039/c4fd90024c

Dreher, Matthieu; Prevoteau-Jonquet, Jessica; Trellet, Mikael; Piuzzi, Marc; Baaden, Marc; Raffin, Bruno; Ferey, Nicolas; Robert, Sophie; Limet, Sebastien
ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations
FARADAY DISCUSSIONS, 169:119-142, 2014
abstract, full text, DOI:10.1039/c3fd00142c

Stone, John E.; McGreevy, Ryan; Isralewitz, Barry; Schulten, Klaus
GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting
FARADAY DISCUSSIONS, 169:265-283, 2014
abstract, full text, TCBG publications, DOI:10.1039/c4fd00005f

Kukkurainen, Sampo; Maatta, Juha A.; Saeger, John; Valjakka, Jarkko; Vogel, Viola; Hytonen, Vesa P.
The talin-integrin interface under mechanical stress
MOLECULAR BIOSYSTEMS, 10:3217-3228, 2014
abstract, full text, DOI:10.1039/c4mb00341a

Sikdar, Samapan; Chakrabarti, J.; Ghosh, Mahua
A microscopic insight from conformational thermodynamics to functional ligand binding in proteins
MOLECULAR BIOSYSTEMS, 10:3280-3289, 2014
abstract, full text, DOI:10.1039/c4mb00434e

Liu, Peng; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:24169-24172, 2014
abstract, full text, DOI:10.1039/c4cp04200j

Bai, Qifeng; Zhang, Yang; Li, Xiaomeng; Chen, Wenbo; Liu, Huanxiang; Yao, Xiaojun
Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:24332-24338, 2014
abstract, full text, DOI:10.1039/c4cp03331k

Turpin, Eleanor R.; Mulholland, Sam; Teale, Andrew M.; Bonev, Boyan B.; Hirst, Jonathan D.
New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations
RSC ADVANCES, 4:48621-48631, 2014
abstract, full text, DOI:10.1039/c4ra09897h

Khan, Rashid Ahmed; Liu, Jiyuan; Zhang, Yalin
Catalytic inactivation of alkaline phosphatase by cantharidin, an inhibitor of protein phosphatase
RSC ADVANCES, 4:49987-49994, 2014
abstract, full text, DOI:10.1039/c4ra09285f

Gajula, Kiran S.; Huwe, Peter J.; Mo, Charlie Y.; Crawford, Daniel J.; Stivers, James T.; Radhakrishnan, Ravi; Kohli, Rahul M.
High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase
NUCLEIC ACIDS RESEARCH, 42:9964-9975, 2014
abstract, full text, DOI:10.1093/nar/gku689

del Valle, Luis J.; Bertran, Oscar; Chaves, Gustavo; Revilla-Lopez, Guillermo; Rivas, Manuel; Casas, Maria T.; Casanovas, Jordi; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
DNA adsorbed on hydroxyapatite surfaces
JOURNAL OF MATERIALS CHEMISTRY B, 2:6953-6966, 2014
abstract, full text, DOI:10.1039/c4tb01184h

D'Annessa, Ilda; Coletta, Andrea; Sutthibutpong, Thana; Mitchell, Jonathan; Chillemi, Giovanni; Harris, Sarah; Desideri, Alessandro
Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site
NUCLEIC ACIDS RESEARCH, 42:9304-9312, 2014
abstract, full text, DOI:10.1093/nar/gku654

Lionta, Evanthia; Spyrou, George; Vassilatis, Demetrios K.; Cournia, Zoe
Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 14:1923-1938, 2014
abstract, full text, DOI:10.2174/1568026614666140929124445

Segura-Cabrera, A.; Garcia-Perez, C. A.; Cipres-Flores, F. J.; Cuevas-Hernandez, R. I.; Trujillo-Ferrara, J. G.; Correa-Basurto, J.; Soriano-Ursua, M. A.
Molecular dynamics simulations to explore the active/inactive conformers of guinea pig beta(2) adrenoceptor for the selective design of agonists or antagonists
MOLECULAR SIMULATION, 40:1244-1254, 2014
abstract, full text, DOI:10.1080/08927022.2013.857771

Mendes, Celso L.; Bode, Brett; Bauer, Gregory H.; Enos, Jeremy; Beldica, Cristina; Kramer, William T.
Deploying a Large Petascale System: the Blue Waters Experience
2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29:198-209, 2014
abstract, full text, DOI:10.1016/j.procs.2014.05.018

Ieong, Pek U.; Sorensen, Jesper; Vemu, Prasantha L.; Wong, Celia W.; Demir, Oezlem; Williams, Nadya P.; Wang, Jianwu; Crawl, Daniel; Swift, Robert V.; Malmstrom, Robert D.; Altintas, Ilkay; Amaro, Rommie E.
Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations
2014 INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE, 29:1745-1755, 2014
abstract, full text, DOI:10.1016/j.procs.2014.05.159

Luna-Palencia, Gabriela R.; Martinez-Ramos, Federico; Vasquez-Moctezuma, Ismael; Jonathan Fragoso-Vazquez, Manuel; Elena Mendieta-Wejebe, Jessica; Padilla-Martinez, Itzia I.; Sixto-Lopez, Yudibeth; Mendez-Luna, David; Trujillo-Ferrara, Jose; Meraz-Rios, Marco A.; Fonseca-Sabater, Yadira; Correa-Basurto, Jose
Three Amino Acid Derivatives of Valproic Acid: Design, Synthesis, Theoretical and Experimental Evaluation as Anticancer Agents
ANTI-CANCER AGENTS IN MEDICINAL CHEMISTRY, 14:984-993, 2014
abstract, full text

Jang, Hyunbum; Arce, Fernando Teran; Ramachandran, Srinivasan; Kagan, Bruce L.; Lal, Ratnesh; Nussinov, Ruth
Disordered amyloidogenic peptides may insert into the membrane and assemble into common cyclic structural motifs
CHEMICAL SOCIETY REVIEWS, 43:6750-6764, 2014
abstract, full text, DOI:10.1039/c3cs60459d

Kamath, Ganesh; Narayanan, Badri; Sankaranarayanan, Subramanian K. R. S.
Atomistic origin of superior performance of ionic liquid electrolytes for Al-ion batteries
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:20387-20391, 2014
abstract, full text, DOI:10.1039/c4cp02840f

Bhattacharya, R.; Kanchi, Subbarao; Roobala, C.; Lakshminarayanan, A.; Seeck, Oliver H.; Maiti, Prabal K.; Ayappa, K. G.; Jayaraman, N.; Basu, J. K.
A new microscopic insight into membrane penetration and reorganization by PETIM dendrimers
SOFT MATTER, 10:7577-7587, 2014
abstract, full text, DOI:10.1039/c4sm01112k

Lo, Kin Cheung; Li, Sheung Yin; Chan, Wai Kin
Photoconductivity enhancement and charge transport properties in a conjugated polyelectrolyte/carbon nanotube hybrid studied by scanning probe microscopy
JOURNAL OF MATERIALS CHEMISTRY C, 2:7739-7751, 2014
abstract, full text, DOI:10.1039/c4tc00819g

Espinoza-Fonseca, L. Michel; Colson, Brett A.; Thomas, David D.
Effects of pseudophosphorylation mutants on the structural dynamics of smooth muscle myosin regulatory light chain
MOLECULAR BIOSYSTEMS, 10:2693-2698, 2014
abstract, full text, DOI:10.1039/c4mb00364k

Martinez-Archundia, Marlet; Correa-Basurto, Jose
Molecular dynamics simulations reveal initial structural and dynamic features for the A(2)AR as a result of ligand binding
MOLECULAR SIMULATION, 40:996-1014, 2014
abstract, full text, DOI:10.1080/08927022.2013.835485

Kostopoulou, Ourania N.; Kouvela, Ekaterini C.; Magoulas, George E.; Garnelis, Thomas; Panagoulias, Ioannis; Rodi, Maria; Papadopoulos, Georgios; Mouzaki, Athanasia; Dinos, George P.; Papaioannou, Dionissios; Kalpaxis, Dimitrios L.
Conjugation with polyamines enhances the antibacterial and anticancer activity of chloramphenicol
NUCLEIC ACIDS RESEARCH, 42:8621-8634, 2014
abstract, full text, DOI:10.1093/nar/gku539

Dixit, Anshuman; Verkhivker, Gennady M.
Structure-Functional Prediction and Analysis of Cancer Mutation Effects in Protein Kinases
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, Art. No. 653487, 2014
abstract, full text, DOI:10.1155/2014/653487

Chen, Qile; Kong, Xian; Li, Jipeng; Lu, Diannan; Liu, Zheng
Electrokinetic desalination using honeycomb carbon nanotubes (HC-CNTs): a conceptual study by molecular simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18941-18948, 2014
abstract, full text, DOI:10.1039/c4cp02679a

Walczewska-Szewc, Katarzyna; Corry, Ben
Do bifunctional labels solve the problem of dye diffusion in FRET analysis?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:18949-18954, 2014
abstract, full text, DOI:10.1039/c4cp02110j

Ilizaliturri-Flores, Ian; Correa-Basurto, Jose; Benitez-Cardoza, Claudia G.; Zamorano-Carrillo, Absalom
A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1707-1719, 2014
abstract, full text, DOI:10.1080/07391102.2013.833858

Kondratyev, Maxim S.; Lunin, Sergey M.; Kabanov, Artem V.; Samchenko, Alexandr A.; Komarov, Vladislav M.; Fesenko, Evgeny E.; Novoselova, Elena G.
Structural and dynamic properties of thymopoietin mimetics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1793-1801, 2014
abstract, full text, DOI:10.1080/07391102.2013.834851

Chapron, Yves; Charlet, Laurent; Sahai, Nita
Fate of pathological prion (PrP(sc)92-138) in soil and water: prion-clay nanoparticle molecular dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32:1802-1816, 2014
abstract, full text, DOI:10.1080/07391102.2013.836461

Hudiyanti, Dwi; Radifar, Muhammad; Raharjo, Tri Joko; Narsito, Narsito; Noegrohati, Sri
A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water
JOURNAL OF CHEMISTRY, Art. No. 273084, 2014
abstract, full text, DOI:10.1155/2014/273084

Mura, Cameron; McAnany, Charles E.
An introduction to biomolecular simulations and docking
MOLECULAR SIMULATION, 40:732-764, 2014
abstract, full text, DOI:10.1080/08927022.2014.935372

LeBard, David N.
Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware
MOLECULAR SIMULATION, 40:802-820, 2014
abstract, full text, DOI:10.1080/08927022.2014.899700

des Georges, Amedee; Hashem, Yaser; Buss, Sarah N.; Jossinet, Fabrice; Zhang, Qin; Liao, Hstau Y.; Fu, Jie; Jobe, Amy; Grassucci, Robert A.; Langlois, Robert; Bajaj, Chandrajit; Westhof, Eric; Madison-Antenucci, Susan; Frank, Joachim
High-resolution Cryo-EM Structure of the Trypanosoma brucei Ribosome: A Case Study
COMPUTATIONAL METHODS FOR THREE-DIMENSIONAL MICROSCOPY RECONSTRUCTION, 97-132, 2014
abstract, full text, DOI:10.1007/978-1-4614-9521-5_5

Bai, Qifeng; Perez-Sanchez, Horacio; Zhang, Yang; Shao, Yonghua; Shi, Danfeng; Liu, Huanxiang; Yao, Xiaojun
Ligand induced change of beta(2) adrenergic receptor from active to inactive conformation and its implication for the closed/open state of the water channel: insight from molecular dynamics simulation, free energy calculation and Markov state model analysis
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:15874-15885, 2014
abstract, full text, DOI:10.1039/c4cp01185f

MacDonald, Corey A.; Bushnell, Eric A. C.; Gauld, James W.; Boyd, Russell J.
The catalytic formation of leukotriene C-4: a critical step in inflammatory processes
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:16284-16289, 2014
abstract, full text, DOI:10.1039/c4cp01984a

Kumar, Amit; Melis, Paola; Genna, Vito; Cocco, Eleonora; Marrosu, Maria Giovanna; Pieroni, Enrico
Antigenic peptide molecular recognition by the DRB1-DQB1 haplotype modulates multiple sclerosis susceptibility
MOLECULAR BIOSYSTEMS, 10:2043-2054, 2014
abstract, full text, DOI:10.1039/c4mb00203b

Zorzini, Valentina; Buts, Lieven; Sleutel, Mike; Garcia-Pino, Abel; Talavera, Ariel; Haesaerts, Sarah; De Greve, Henri; Cheung, Ambrose; van Nuland, Nico A. J.; Loris, Remy
Structural and biophysical characterization of Staphylococcus aureus SaMazF shows conservation of functional dynamics
NUCLEIC ACIDS RESEARCH, 42:6709-6725, 2014
abstract, full text, DOI:10.1093/nar/gku266

Orozco, Modesto
A theoretical view of protein dynamics
CHEMICAL SOCIETY REVIEWS, 43:5051-5066, 2014
abstract, full text, DOI:10.1039/c3cs60474h

Abeyrathne, Chathurika D.; Halgamuge, Malka N.; Farrell, Peter M.; Skafidas, Efstratios
Dielectric properties of liquid phase molecular clusters using the external field method: molecular dynamics study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:13943-13947, 2014
abstract, full text, DOI:10.1039/c4cp00716f

Chen, Xin; Duan, Danhui; Zhu, Shuyan; Liu, Yafang
Dynamics study on the stability of animal prion proteins
TURKISH JOURNAL OF BIOCHEMISTRY-TURK BIYOKIMYA DERGISI, 39:188-195, 2014
abstract, full text, DOI:10.5505/tjb.2014.21033

Jin, Lu; Ye, Fei; Zhao, Dan; Chen, Shijie; Zhu, Kongkai; Zheng, Mingyue; Jiang, Ren-Wang; Jiang, Hualiang; Luo, Cheng
Metadynamics Simulation Study on the Conformational Transformation of HhaI Methyltransferase: An Induced-Fit Base-Flipping Hypothesis
BIOMED RESEARCH INTERNATIONAL, Art. No. 304563, 2014
abstract, full text, DOI:10.1155/2014/304563

Kumar, Vikash; Chandra, Sharat; Siddiqi, Mohammad Imran
Recent Advances in the Development of Antiviral Agents Using Computer-aided Structure Based Approaches
CURRENT PHARMACEUTICAL DESIGN, 20:3488-3499, 2014
abstract, full text

Xu, Jia-Jia; Yi, Hai-Bo; Li, Hui-Ji; Chen, Yun
Ionic solvation and association in LiCl aqueous solution: a density functional theory, polarised continuum model and molecular dynamics investigation
MOLECULAR PHYSICS, 112:1710-1723, 2014
abstract, full text, DOI:10.1080/00268976.2013.860244

Plehn, Thomas; Megow, Joerg; May, Volkhard
Concerted charge and energy transfer processes in a highly flexible fullerene-dye system: a mixed quantum-classical study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:12949-12958, 2014
abstract, full text, DOI:10.1039/c4cp01081g

Murase, Sara K.; Haspel, Nurit; del Valle, Luis J.; Perpete, Eric A.; Michaux, Catherine; Nussinov, Ruth; Puiggali, Jordi; Aleman, Carlos
Molecular characterization of L-phenylalanine terminated poly(L-lactide) conjugates
RSC ADVANCES, 4:23231-23241, 2014
abstract, full text, DOI:10.1039/c4ra01534g

Liu, Yingting; Radhakrishnan, Ravi
Computational delineation of tyrosyl-substrate recognition and catalytic landscapes by the epidermal growth factor receptor tyrosine kinase domain
MOLECULAR BIOSYSTEMS, 10:1890-1904, 2014
abstract, full text, DOI:10.1039/c3mb70620f

Bai, Qifeng; Shi, Danfeng; Zhang, Yang; Liu, Huanxiang; Yao, Xiaojun
Exploration of the antagonist CP-376395 escape pathway for the corticotropin-releasing factor receptor 1 by random acceleration molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 10:1958-1967, 2014
abstract, full text, DOI:10.1039/c4mb00037d

Wineman-Fisher, Vered; Simkovitch, Ron; Shomer, Shay; Gepshtein, Rinat; Huppert, Dan; Saif, Mari; Kallio, Karen; Remington, S. James; Miller, Yifat
Insight into the structure and the mechanism of the slow proton transfer in the GFP double mutant T203V/S205A
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:11196-11208, 2014
abstract, full text, DOI:10.1039/c4cp00311j

Weng, Lindong; Elliott, Gloria D.
Dynamic and thermodynamic characteristics associated with the glass transition of amorphous trehalose-water mixtures
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:11555-11565, 2014
abstract, full text, DOI:10.1039/c3cp55418j

Walczewska-Szewc, Katarzyna; Corry, Ben
Accounting for dye diffusion and orientation when relating FRET measurements to distances: three simple computational methods
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:12317-12326, 2014
abstract, full text, DOI:10.1039/c4cp01222d

Pan, Jianjun; Cheng, Xiaolin; Monticelli, Luca; Heberle, Frederick A.; Kucerka, Norbert; Tieleman, D. Peter; Katsaras, John
The molecular structure of a phosphatidylserine bilayer determined by scattering and molecular dynamics simulations
SOFT MATTER, 10:3716-3725, 2014
abstract, full text, DOI:10.1039/c4sm00066h

Di Leva, Francesco Saverio; Novellino, Ettore; Cavalli, Andrea; Parrinello, Michele; Limongelli, Vittorio
Mechanistic insight into ligand binding to G-quadruplex DNA
NUCLEIC ACIDS RESEARCH, 42:5447-5455, 2014
abstract, full text, DOI:10.1093/nar/gku247

Cardamone, Salvatore; Hughes, Timothy J.; Popelier, Paul L. A.
Multipolar electrostatics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:10367-10387, 2014
abstract, full text, DOI:10.1039/c3cp54829e

Binkowski, T. Andrew; Jiang, Wei; Roux, Benoit; Anderson, Wayne F.; Joachimiak, Andrzej
Virtual High-Throughput Ligand Screening
STRUCTURAL GENOMICS AND DRUG DISCOVERY: METHODS AND PROTOCOLS, 1140:251-261, 2014
abstract, full text, DOI:10.1007/978-1-4939-0354-2_19

Seitz, Patrick; Modarres, Hassan Pezeshgi; Borgeaud, Sandrine; Bulushev, Roman D.; Steinbock, Lorenz J.; Radenovic, Aleksandra; Dal Peraro, Matteo; Blokesch, Melanie
ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells
PLOS GENETICS, 10 Art. No. e1004066, JAN 2014
abstract, full text, DOI:10.1371/journal.pgen.1004066

Nayar, Divya; Chakravarty, Charusita
Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:10199-10213, 2014
abstract, full text, DOI:10.1039/c3cp55147d

Doss, C. George Priya; Chakraborty, Chiranjib; Narayan, Vaishnavi; Kumar, D. Thirumal
Computational Approaches and Resources in Single Amino Acid Substitutions Analysis Toward Clinical Research
ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY, VOL 94, 94:365-423, 2014
abstract, full text, DOI:10.1016/B978-0-12-800168-4.00010-X

Chen, Yi; Liu, Logan
Low cost, high sensitivity SERS nano-bio-chip for kinase profiling, drug monitoring and environmental detection: a translational platform technology
PLASMONICS IN BIOLOGY AND MEDICINE XI, 8957 Art. No. 895702, 2014
abstract, full text, DOI:10.1117/12.2062790

Vitorovic, Aleksandar; Tomasevic, Milo V.; Milutinovic, Veljko M.
Manual Parallelization Versus State-of-the-Art Parallelization Techniques: The SPEC CPU2006 as a Case Study
ADVANCES IN COMPUTERS, VOL 92, 92:203-251, 2014
abstract, full text, DOI:10.1016/B978-0-12-420232-0.00005-2

Frankevich, Vladimir; Chagovets, Vitaliy; Widjaja, Fanny; Barylyuk, Konstantin; Yang, Zhiyi; Zenobi, Renato
Fluorescence resonance energy transfer of gas-phase ions under ultra high vacuum and ambient conditions
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:8911-8920, 2014
abstract, full text, DOI:10.1039/c3cp54521k

Raz, Yoav; Adler, Juliane; Vogel, Alexander; Scheidt, Holger A.; Haeupl, Tilmann; Abel, Bernd; Huster, Daniel; Miller, Yifat
The influence of the triangle K280 mutation and N- or C-terminal extensions on the structure, dynamics, and fibril morphology of the tau R2 repeat
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:7710-7717, 2014
abstract, full text, DOI:10.1039/c3cp54890b

Johnston, Jennifer M.; Filizola, Marta
Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods
G PROTEIN-COUPLED RECEPTORS - MODELING AND SIMULATION, 796:95-125, 2014
abstract, full text, DOI:10.1007/978-94-007-7423-0_6

Lin, Jong-Chin; Hyeon, Changbong; Thirumalai, D.
Sequence-dependent folding landscapes of adenine riboswitch aptamers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:6376-6382, 2014
abstract, full text, DOI:10.1039/c3cp53932f

Miao, Yinglong; Nichols, Sara E.; McCammon, J. Andrew
Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:6398-6406, 2014
abstract, full text, DOI:10.1039/c3cp53962h

He, Jia; Wu, Ming; Feng, Xizeng; Shao, Xueguang; Cai, Wensheng
Immobilization of papain on nanoporous silica
RSC ADVANCES, 4:13304-13312, 2014
abstract, full text, DOI:10.1039/c3ra47346e

Caruso, Mario; Gatto, Emanuela; Placidi, Ernesto; Ballano, Gema; Formaggio, Fernando; Toniolo, Claudio; Zanuy, David; Aleman, Carlos; Venanzi, Mariano
A single-residue substitution inhibits fibrillization of Ala-based pentapeptides. A spectroscopic and molecular dynamics investigation
SOFT MATTER, 10:2508-2519, 2014
abstract, full text, DOI:10.1039/c3sm52831f

Zhang, Kai; Zhao, Wei-Jie; Leng, Xiao-Yao; Wang, Sha; Yao, Ke; Yan, Yong-Bin
The importance of the last strand at the C-terminus in beta B2-crystallin stability and assembly
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE, 1842:44-55, JAN 2014
abstract, full text, DOI:10.1016/j.bbadis.2013.10.001

Tsigelny, Igor F.; Sharikov, Yuriy; Kouznetsova, Valentina L.; Greenberg, Jerry P.; Wrasidlo, Wolfgang; Gonzalez, Tania; Desplats, Paula; Michael, Sarah E.; Trejo-Morales, Margarita; Overk, Cassia R.; Masliah, Eliezer
Structural Diversity of Alzheimer's Disease Amyloid-beta Dimers and Their Role in Oligomerization and Fibril Formation
JOURNAL OF ALZHEIMERS DISEASE, 39:583-600, 2014
abstract, full text, DOI:10.3233/JAD-131589

Martin, Lewis J.; Chao, Rebecca; Corry, Ben
Molecular dynamics simulation of the partitioning of benzocaine and phenytoin into a lipid bilayer
BIOPHYSICAL CHEMISTRY, 185:98-107, JAN 2014
abstract, full text, DOI:10.1016/j.bpc.2013.12.003

Sun, Tian-Yang; Liang, Li-Jun; Wang, Qi; Laaksonen, Aatto; Wu, Tao
A molecular dynamics study on pH response of protein adsorbed on peptide-modified polyvinyl alcohol hydrogel
BIOMATERIALS SCIENCE, 2:419-426, 2014
abstract, full text, DOI:10.1039/c3bm60213c

Telpoukhovskaia, Maria A.; Rodriguez-Rodriguez, Cristina; Cawthray, Jacqueline F.; Scott, Lauren E.; Page, Brent D. G.; Ali-Torres, Jorge; Sodupe, Mariona; Bailey, Gwendolyn A.; Patrick, Brian O.; Orvig, Chris
3-Hydroxy-4-pyridinone derivatives as metal ion and amyloid binding agents
METALLOMICS, 6:249-262, 2014
abstract, full text, DOI:10.1039/c3mt00135k

Das, Amit; Chakrabarti, Jaydeb; Ghosh, Mahua
Thermodynamics of interfacial changes in a protein-protein complex
MOLECULAR BIOSYSTEMS, 10:437-445, 2014
abstract, full text, DOI:10.1039/c3mb70249a

Kalyaanamoorthy, Subha; Chen, Yi-Ping Phoebe
A steered molecular dynamics mediated hit discovery for histone deacetylases
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:3777-3791, 2014
abstract, full text, DOI:10.1039/c3cp53511h

Alsharif, Shada A.; Chen, Liao Y.; Tlahuice-Flores, Alfredo; Whetten, Robert L.; Yacaman, Miguel Jose
Interaction between functionalized gold nanoparticles in physiological saline
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:3909-3913, 2014
abstract, full text, DOI:10.1039/c3cp54503b

Chen, Xuebo; Fang, Weihai; Wang, Haobin
Slow deactivation channels in UV-photoexcited adenine DNA
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:4210-4219, 2014
abstract, full text, DOI:10.1039/c3cp55020f

Juntadech, Thanate; Kanintronkul, Yodsoi; Kanchanawarin, Chalermpol; Katzenmeier, Gerd; Angsuthanasombat, Chanan
Importance of polarity of the alpha 4-alpha 5 loop residue-Asn(166) in the pore-forming domain of the Bacillus thuringiensis Cry4Ba toxin: Implications for ion permeation and pore opening
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:319-327, JAN 2014
abstract, full text, DOI:10.1016/j.bbamem.2013.10.002

Basu, Ipsita; Chattopadhyay, Amitabha; Mukhopadhyay, Chaitali
Ion channel stability of Gramicidin A in lipid bilayers: Effect of hydrophobic mismatch
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:328-338, JAN 2014
abstract, full text, DOI:10.1016/j.bbamem.2013.10.005

Hinsen, Konrad
MOSAIC: A Data Model and File Formats for Molecular Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:131-137, JAN 2014
abstract, full text, DOI:10.1021/ci400599y

Koukos, Panagiotis I.; Glykos, Nicholas M.
On the Application of Good-Turing Statistics to Quantify Convergence of Biomolecular Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54:209-217, JAN 2014
abstract, full text, DOI:10.1021/ci4005817

Shams, Hengameh; Holt, Brian D.; Mahboobi, Seyed Hanif; Jahed, Zeinab; Islam, Mohammad F.; Dahl, Kris Noel; Mofrad, Mohammad R. K.
Actin Reorganization through Dynamic Interactions with Single-Wall Carbon Nanotubes
ACS NANO, 8:188-197, JAN 2014
abstract, full text, DOI:10.1021/nn402865e

Abrams, Cameron; Bussi, Giovanni
Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
ENTROPY, 16:163-199, JAN 2014
abstract, full text, DOI:10.3390/e16010163

Carlotto, Silvia; Zerbetto, Mirco
Computational Study of Environmental Effects on Torsional Free Energy Surface of N-Acetyl-N '-methyl-L-alanylamide Dipeptide
JOURNAL OF CHEMICAL EDUCATION, 91:96-102, JAN 2014
abstract, full text, DOI:10.1021/ed400346v

Lee, Tai-Sung; Radak, Brian K.; Huang, Ming; Wong, Kin-Yiu; York, Darrin M.
Roadmaps through Free Energy Landscapes Calculated Using the Multidimensional vFEP Approach
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:24-34, JAN 2014
abstract, full text, DOI:10.1021/ct400691f

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian
Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:122-133, JAN 2014
abstract, full text, DOI:10.1021/ct400713t

Doemer, Manuel; Maurer, Patrick; Campomanes, Pablo; Tavernelli, Ivano; Rothlisberger, Ursula
Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:412-422, JAN 2014
abstract, full text, DOI:10.1021/ct400697n

Grime, John. M. A.; Voth, Gregory A.
Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:423-431, JAN 2014
abstract, full text, DOI:10.1021/ct400727q

Xing, Yan-Fei; Yang, Chuan-Lu; Mo, Yong-Fang; Wang, Mei-Shan; Ma, Xiao-Guang
Spontaneous nanoinjection with carbon nanotubes: a molecular dynamics simulation study
JOURNAL OF MATERIALS CHEMISTRY B, 2:859-867, 2014
abstract, full text, DOI:10.1039/c3tb21468k

Yang, Zaixing; Xia, Zhen; Tien Huynh; King, Jonathan A.; Zhou, Ruhong
Dissecting the contributions of beta-hairpin tyrosine pairs to the folding and stability of long-lived human gamma-crystallins
NANOSCALE, 6:1797-1807, 2014
abstract, full text, DOI:10.1039/c3nr03782g

Cordova-Mateo, Esther; Bertran, Oscar; Zhang, Baozhong; Vlassopoulos, Dimitris; Pasquino, Rossana; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Interactions in dendronized polymers: intramolecular dominates intermolecular
SOFT MATTER, 10:1032-1044, 2014
abstract, full text, DOI:10.1039/c3sm52343h

Xiao, Shiyan; Zhu, Hong; Wang, Lei; Liang, Haojun
DNA conformational flexibility study using phosphate backbone neutralization model
SOFT MATTER, 10:1045-1055, 2014
abstract, full text, DOI:10.1039/c3sm52345d

Ban, Ehsan; Picu, Catalin R.
Strength of DNA Sticky End Links
BIOMACROMOLECULES, 15:143-149, JAN 2014
abstract, full text, DOI:10.1021/bm401425k

Nishino, Noriko; Hollingsworth, Scott A.; Stern, Abraham C.; Roeselova, Martina; Tobias, Douglas J.; Finlayson-Pitts, Barbara J.
Interactions of gaseous HNO3 and water with individual and mixed alkyl self-assembled monolayers at room temperature
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:2358-2367, 2014
abstract, full text, DOI:10.1039/c3cp54118e

Zhao, Jun; Hu, Rundong; Sciacca, Michele F. M.; Brender, Jeffrey R.; Chen, Hong; Ramamoorthy, Ayyalusamy; Zheng, Jie
Non-selective ion channel activity of polymorphic human islet amyloid polypeptide (amylin) double channels
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:2368-2377, 2014
abstract, full text, DOI:10.1039/c3cp53345j

Cheng, Chang-Li; Zhang, Ming-Zhen; Zhao, Guang-Jiu
Mechanical stability and thermal conductivity of beta-barrel in green fluorescent protein by steered molecular dynamics
RSC ADVANCES, 4:6513-6516, 2014
abstract, full text, DOI:10.1039/c3ra42679c

Gillespie, C. M.; Asthagiri, D.; Lenhoff, A. M.
Polymorphic Protein Crystal Growth: Influence of Hydration and Ions in Glucose Isomerase
CRYSTAL GROWTH & DESIGN, 14:46-57, JAN 2014
abstract, full text, DOI:10.1021/cg401063b

Myat, Darli T.; Stewart, Matthew B.; Mergen, Max; Zhao, Oliver; Orbell, John D.; Gray, Stephen
Experimental and computational investigations of the interactions between model organic compounds and subsequent membrane fouling
WATER RESEARCH, 48:108-118, JAN 1 2014
abstract, full text, DOI:10.1016/j.watres.2013.09.020

Du, Kun; Liu, Zhongmei; Cui, Wenjing; Zhou, Li; Liu, Yi; Du, Guocheng; Chen, Jian; Zhou, Zhemin
pH-Dependent Activation of Streptomyces hygroscopicus Transglutaminase Mediated by Inteinle
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 80:723-729, JAN 2014
abstract, full text, DOI:10.1128/AEM.02820-13

Andersson, Magnus; Mattle, Daniel; Sitsel, Oleg; Klymchuk, Tetyana; Nielsen, Anna Marie; Moller, Lisbeth Birk; White, Stephen H.; Nissen, Poul; Gourdon, Pontus
Copper-transporting P-type ATPases use a unique ion-release pathway
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 21:43-+, JAN 2014
abstract, full text, DOI:10.1038/nsmb.2721

Loison, Claire; Nasir, Mehmet Nail; Benichou, Emmanuel; Besson, Francoise; Brevet, Pierre-Francois
Multi-scale modeling of mycosubtilin lipopeptides at the air/water interface: structure and optical second harmonic generation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:2136-2148, 2014
abstract, full text, DOI:10.1039/c3cp53101e

Gorny, Krzysztof; Dendzik, Zbigniew; Sawicki, Bogdan; Dawid, Aleksander; Gburski, Zygmunt
Thermal activation of ethylene glycol embedded in carbon nanotubes - Computer simulation study
SOLID STATE COMMUNICATIONS, 177:117-122, JAN 2014
abstract, full text, DOI:10.1016/j.ssc.2013.10.013

Koseki, Yuji; Aoki, Shunsuke
Computational Medicinal Chemistry for Rational Drug Design: Identification of Novel Chemical Structures with Potential Anti-Tuberculosis Activity
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 14:176-188, JAN 2014
abstract, full text

Unlu, Ayhan
Computational prediction of actin-actin interaction
MOLECULAR BIOLOGY REPORTS, 41:355-364, JAN 2014
abstract, full text, DOI:10.1007/s11033-013-2869-8

Schramm, Oana G.; Lopez-Cortes, Xaviera; Santos, Leonardo S.; Felipe Laurie, V.; Gonzalez Nilo, Fernando Danilo; Krolik, Michal; Fischer, Rainer; Di Fiore, Stefano
pH-dependent nano-capturing of tartaric acid using dendrimers
SOFT MATTER, 10:600-608, 2014
abstract, full text, DOI:10.1039/c3sm52255e

Ginovska-Pangovska, Bojana; Ho, Ming-Hsun; Linehan, John C.; Cheng, Yuhui; Dupuis, Michel; Raugei, Simone; Shaw, Wendy J.
Molecular dynamics study of the proposed proton transport pathways in [FeFe]-hydrogenase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:131-138, JAN 2014
abstract, full text, DOI:10.1016/j.bbabio.2013.08.004

Chylek, Lily A.; Harris, Leonard A.; Tung, Chang-Shung; Faeder, James R.; Lopez, Carlos F.; Hlavacek, William S.
Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems
WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE, 6:13-36, JAN 2014
abstract, full text, DOI:10.1002/wsbm.1245

Chaudhry, Jehanzeb Hameed; Comer, Jeffrey; Aksimentiev, Aleksei; Olson, Luke N.
A Stabilized Finite Element Method for Modified Poisson-Nernst-Planck Equations to Determine Ion Flow Through a Nanopore
COMMUNICATIONS IN COMPUTATIONAL PHYSICS, 15:93-125, JAN 2014
abstract, full text, DOI:10.4208/cicp.101112.100413a

Banks, David C.; Huff, Israel J.
Halo Water: Ensemble Visualization Distinguishes Configurations Near Nanotubes
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 11:8-14, JAN 2014
abstract, full text, DOI:10.1166/jctn.2014.3310

Bertran, Oscar; del Valle, Luis J.; Revilla-Lopez, Guillermo; Chaves, Gustavo; Cardus, Lluis; Casas, Maria T.; Casanovas, Jordi; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
Mineralization of DNA into nanoparticles of hydroxyapatite
DALTON TRANSACTIONS, 43:317-327, 2014
abstract, full text, DOI:10.1039/c3dt52112e

Bouvier, Benjamin
Decoding the patterns of ubiquitin recognition by ubiquitin-associated domains from free energy simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16:48-60, 2014
abstract, full text, DOI:10.1039/c3cp52436a

Timucin, Emel; Sezerman, O. Ugur
The Conserved Lid Tryptophan, W211, Potentiates Thermostability and Thermoactivity in Bacterial Thermoalkalophilic Lipases
PLOS ONE, 8 Art. No. e85186, DEC 31 2013
abstract, full text, DOI:10.1371/journal.pone.0085186

Denning, Elizabeth J.; Thirumalai, D.; MacKerell, Alexander D., Jr.
Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure
BIOPHYSICAL CHEMISTRY, 184:8-16, DEC 31 2013
abstract, full text, DOI:10.1016/j.bpc.2013.08.002

Jana, Asis K.; Sengupta, Neelanjana
Surface induced collapse of A beta(1-42) with the F19A replacement following adsorption on a single walled carbon nanotube
BIOPHYSICAL CHEMISTRY, 184:108-115, DEC 31 2013
abstract, full text, DOI:10.1016/j.bpc.2013.09.008

Noskov, Sergei Yu.; Rostovtseva, Tatiana K.; Bezrukov, Sergey M.
ATP Transport through VDAC and the VDAC-Tubulin Complex Probed by Equilibrium and Nonequilibrium MD Simulations
BIOCHEMISTRY, 52:9246-9256, DEC 24 2013
abstract, full text, DOI:10.1021/bi4011495

Vukovic, Lela; Madriaga, Antonett; Kuzmis, Antonina; Banerjee, Amrita; Tang, Alan; Tao, Kevin; Shah, Neil; Kral, Petr; Onyuksel, Hayat
Solubilization of Therapeutic Agents in Micellar Nanomedicines
LANGMUIR, 29:15747-15754, DEC 24 2013
abstract, full text, DOI:10.1021/la403264w

Liu, Jian; Wang, Chunlei; Guo, Pan; Shi, Guosheng; Fang, Haiping
Linear relationship between water wetting behavior and microscopic interactions of super-hydrophilic surfaces
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 234703, DEC 21 2013
abstract, full text, DOI:10.1063/1.4841815

Pal, Somedatta; Bandyopadhyay, Sanjoy
Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 235101, DEC 21 2013
abstract, full text, DOI:10.1063/1.4844255

Xue, Minmin; Qiu, Hu; Guo, Wanlin
Exceptionally fast water desalination at complete salt rejection by pristine graphyne monolayers
NANOTECHNOLOGY, 24 Art. No. 505720, DEC 20 2013
abstract, full text, DOI:10.1088/0957-4484/24/50/505720

Song, Jianing; Ji, Changge; Zhang, John Z. H.
Unveiling the gating mechanism of ECF Transporter RibU
SCIENTIFIC REPORTS, 3 Art. No. 3566, DEC 20 2013
abstract, full text, DOI:10.1038/srep03566

Lu, Jing; Modi, Niraj; Kleinekathoefer, Ulrich
Simulation of Ion Transport through an N-Acetylneuraminic Acid-Inducible Membrane Channel: From Understanding to Engineering
JOURNAL OF PHYSICAL CHEMISTRY B, 117:15966-15975, DEC 19 2013
abstract, full text, DOI:10.1021/jp408495v

Profantova, Barbora; Profant, Vaclav; Zima, Vlastimil; Kopecky, Vladimir, Jr.; Bednarova, Lucie; Zentz, Christian; Baumruk, Vladimir; Turpin, Pierre-Yves; Stepanek, Josef
Protonation Effect of Tyrosine in a Segment of the SRF Transcription Factor: A Combined Optical Spectroscopy, Molecular Dynamics, and Density Functional Theory Calculation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 117:16086-16095, DEC 19 2013
abstract, full text, DOI:10.1021/jp4099864

Comer, Jeffrey; Dehez, Francois; Cai, Wensheng; Chipot, Christophe
Water Conduction through a Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY C, 117:26797-26803, DEC 19 2013
abstract, full text, DOI:10.1021/jp4088223

Arnold, Axel; Fahrenberger, Florian; Holm, Christian; Lenz, Olaf; Bolten, Matthias; Dachsel, Holger; Halver, Rene; Kabadshow, Ivo; Gaehler, Franz; Heber, Frederik; Iseringhausen, Julian; Hofmann, Michael; Pippig, Michael; Potts, Daniel; Sutmann, Godehard
Comparison of scalable fast methods for long-range interactions
PHYSICAL REVIEW E, 88 Art. No. 063308, DEC 19 2013
abstract, full text, DOI:10.1103/PhysRevE.88.063308

Payne, Christina M.; Jiang, Wei; Shirts, Michael R.; Himmel, Michael E.; Crowley, Michael F.; Beckham, Gregg T.
Glycoside Hydrolase Processivity Is Directly Related to Oligosaccharide Binding Free Energy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:18831-18839, DEC 18 2013
abstract, full text, DOI:10.1021/ja407287f

Lv, Xiaoying; Liu, Huihui; Ke, Meng; Gong, Haipeng
Exploring the pH-Dependent Substrate Transport Mechanism of FocA Using Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 105:2714-2723, DEC 17 2013
abstract, full text, DOI:10.1016/j.bpj.2013.11.006

Singh, Raghvendra Pratap; Blossey, Ralf; Cleri, Fabrizio
Structure and Mechanical Characterization of DNA i-Motif Nanowires by Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 105:2820-2831, DEC 17 2013
abstract, full text, DOI:10.1016/j.bpj.2013.10.021

Pessoa-Mahana, Hernan; Gonzalez-Lira, Christian; Fierro, Angelica; Zapata-Torres, Gerald; David Pessoa-Mahana, C.; Ortiz-Severin, Javiera; Iturriaga-Vasquez, Patricio; Reyes-Parada, Miguel; Silva-Matus, Paul; Saitz-Barria, Claudio; Araya-Maturana, Ramiro
Synthesis, docking and pharmacological evaluation of novel homo- and hetero-bis 3-piperazinylpropylindole derivatives at SERT and 5-HT1A receptor
BIOORGANIC & MEDICINAL CHEMISTRY, 21:7604-7611, DEC 15 2013
abstract, full text, DOI:10.1016/j.bmc.2013.10.036

Whiteley, Chris G.; Lee, Duu-Jong
Enzymes for energy. Structural computational analysis, substrate association and product dissociation from the thermophilic esterase of Alicyclobacillus acidocaldarius: Implications in biodiesel production
JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 97:156-168, DEC 15 2013
abstract, full text, DOI:10.1016/j.molcatb.2013.08.008

Mayne, Christopher G.; Saam, Jan; Schulten, Klaus; Tajkhorshid, Emad; Gumbart, James C.
Rapid Parameterization of Small Molecules Using the Force Field Toolkit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2757-2770, DEC 15 2013
abstract, full text, TCBG publications, DOI:10.1002/jcc.23422

Chang, Shan-Yan; Liu, Fu-Feng; Dong, Xiao-Yan; Sun, Yan
Molecular insight into conformational transmission of human P-glycoprotein
JOURNAL OF CHEMICAL PHYSICS, 139, DEC 14 2013
abstract, full text, DOI:10.1063/1.4832740

Lam, A. R.; Moran, S. D.; Preketes, N. K.; Zhang, T. O.; Zanni, M. T.; Mukamel, S.
Study of the gamma D-Crystallin Protein Using Two-Dimensional Infrared (2DIR) Spectroscopy: Experiment and Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 117:15436-15443, DEC 12 2013
abstract, full text, DOI:10.1021/jp405159v

Singharoy, Abhishek; Polavarapu, Abhigna; Joshi, Harshad; Baik, Mu-Hyun; Ortoleva, Peter
Epitope Fluctuations in the Human Papillomavirus Are Under Dynamic Allosteric Control: A Computational Evaluation of a New Vaccine Design Strategy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:18458-18468, DEC 11 2013
abstract, full text, DOI:10.1021/ja407489r

Jha, Narendra Nath; Anoop, A.; Ranganathan, Srivastav; Mohite, Ganesh M.; Padinhateeri, Ranjith; Maji, Samir K.
Characterization of Amyloid Formation by Glucagon-Like Peptides: Role of Basic Residues in Heparin-Mediated Aggregation
BIOCHEMISTRY, 52:8800-8810, DEC 10 2013
abstract, full text, DOI:10.1021/bi401398k

Yoo, Jejoong; Aksimentiev, Aleksei
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:20099-20104, DEC 10 2013
abstract, full text, DOI:10.1073/pnas.1316521110

Hashemian, Behrooz; Millan, Daniel; Arroyo, Marino
Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 214101, DEC 7 2013
abstract, full text, DOI:10.1063/1.4830403

Ikeda, Atsushi; Hirata, Akiko; Ishikawa, Michiko; Kikuchi, Jun-ichi; Mieda, Shunsuke; Shinoda, Wataru
Effect of different substituents on the water-solubility and stability properties of 1: 2 [60]fullerene derivative-gamma-cyclodextrin complexes
ORGANIC & BIOMOLECULAR CHEMISTRY, 11:7843-7851, DEC 7 2013
abstract, full text, DOI:10.1039/c3ob41513a

Shi, Guosheng; Liu, Jian; Wang, Chunlei; Song, Bo; Tu, Yusong; Hu, Jun; Fang, Haiping
Ion Enrichment on the Hydrophobic Carbon-based Surface in Aqueous Salt Solutions due to Cation-pi Interactions
SCIENTIFIC REPORTS, 3 Art. No. 3436, DEC 6 2013
abstract, full text, DOI:10.1038/srep03436

Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi
Exploring the Dynamic Behaviors and Transport Properties of Gas Molecules in a Transmembrane Cyclic Peptide Nanotube
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14916-14927, DEC 5 2013
abstract, full text, DOI:10.1021/jp408769u

Grigoryan, Gevorg
Absolute Free Energies of Biomolecules from Unperturbed Ensembles
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34:2726-2741, DEC 5 2013
abstract, full text, DOI:10.1002/jcc.23448

Smith, Jeremy C.; Roux, Benoit
Eppur Si Muove! The 2013 Nobel Prize in Chemistry
STRUCTURE, 21:2102-2105, DEC 3 2013
full text, DOI:10.1016/j.str.2013.11.005

Benitez, Benedetta Sampoli; Barbati, Zachary R.; Arora, Karunesh; Bogdanovic, Jasmina; Schlick, Tamar
How DNA Polymerase X Preferentially Accommodates Incoming dATP Opposite 8-Oxoguanine on the Template
BIOPHYSICAL JOURNAL, 105:2559-2568, DEC 3 2013
abstract, full text, DOI:10.1016/j.bpj.2013.10.014

Bonaiuto, Emanuela; Milelli, Andrea; Cozza, Giorgio; Tumiatti, Vincenzo; Marchetti, Chiara; Agostinelli, Enzo; Fimognari, Carmela; Hrelia, Patrizia; Minarini, Anna; Di Paolo, Maria Luisa
Novel polyamine analogues: From substrates towards potential inhibitors of monoamine oxidases
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 70:88-101, DEC 2013
abstract, full text, DOI:10.1016/j.ejmech.2013.07.005

Tan, Xiao; Bertonati, Claudia; Qin, Lixian; Furio, Laetitia; El Amri, Chahrazade; Hovnanian, Alain; Reboud-Ravaux, Michele; Villoutreix, Bruno O.
Identification by in silico and in vitro screenings of small organic molecules acting as reversible inhibitors of kallikreins
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 70:661-668, DEC 2013
abstract, full text, DOI:10.1016/j.ejmech.2013.10.040

Gursky, Olga; Jones, Martin K.; Mei, Xiaohu; Segrest, Jere P.; Atkinson, David
Structural basis for distinct functions of the naturally occurring Cys mutants of human apolipoprotein A-I
JOURNAL OF LIPID RESEARCH, 54:3244-3257, DEC 2013
abstract, full text, DOI:10.1194/jlr.R037911

Roy, Sophie; Boiteux, Celine; Alijevic, Omar; Liang, Chungwen; Berneche, Simon; Kellenberger, Stephan
Molecular determinants of desensitization in an ENaC/degenerin channel
FASEB JOURNAL, 27:5034-5045, DEC 2013
abstract, full text, DOI:10.1096/fj.13-230680

Bossis, Fabrizio; Palese, Luigi L.
Amyloid beta(1-42) in aqueous environments: Effects of ionic strength and E22Q (Dutch) mutation
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:2486-2493, DEC 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.08.010

Gupta, Arun A.; Chou, Ruey-Hwang; Li, Hongchun; Yang, Lee-Wei; Yu, Chin
Structural insights into the interaction of human S100B and basic fibroblast growth factor (FGF2): Effects on FGFR1 receptor signaling
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:2606-2619, DEC 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.09.012

Underhaug, Jan; Koldso, Heidi; Runager, Kasper; Nielsen, Jakob Toudahl; Sorensen, Charlotte S.; Kristensen, Torsten; Otzen, Daniel E.; Karring, Henrik; Malmendal, Anders; Schiott, Birgit; Enghild, Jan J.; Nielsen, Niels Chr.
Mutation in transforming growth factor beta induced protein associated with granular corneal dystrophy type 1 reduces the proteolytic susceptibility through local structural stabilization
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834:2812-2822, DEC 2013
abstract, full text, DOI:10.1016/j.bbapap.2013.10.008

Xu, Xiaojun; Guardiani, Carlo; Yan, Chunli; Ivanov, Ivaylo
Opening pathways of the DNA clamps proliferating cell nuclear antigen and Rad9-Rad1-Hus1
NUCLEIC ACIDS RESEARCH, 41:10020-10031, DEC 2013
abstract, full text, DOI:10.1093/nar/gkt810

Aykut, Ayse Ozlem; Atilgan, Ali Rana; Atilgan, Canan
Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003366, DEC 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003366

Candotti, Michela; Perez, Alberto; Ferrer-Costa, Carles; Rueda, Manuel; Meyer, Tim; Lluis Gelpi, Josep; Orozco, Modesto
Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003393, DEC 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003393

Iakhiaev, Mikhail A.; Iakhiaev, Alexei V.
Mapping the intramolecular signal propagation pathways in protein using Bayesian change point analysis of atomic motions
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 47:89-95, DEC 2013
abstract, full text, DOI:10.1016/j.compbiolchem.2013.08.004

Borozan, Suncica Z.; Dimitrijevic, Blagoje P.; Stojanovic, Srdan D.
Cation-pi interactions in high resolution protein-RNA complex crystal structures
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 47:105-112, DEC 2013
abstract, full text, DOI:10.1016/j.compbiolchem.2013.08.005

Bellucci, Luca; Angeli, Lucilla; Tafi, Andrea; Radi, Marco; Botta, Maurizio
Unconventional Plasticity of HIV-1 Reverse Transcriptase: How Inhibitors Could Open a Connection "Gate" between Allosteric and Catalytic Sites
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3117-3122, DEC 2013
abstract, full text, DOI:10.1021/ci400414s

Chen, Qi; Buolamwini, John K.; Smith, Jeremy C.; Li, Aixiu; Xu, Qin; Cheng, Xiaolin; Wei, Dongqing
Impact of Resistance Mutations on Inhibitor Binding to HIV-1 Integrase
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3297-3307, DEC 2013
abstract, full text, DOI:10.1021/ci400537n

Sun, Hui-Yong; Ji, Feng-Qin; Fu, Liang-Yu; Wang, Zhong-Yi; Zhang, Hong-Yu
Structural and Energetic Analyses of SNPs in Drug Targets and Implications for Drug Therapy
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3343-3351, DEC 2013
abstract, full text, DOI:10.1021/ci400457v

Vashisth, Harish; Storaska, Andrew J.; Neubig, Richard R.; Brooks, Charles L., I.I.I.
Conformational Dynamics of a Regulator of G-Protein Signaling Protein Reveals a Mechanism of Allosteric Inhibition by a Small Molecule
ACS CHEMICAL BIOLOGY, 8:2778-2784, DEC 2013
abstract, full text, DOI:10.1021/cb400568g

Telesco, Shannon E.; Vadigepalli, Rajanikanth; Radhakrishnan, Ravi
Molecular modeling of ErbB4/HER4 kinase in the context of the HER4 signaling network helps rationalize the effects of clinically identified HER4 somatic mutations on the cell phenotype
BIOTECHNOLOGY JOURNAL, 8:1452-1464, DEC 2013
abstract, full text, DOI:10.1002/biot.201300022

Straatsma, T. P.; Chavarria-Miranda, Daniel G.
On eliminating synchronous communication in molecular simulations to improve scalability
COMPUTER PHYSICS COMMUNICATIONS, 184:2634-2640, DEC 2013
abstract, full text, DOI:10.1016/j.cpc.2013.01.009

Pall, Szilard; Hess, Berk
A flexible algorithm for calculating pair interactions on SIMD architectures
COMPUTER PHYSICS COMMUNICATIONS, 184:2641-2650, DEC 2013
abstract, full text, DOI:10.1016/j.cpc.2013.06.003

Mick, Jason; Hailat, Eyad; Russo, Vincent; Rushaidat, Kamel; Schwiehert, Loren; Potoff, Jeffrey
GPU-accelerated Gibbs ensemble Monte Carlo simulations of Lennard-Jonesium
COMPUTER PHYSICS COMMUNICATIONS, 184:2662-2669, DEC 2013
abstract, full text, DOI:10.1016/j.cpc.2013.06.020

Zhang, Ji-Long; Zheng, Qing-Chuan; Chu, Wen-Ting; Zhang, Hong-Xing
Drug Design Benefits from Molecular Dynamics: Some Examples
CURRENT COMPUTER-AIDED DRUG DESIGN, 9:532-546, DEC 2013
abstract, full text

Immadisetty, Kalyan; Madura, Jeffry D.
A Review of Monoamine Transporter-Ligand Interactions
CURRENT COMPUTER-AIDED DRUG DESIGN, 9:556-568, DEC 2013
abstract, full text

Riley, Julie M.; Kim, Hyunjin; Averch, Timothy D.; Kim, Hyung J.
Effect of Magnesium on Calcium and Oxalate Ion Binding
JOURNAL OF ENDOUROLOGY, 27:1487-1492, DEC 1 2013
abstract, full text, DOI:10.1089/end.2013.0173

Cui, Guanglei; Swails, Jason M.; Manas, Eric S.
SPAM: A Simple Approach for Profiling Bound Water Molecules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5539-5549, DEC 2013
abstract, full text, DOI:10.1021/ct400711g

Bulo, Rosa E.; Michel, Carine; Fleurat-Lessard, Paul; Sautet, Philippe
Multiscale Modeling of Chemistry in Water: Are We There Yet?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5567-5577, DEC 2013
abstract, full text, DOI:10.1021/ct4005596

Fugebakk, Edvin; Reuter, Nathalie; Hinsen, Konrad
Evaluation of Protein Elastic Network Models Based on an Analysis of Collective Motions
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5618-5628, DEC 2013
abstract, full text, DOI:10.1021/ct400399x

Bonhenry, Daniel; Tarek, Mounir; Dehez, Francois
Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5675-5684, DEC 2013
abstract, full text, DOI:10.1021/ct400576e

Palmer, David S.; Sorensen, Jesper; Schiott, Birgit; Fedorov, Maxim V.
Solvent Binding Analysis and Computational Alanine Scanning of the Bovine Chymosin-Bovine kappa-Casein Complex Using Molecular Integral Equation Theory
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5706-5717, DEC 2013
abstract, full text, DOI:10.1021/ct400605x

Toy, Weiyi; Shen, Yang; Won, Helen; Green, Bradley; Sakr, Rita A.; Will, Marie; Li, Zhiqiang; Gala, Kinisha; Fanning, Sean; King, Tari A.; Hudis, Clifford; Chen, David; Taran, Tetiana; Hortobagyi, Gabriel; Greene, Geoffrey; Berger, Michael; Baselga, Jose; Chandarlapaty, Sarat
ESR1 ligand-binding domain mutations in hormone-resistant breast cancer
NATURE GENETICS, 45:1439-U189, DEC 2013
abstract, full text, DOI:10.1038/ng.2822

Nunes, Alexandro Silva; Campos, Vicente Paulo; Mascarello, Alessandra; Stumpf, Taisa Regina; Chiaradia-Delatorre, Louise Domenghini; Teixeira Machado, Alan Rodrigues; Santos Junior, Helvecio Martins; Yunes, Rosendo Augusto; Nunes, Ricardo Jose; Oliveira, Denilson Ferreira
Activity of chalcones derived from 2,4,5-trimethoxybenzaldehyde against Meloidogyne exigua and in silico interaction of one chalcone with a putative caffeic acid 3-O-methyltransferase from Meloidogyne incognita
EXPERIMENTAL PARASITOLOGY, 135:661-668, DEC 2013
abstract, full text, DOI:10.1016/j.exppara.2013.10.003

Chen, Xin; Zhu, Shuyan; Duan, Danhui; Wu, Tao; Wang, Qi
Investigation of the binding network of IGF-I on the cavity surface of IGFBP4
JOURNAL OF MOLECULAR MODELING, 19:5257-5266, DEC 2013
abstract, full text, DOI:10.1007/s00894-013-2020-8

Fiorin, Giacomo; Klein, Michael L.; Henin, Jerome
Using collective variables to drive molecular dynamics simulations
MOLECULAR PHYSICS, 111:3345-3362, DEC 1 2013
abstract, full text, DOI:10.1080/00268976.2013.813594

Biocca, Silvia; Arcangeli, Tania; Tagliaferri, Elisa; Testa, Barbara; Vindigni, Giulia; Oteri, Francesco; Giorgi, Alessandra; Iacovelli, Federico; Novelli, Giuseppe; Desideri, Alessandro; Falconi, Mattia
Simulative and experimental investigation on the cleavage site that generates the soluble human LOX-1
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 540:9-18, DEC 2013
abstract, full text, DOI:10.1016/j.abb.2013.10.001

Cristina Ravanal, Maria; Alegria-Arcos, Melissa; Danilo Gonzalez-Nilo, Fernando; Eyzaguirre, Jaime
Penicillium purpurogenum produces two GH family 43 enzymes with beta-xylosidase activity, one monofunctional and the other bifunctional: Biochemical and structural analyses explain the difference
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 540:117-124, DEC 2013
abstract, full text, DOI:10.1016/j.abb.2013.10.017

Barakat, Khaled H.; Huzil, J. Torin; Jordan, Kirk E.; Evangelinos, Constantinos; Houghton, Michael; Tuszynski, Jack
A Computational Model for Overcoming Drug Resistance Using Selective Dual-Inhibitors for Aurora Kinase A and Its T217D Variant
MOLECULAR PHARMACEUTICS, 10:4572-4589, DEC 2013
abstract, full text, DOI:10.1021/mp4003893

Bellesia, Giovanni; Gnanakaran, S.
Sodium chloride interaction with solvated and crystalline cellulose: sodium ion affects the cellotetraose molecule and the cellulose fibril in aqueous solution
CELLULOSE, 20:2695-2702, DEC 2013
abstract, full text, DOI:10.1007/s10570-013-0063-8

Wood, Irene; Pickholz, Monica
Concentration effects of sumatriptan on the properties of model membranes by molecular dynamics simulations
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 42:833-841, DEC 2013
abstract, full text, DOI:10.1007/s00249-013-0932-y

Wu, Qing-Yun; Guo, Hua-Yan; Li, Feng; Li, Zhen-Yu; Zeng, Ling-Yu; Xu, Kai-Lin
Disruption of E627 and R683 interaction is responsible for B-cell acute lymphoblastic leukemia caused by JAK2 R683G(S) mutations
LEUKEMIA & LYMPHOMA, 54:2693-2700, DEC 2013
abstract, full text, DOI:10.3109/10428194.2013.781171

Guemral, Devrim; Fogolari, Federico; Corazza, Alessandra; Viglino, Paolo; Giorgetti, Sofia; Stoppini, Monica; Bellotti, Vittorio; Esposito, Gennaro
Reduction of conformational mobility and aggregation in W60G beta(2)-microglobulin: assessment by N-15 NMR relaxation
MAGNETIC RESONANCE IN CHEMISTRY, 51:795-807, DEC 2013
abstract, full text, DOI:10.1002/mrc.4018

Chempath, Shaji; Dueren, Tina; Sarkisov, Lev; Snurr, Randall Q.
Experiences with the publicly available multipurpose simulation code, Music
MOLECULAR SIMULATION, 39:1195-1204, DEC 1 2013
abstract, full text, DOI:10.1080/08927022.2013.819103

Dewdney, Tamaria G.; Wang, Yong; Liu, Zhigang; Sharma, Shiv K.; Reiter, Samuel J.; Brunzelle, Joseph S.; Kovari, Iulia A.; Woster, Patrick M.; Kovari, Ladislau C.
Ligand modifications to reduce the relative resistance of multi-drug resistant HIV-1 protease
BIOORGANIC & MEDICINAL CHEMISTRY, 21:7430-7434, DEC 1 2013
abstract, full text, DOI:10.1016/j.bmc.2013.09.045

Unno, Masaki; Ardevol, Albert; Rovira, Carme; Ikeda-Saito, Masao
Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae X-RAY CRYSTALLOGRAPHY AND MOLECULAR DYNAMICS INVESTIGATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:34443-34458, NOV 29 2013
abstract, full text, DOI:10.1074/jbc.M113.486936

Politis, Argyris; Park, Ah Young; Hall, Zoe; Ruotolo, Brandon T.; Robinson, Carol V.
Integrative Modelling Coupled with Ion Mobility Mass Spectrometry Reveals Structural Features of the Clamp Loader in Complex with Single-Stranded DNA Binding Protein
JOURNAL OF MOLECULAR BIOLOGY, 425:4790-4801, NOV 29 2013
abstract, full text, DOI:10.1016/j.jmb.2013.04.006

De Luna, Phil; Bushnell, Eric A. C.; Gauld, James W.
A Molecular Dynamics Examination on Mutation-Induced Catalase Activity in Coral Allene Oxide Synthase
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14635-14641, NOV 28 2013
abstract, full text, DOI:10.1021/jp408486n

Kubiak-Ossowska, Karina; Burley, Glenn; Patwardhan, Siddharth V.; Mulheran, Paul A.
Spontaneous Membrane-Translocating Peptide Adsorption at Silica Surfaces: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14666-14675, NOV 28 2013
abstract, full text, DOI:10.1021/jp409130s

Markiewicz, Beatrice N.; Jo, Hyunil; Culik, Robert M.; DeGrado, William F.; Gai, Feng
Assessment of Local Friction in Protein Folding Dynamics Using a Helix Cross-Linker
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14688-14696, NOV 28 2013
abstract, full text, DOI:10.1021/jp409334h

Nichols, Matthew; Kuljanin, Miljan; Nategholeslam, Mostafa; Hoang, Tuan; Vafaei, Shaghayegh; Tomberli, Bruno; Gray, C. G.; DeBruin, Lillian; Jelokhani-Niaraki, Masoud
Dynamic Turn Conformation of a Short Tryptophan-Rich Cationic Antimicrobial Peptide and Its Interaction with Phospholipid Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14697-14708, NOV 28 2013
abstract, full text, DOI:10.1021/jp4096985

Shonberg, Jeremy; Herenbrink, Carmen Klein; Lopez, Laura; Christopoulos, Arthur; Scammells, Peter J.; Capuano, Ben; Lane, J. Robert
A Structure-Activity Analysis of Biased Agonism at the Dopamine D2 Receptor
JOURNAL OF MEDICINAL CHEMISTRY, 56:9199-9221, NOV 28 2013
abstract, full text, DOI:10.1021/jm401318w

Reale, Riccardo; English, Niall J.; Garate, Jose-Antonio; Marracino, Paolo; Liberti, Micaela; Apollonio, Francesca
Human aquaporin 4 gating dynamics under and after nanosecond-scale static and alternating electric-field impulses: A molecular dynamics study of field effects and relaxation
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 205101, NOV 28 2013
abstract, full text, DOI:10.1063/1.4832383

Hashem, Yaser; des Georges, Amedee; Dhote, Vidya; Langlois, Robert; Liao, Hstau Y.; Grassucci, Robert A.; Pestova, Tatyana V.; Hellen, Christopher U. T.; Frank, Joachim
Hepatitis-C-virus-like internal ribosome entry sites displace eIF3 to gain access to the 40S subunit
NATURE, 503:539-+, NOV 28 2013
abstract, full text, DOI:10.1038/nature12658

Li, Minghui; Zheng, Wenjun
All-Atom Molecular Dynamics Simulations of Actin-Myosin Interactions: A Comparative Study of Cardiac alpha Myosin, beta Myosin, and Fast Skeletal Muscle Myosin
BIOCHEMISTRY, 52:8393-8405, NOV 26 2013
abstract, full text, DOI:10.1021/bi4006896

Goh, Boon Chong; Rynkiewicz, Michael J.; Cafarella, Tanya R.; White, Mitchell R.; Hartshorn, Kevan L.; Allen, Kimberly; Crouch, Erika C.; Calin, Oliviana; Seeberger, Peter H.; Schulten, Klaus; Seaton, Barbara A.
Molecular Mechanisms of Inhibition of Influenza by Surfactant Protein D Revealed by Large-Scale Molecular Dynamics Simulation
BIOCHEMISTRY, 52:8527-8538, NOV 26 2013
abstract, full text, TCBG publications, DOI:10.1021/bi4010683

Diaz, Natalia; Suarez, Dimas; Valdes, Haydee
Unraveling the Molecular Structure of the Catalytic Domain of Matrix Metalloproteinase-2 in Complex with a Triple-Helical Peptide by Means of Molecular Dynamics Simulations
BIOCHEMISTRY, 52:8556-8569, NOV 26 2013
abstract, full text, DOI:10.1021/bi401144p

Wicky, Basile I. M.; Stenta, Marco; Dal Peraro, Matteo
TAL Effectors Specificity Stems from Negative Discrimination
PLOS ONE, 8 Art. No. e80261, NOV 25 2013
abstract, full text, DOI:10.1371/journal.pone.0080261

Abad, Enrique; Zenn, Roland K.; Kaestner, Johannes
Reaction Mechanism of Monoamine Oxidase from QM/MM Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14238-14246, NOV 21 2013
abstract, full text, DOI:10.1021/jp4061522

Jiang, Jun; Golchert, Kory J.; Kingsley, Carolyn N.; Brubaker, William D.; Martin, Rachel W.; Mukamel, Shaul
Exploring the Aggregation Propensity of gamma S-Crystallin Protein Variants Using Two-Dimensional Spectroscopic Tools
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14294-14301, NOV 21 2013
abstract, full text, DOI:10.1021/jp408000k

Akimov, Alexey V.; Prezhdo, Oleg V.
Persistent Electronic Coherence Despite Rapid Loss of Electron-Nuclear Correlation
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:3857-3864, NOV 21 2013
abstract, full text, DOI:10.1021/jz402035z

Boynton, P.; Di Ventra, M.
Probing Water Structures in Nanopores Using Tunneling Currents
PHYSICAL REVIEW LETTERS, 111 Art. No. 216804, NOV 20 2013
abstract, full text, DOI:10.1103/PhysRevLett.111.216804

Villanueva, Diana Y.; Lim, Joseph B.; Klauda, Jeffery B.
Influence of Ester-Modified Lipids on Bilayer Structure
LANGMUIR, 29:14196-14203, NOV 19 2013
abstract, full text, DOI:10.1021/la403919h

Zhang, Liqun; Buck, Matthias
Molecular Simulations of a Dynamic Protein Complex: Role of Salt-Bridges and Polar Interactions in Configurational Transitions
BIOPHYSICAL JOURNAL, 105:2412-2417, NOV 19 2013
abstract, full text, DOI:10.1016/j.bpj.2013.09.052

Demirci, Erhan; Junne, Tina; Baday, Sefer; Berneche, Simon; Spiess, Martin
Functional asymmetry within the Sec61p translocon
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110:18856-18861, NOV 19 2013
abstract, full text, DOI:10.1073/pnas.1318432110

Lima, Marisa A.; Oliveira-Neto, Mario; Kadowaki, Marco Antonio S.; Rosseto, Flavio R.; Prates, Erica T.; Squina, Fabio M.; Leme, Adriana F. P.; Skaf, Munir S.; Polikarpov, Igor
Aspergillus niger beta-Glucosidase Has a Cellulase-like Tadpole Molecular Shape INSIGHTS INTO GLYCOSIDE HYDROLASE FAMILY 3 (GH3) beta-GLUCOSIDASE STRUCTURE AND FUNCTION
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:32991-33005, NOV 15 2013
abstract, full text, DOI:10.1074/jbc.M113.479279

Wu, Miao; Bu, Lintao; Vuong, Thu V.; Wilson, David B.; Crowley, Michael F.; Sandgren, Mats; Stahlberg, Jerry; Beckham, Gregg T.; Hansson, Henrik
Loop Motions Important to Product Expulsion in the Thermobifida fusca Glycoside Hydrolase Family 6 Cellobiohydrolase from Structural and Computational Studies
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:33107-33117, NOV 15 2013
abstract, full text, DOI:10.1074/jbc.M113.502765

Hsin, Jen; Fu, Rui; Huang, Kerwyn Casey
Dimer Dynamics and Filament Organization of the Bacterial Cell Division Protein FtsA
JOURNAL OF MOLECULAR BIOLOGY, 425:4415-4426, NOV 15 2013
abstract, full text, DOI:10.1016/j.jmb.2013.07.016

Rathore, Anurag; Carpenter, Michael A.; Demir, Oeziem; Ikeda, Terumasa; Li, Ming; Shaban, Nadine M.; Law, Emily K.; Anokhin, Dmitry; Brown, William L.; Amaro, Rommie E.; Harris, Reuben S.
The Local Dinucleotide Preference of APOBEC3G Can Be Altered from 5 '-CC to 5 '-TC by a Single Amino Acid Substitution
JOURNAL OF MOLECULAR BIOLOGY, 425:4442-4454, NOV 15 2013
abstract, full text, DOI:10.1016/j.jmb.2013.07.040

Sousa, Duncan R.; Stagg, Scott M.; Stroupe, M. Elizabeth
Cryo-EM Structures of the Actin:Tropomyosin Filament Reveal the Mechanism for the Transition from C- to M-State
JOURNAL OF MOLECULAR BIOLOGY, 425:4544-4555, NOV 15 2013
abstract, full text, DOI:10.1016/j.jmb.2013.08.020

Turecek, Frantisek; Moss, Christopher L.; Pikalov, Ioannis; Pepin, Robert; Gulyuz, Kerim; Polfer, Nicolas C.; Bush, Matthew F.; Brown, Jeffery; Williams, Jonathan; Richardson, Keith
Gas-phase structures of phosphopeptide ions: A difficult case
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY, 354:249-256, NOV 15 2013
abstract, full text, DOI:10.1016/j.ijms.2013.06.021

Clark, Nicholas J.; Zhang, Hailiang; Krueger, Susan; Lee, Hyo Jin; Ketchem, Randal R.; Kerwin, Bruce; Kanapuram, Sekhar R.; Treuheit, Michael J.; McAuley, Arnold; Curtis, Joseph E.
Small-Angle Neutron Scattering Study of a Monoclonal Antibody Using Free-Energy Constraints
JOURNAL OF PHYSICAL CHEMISTRY B, 117:14029-14038, NOV 14 2013
abstract, full text, DOI:10.1021/jp408710r

Ningshen, Thuirei Jacob; Aparoy, Polamarasetty; Ventaku, Venkat Rao; Dutta-Gupta, Aparna
Functional Interpretation of a Non-Gut Hemocoelic Tissue Aminopeptidase N (APN) in a Lepidopteran Insect Pest Achaea janata
PLOS ONE, 8 Art. No. e79468, NOV 14 2013
abstract, full text, DOI:10.1371/journal.pone.0079468

Zhao, Junjie; Srajer, Vukica; Franzen, Stefan
Functional Consequences of the Open Distal Pocket of Dehaloperoxidase-Hemoglobin Observed by Time-Resolved X-ray Crystallography
BIOCHEMISTRY, 52:7943-7950, NOV 12 2013
abstract, full text, DOI:10.1021/bi401118q

Parulek, Julius; Turkay, Cagatay; Reuter, Nathalie; Viola, Ivan
Visual cavity analysis in molecular simulations
BMC BIOINFORMATICS, 14 Art. No. S4, NOV 12 2013
abstract, full text, DOI:10.1186/1471-2105-14-S19-S4

Mandal, Manoj; Mukhopadhyay, Chaitali
Concentration-dependent like-charge pairing of guanidinium ions and effect of guanidinium chloride on the structure and dynamics of water from all-atom molecular dynamics simulation
PHYSICAL REVIEW E, 88 Art. No. 052708, NOV 11 2013
abstract, full text, DOI:10.1103/PhysRevE.88.052708

Ozcan, Ozer; Uyar, Arzu; Doruker, Pemra; Akten, Ebru Demet
Effect of intracellular loop 3 on intrinsic dynamics of human beta(2)-adrenergic receptor
BMC STRUCTURAL BIOLOGY, 13 Art. No. 29, NOV 9 2013
abstract, full text, DOI:10.1186/1472-6807-13-29

Akbal-Delibas, Bahar; Haspel, Nurit
A conservation and biophysics guided stochastic approach to refining docked multimeric proteins
BMC STRUCTURAL BIOLOGY, 13 Art. No. S7, NOV 8 2013
abstract, full text, DOI:10.1186/1472-6807-13-S1-S7

Sabit, Hairat; Mallajosyula, Sairam S.; MacKerell, Alexander D., Jr.; Swaan, Peter W.
Transmembrane Domain II of the Human Bile Acid Transporter SLC10A2 Coordinates Sodium Translocation
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:32394-32404, NOV 8 2013
abstract, full text, DOI:10.1074/jbc.M113.518555

Shim, Joong-Youn; Ahn, Kwang H.; Kendall, Debra A.
Molecular Basis of Cannabinoid CB1 Receptor Coupling to the G Protein Heterotrimer G alpha(i)beta gamma IDENTIFICATION OF KEY CB1 CONTACTS WITH THE C-TERMINAL HELIX alpha(5) OF G alpha(i)
JOURNAL OF BIOLOGICAL CHEMISTRY, 288:32449-32465, NOV 8 2013
abstract, full text, DOI:10.1074/jbc.M113.489153

Rashid, M. Harunur; Heinzelmann, Germano; Huq, Redwan; Tajhya, Rajeev B.; Chang, Shih Chieh; Chhabra, Sandeep; Pennington, Michael W.; Beeton, Christine; Norton, Raymond S.; Kuyucak, Serdar
A Potent and Selective Peptide Blocker of the Kv1.3 Channel: Prediction from Free-Energy Simulations and Experimental Confirmation
PLOS ONE, 8 Art. No. e78712, NOV 7 2013
abstract, full text, DOI:10.1371/journal.pone.0078712

Yi, Zheng; Lindner, Benjamin; Prinz, Jan-Hendrik; Noe, Frank; Smith, Jeremy C.
Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling
JOURNAL OF CHEMICAL PHYSICS, 139 Art. No. 175102, NOV 7 2013
abstract, full text, DOI:10.1063/1.4824071

Bidon-Chanal, Axel; Krammer, Eva-Maria; Bolt, Delphine; Pebay-Peyroula, Eva; Chipot, Christophe; Ravaud, Stephanie; Dehez, Francois
How Do Membrane Transporters Sense pH? The Case of the Mitochondrial ADP-ATP Carrier
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 4:3787-3791, NOV 7 2013
abstract, full text, DOI:10.1021/jz401847d

Dhakshnamoorthy, Balasundaresan; Ziervogel, Brigitte K.; Blachowicz, Lydia; Roux, Benoit
A Structural Study of Ion Permeation in OmpF Porin from Anomalous X-ray Diffraction and Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135:16561-16568, NOV 6 2013
abstract, full text, DOI:10.1021/ja407783a

Wei, Chenyu; Pohorille, Andrew
Activation and Proton Transport Mechanism in Influenza A M2 Channel
BIOPHYSICAL JOURNAL, 105:2036-2045, NOV 5 2013
abstract, full text, DOI:10.1016/j.bpj.2013.08.030

Gupta, Kshitij; Jang, Hyunbum; Harlen, Kevin; Puri, Anu; Nussinov, Ruth; Schneider, Joel P.; Blumenthal, Robert
Mechanism of Membrane Permeation Induced by Synthetic beta-Hairpin Peptides
BIOPHYSICAL JOURNAL, 105:2093-2103, NOV 5 2013
abstract, full text, DOI:10.1016/j.bpj.2013.09.040

Ma, Chunlong; Fiorin, Giacomo; Carnevale, Vincenzo; Wang, Jun; Lamb, Robert A.; Klein, Michael L.; Wu, Yibing; Pinto, Lawrence H.; DeGrado, William F.
Asp44 Stabilizes the Trp41 Gate of the M2 Proton Channel of Influenza A Virus
STRUCTURE, 21:2033-2041, NOV 5 2013
abstract, full text, DOI:10.1016/j.str.2013.08.029

Dolores Elola, M.; Rodriguez, Javier
Structure and Dynamics of Nonionic Surfactants Adsorbed at Vacuum/Ionic Liquid Interfaces
LANGMUIR, 29:13379-13387, NOV 5 2013
abstract, full text, DOI:10.1021/la402683j

Giudice, Emmanuel; Molza, Anne-Elisabeth; Laurin, Yoann; Nicolas, Aurelie; Le Rumeur, Elisabeth; Delalande, Olivier
Molecular Clues about the Dystrophin-Neuronal Nitric Oxide Synthase Interaction: A Theoretical Approach
BIOCHEMISTRY, 52:7777-7784, NOV 5 2013
abstract, full text, DOI:10.1021/bi400794p

Lushchekina, S. V.; Polomskikh, V. S.; Varfolomeev, S. D.; Masson, P.
Molecular modeling of butyrylcholinesterase inhibition by cresyl saligenin phosphate
RUSSIAN CHEMICAL BULLETIN, 62:2527-2537, NOV 2013
abstract, full text

Ortega, Davi R.; Mo, Guoya; Lee, Kwangwoon; Zhou, Hongjun; Baudry, Jerome; Dahlquist, Frederick W.; Zhulin, Igor B.
Conformational Coupling between Receptor and Kinase Binding Sites through a Conserved Salt Bridge in a Signaling Complex Scaffold Protein
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003337, NOV 2013
abstract, full text, DOI:10.1371/journal.pcbi.1003337

Ganoth, Assaf; Tsfadia, Yossi; Wiener, Reuven
Ubiquitin: Molecular modeling and simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 46:29-40, NOV 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.09.006

Chen, Xin; Yu, Xiaohan; Liu, Yafang; Zhang, Jinglai
Stepwise design of non-covalent wrapping of large diameter carbon nanotubes by peptides
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 46:83-92, NOV 2013
abstract, full text, DOI:10.1016/j.jmgm.2013.09.012

Juul, Sissel; Iacovelli, Federico; Falconi, Mattia; Kragh, Sofie L.; Christensen, Brian; Frohlich, Rikke; Franch, Oskar; Kristoffersen, Emil L.; Stougaard, Magnus; Leong, Kam W.; Ho, Yi-Ping; Sorensen, Esben S.; Birkedal, Victoria; Desideri, Alessandro; Knudsen, Birgitta R.
Temperature-Controlled Encapsulation and Release of an Active Enzyme in the Cavity of a Self-Assembled DNA Nanocage
ACS NANO, 7:9724-9734, NOV 2013
abstract, full text, DOI:10.1021/nn4030543

Arias, Hugo R.; Lopez, Jhon J.; Feuerbach, Dominik; Fierro, Angelica; Ortells, Marcelo O.; Perez, Edwin G.
Novel 2-(substituted benzyl)quinuclidines inhibit human alpha 7 and alpha 4 beta 2 nicotinic receptors by different mechanisms
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 45:2420-2430, NOV 2013
abstract, full text, DOI:10.1016/j.biocel.2013.08.003

Blacklock, Kristin; Verkhivker, Gennady M.
Experimentally Guided Structural Modeling and Dynamics Analysis of Hsp90-p53 Interactions: Allosteric Regulation of the Hsp90 Chaperone by a Client Protein
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2962-2978, NOV 2013
abstract, full text, DOI:10.1021/ci400434g

Tarcsay, Akos; Paragi, Gabor; Vass, Marton; Jojart, Balazs; Bogar, Ferenc; Keseru, Gyoergy M.
The Impact of Molecular Dynamics Sampling on the Performance of Virtual Screening against GPCRs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:2990-2999, NOV 2013
abstract, full text, DOI:10.1021/ci400087b

Barakat, Khaled H.; Law, John; Prunotto, Alessio; Magee, Wendy C.; Evans, David H.; Tyrrell, D. Lorne; Tuszynski, Jack; Houghton, Michael
Detailed Computational Study of the Active Site of the Hepatitis C Viral RNA Polymerase to Aid Novel Drug Design
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 53:3031-3043, NOV 2013
abstract, full text, DOI:10.1021/ci4003969

Hobbs, Joanne K.; Jiao, Wanting; Easter, Ashley D.; Parker, Emily J.; Schipper, Louis A.; Arcus, Vickery L.
Change in Heat Capacity for Enzyme Catalysis Determines Temperature Dependence of Enzyme Catalyzed Rates
ACS CHEMICAL BIOLOGY, 8:2388-2393, NOV 2013
abstract, full text, DOI:10.1021/cb4005029

Leonarski, Filip; Trovato, Fabio; Tozzini, Valentina; Les, Andrzej; Trylska, Joanna
Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:4874-4889, NOV 2013
abstract, full text, DOI:10.1021/ct4005036

Calero, C.; Marti, J.; Guardia, E.; Masia, Marco
Characterization of the Methane-Graphene Hydrophobic Interaction in Aqueous Solution from Ab Initio Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5070-5075, NOV 2013
abstract, full text, DOI:10.1021/ct400554q

Damas, Joao M.; Filipe, Luis C. S.; Campos, Sara R. R.; Lousa, Diana; Victor, Bruno L.; Baptista, Antonio M.; Soares, Claudio M.
Predicting the Thermodynamics and Kinetics of Helix Formation in a Cyclic Peptide Model
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5148-5157, NOV 2013
abstract, full text, DOI:10.1021/ct400529k

Fowler, Philip W.; Abad, Enrique; Beckstein, Oliver; Sansom, Mark S. P.
Energetics of Multi-Ion Conduction Pathways in Potassium Ion Channels
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9:5176-5189, NOV 2013
abstract, full text, DOI:10.1021/ct4005933

Bagatin, Mariane C.; Candido, Augusto A.; Pinheiro, Glaucia M. S.; Hoeehr, Nelci F.; Machinski, Miguel, Jr.; Mossini, Simone A. G.; Basso, Ernani A.; Gauze, Gisele F.
Molecular Modeling and Anticholinesterasic Activity of Novel 2-Arylaminocyclohexyl N,N-Dimethylcarbamates
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 24:1798-1807, NOV 2013
abstract, full text, DOI:10.5935/0103-5053.20130225

Gun'ko, Vladimir M.
MODELING OF INTERFACIAL BEHAVIOR OF WATER AND ORGANICS
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 12 Art. No. 1350059, NOV 2013
abstract, full text, DOI:10.1142/S0219633613500594

Buck, Patrick M.; Kumar, Sandeep; Singh, Satish K.
Consequences of glycan truncation on Fc structural integrity
MABS, 5:904-916, NOV 1 2013
abstract, full text,