Papers Citing VMD

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VMD citations, February 2012.

Ahadi, Elias, Konermann, Lars
Modeling the Behavior of Coarse-Grained Polymer Chains in Charged Water Droplets: Implications for the Mechanism of Electrospray Ionization
JOURNAL OF PHYSICAL CHEMISTRY B, 116:104-112, JAN 12 2012 2012
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Kucerka, Norbert, Holland, Bryan W., Gray, Chris G., Tomberli, Bruno, Katsaras, John
Scattering Density Profile Model of POPG Bilayers As Determined by Molecular Dynamics Simulations and Small-Angle Neutron and X-ray Scattering Experiments
JOURNAL OF PHYSICAL CHEMISTRY B, 116:232-239, JAN 12 2012 2012
abstract, full text

Morrone, Joseph A., Li, Jingyuan, Berne, B. J.
Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes
JOURNAL OF PHYSICAL CHEMISTRY B, 116:378-389, JAN 12 2012 2012
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Pongprayoon, Prapasiri, Beckstein, Oliver, Sansom, Mark S. P.
Biomimetic Design of a Brush-Like Nanopore: Simulation Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 116:462-468, JAN 12 2012 2012
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Mondal, Jagannath, Zhu, Xiao, Cui, Qiang, Yethiraj, Arun
Sequence-Dependent pK(a) Shift Induced by Molecular Self-Assembly: Insights from Computer Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:491-495, JAN 12 2012 2012
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Huang, Xiaoqin, Zheng, Guangrong, Zhani, Chang-Guo
Microscopic Binding of M5 Muscarinic Acetylcholine Receptor with Antagonists by Homology Modeling, Molecular Docking, and Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 116:532-541, JAN 12 2012 2012
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Chen, Pan, Nishiyama, Yoshiharu, Mazeau, Karim
Torsional Entropy at the Origin of the Reversible Temperature-Induced Phase Transition of Cellulose
MACROMOLECULES, 45:362-368, JAN 10 2012 2012
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Dhamodharan, V., Harikrishna, S., Jagadeeswaran, C., Halder, K., Pradeepkumar, P. I.
Selective G-quadruplex DNA Stabilizing Agents Based on Bisquinolinium and Bispyridinium Derivatives of 1,8-Naphthyridine
JOURNAL OF ORGANIC CHEMISTRY, 77:229-242, JAN 6 2012 2012
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Khabiri, Morteza, Roeselova, Martina, Cwiklik, Lukasz
Properties of oxidized phospholipid monolayers: An atomistic molecular dynamics study
CHEMICAL PHYSICS LETTERS, 519-20:93-99, JAN 5 2012 2012
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Kang, Yingyong, Lu, Shouqin, Ren, Peng, Huo, Bo, Long, Mian
Molecular Dynamics Simulation of Shear- and Stretch-Induced Dissociation of P-Selectin/PSGL-1 Complex
BIOPHYSICAL JOURNAL, 102:112-120, JAN 4 2012 2012
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Goerl, Julian, Timm, Malte, Seibel, Juergen
Mechanism-Oriented Redesign of an Isomaltulose Synthase to an Isomelezitose Synthase by Site-Directed Mutagenesis
CHEMBIOCHEM, 13:149-156, JAN 2 2012 2012
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Kuchta, Alison L., Parikh, Hardik, Zhu, Yali, Kellogg, Glen E., Parris, Deborah S., McVoy, Michael A.
Structural modelling and mutagenesis of human cytomegalovirus alkaline nuclease UL98
JOURNAL OF GENERAL VIROLOGY, 93:130-138, JAN 2012 2012
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Altman, Roger B., Terry, Daniel S., Zhou, Zhou, Zheng, Qinsi, Geggier, Peter, Kolster, Rachel A., Zhao, Yongfang, Javitch, Jonathan A., Warren, J. David, Blanchard, Scott C.
Cyanine fluorophore derivatives with enhanced photostability
NATURE METHODS, 9:68-U178, JAN 2012 2012
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Girard, Peter M., Laughton, Charles, Nikjoo, Hooshang
Determination of DNA structural detail using radioprobing
INTERNATIONAL JOURNAL OF RADIATION BIOLOGY, 88:123-128, JAN 2012 2012
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Filippi, Claudia, Buda, Francesco, Guidoni, Leonardo, Sinicropi, Adalgisa
Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:112-124, JAN 2012 2012
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Harada, Ryuhei, Kitao, Akio
The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:290-299, JAN 2012 2012
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Vitalis, Andreas, Caflisch, Amedeo
50 Years of Lifson-Roig Models: Application to Molecular Simulation Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 8:363-373, JAN 2012 2012
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Plazinski, Wojciech, Knys-Dzieciuch, Agnieszka
Interactions between CD44 protein and hyaluronan: insights from the computational study
MOLECULAR BIOSYSTEMS, 8:543-547, 2012 2012
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Guo, Xiaoqing, Su, Jiaye, Guo, Hongxia
Electric field induced orientation and self-assembly of carbon nanotubes in water
SOFT MATTER, 8:1010-1016, 2012 2012
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Jose Valle-Delgado, Juan, Liepina, Inta, Lapidus, Dmitrijs, Sabate, Raimon, Ventura, Salvador, Samitier, Josep, Fernandez-Busquets, Xavier
Self-assembly of human amylin-derived peptides studied by atomic force microscopy and single molecule force spectroscopy
SOFT MATTER, 8:1234-1242, 2012 2012
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Kovalenko, Andriy, Kobryn, Alexander E., Gusarov, Sergey, Lyubimova, Olga, Liu, Xiangjun, Blinov, Nikolay, Yoshida, Masaru
Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators
SOFT MATTER, 8:1508-1520, 2012 2012
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Ramon Peregrina, Jose, Lans, Isaias, Medina, Milagros
The transient catalytically competent coenzyme allocation into the active site of Anabaena ferredoxin NADP(+)-reductase
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 41:117-128, JAN 2012 2012
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Frolov, Andrey I., Arif, Raz N., Kolar, Martin, Romanova, Anastasia O., Fedorov, Maxim V., Rozhin, Aleksey G.
Molecular mechanisms of salt effects on carbon nanotube dispersions in an organic solvent (N-methyl-2-pyrrolidone)
CHEMICAL SCIENCE, 3:541-548, 2012 2012
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Mueh, Frank, Gloeckner, Carina, Hellmich, Julia, Zouni, Athina
Light-induced quinone reduction in photosystem II
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1817:44-65, JAN 2012 2012
abstract, full text

Xu, Huai-long, Li, Chun-yang, He, Xue-mei, Niu, Ke-qin, Peng, Hao, Li, Wen-wen, Zhou, Cheng-cheng, Bao, Jin-ku
Molecular modeling, docking and dynamics simulations of GNA-related lectins for potential prevention of influenza virus (H1N1)
JOURNAL OF MOLECULAR MODELING, 18:27-37, JAN 2012 2012
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Xu, Sichuan, Chi, Shaoming, Jin, Yi, Shi, Qiang, Ge, Maofa, Wang, Shu, Zhang, Xingkang
Molecular dynamics simulation and density functional theory studies on the active pocket for the binding of paclitaxel to tubulin
JOURNAL OF MOLECULAR MODELING, 18:377-391, JAN 2012 2012
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Piechowiak, M. A., Videcoq, A., Ferrando, R., Bochicchio, D., Pagnoux, C., Rossignol, F.
Aggregation kinetics and gel formation in modestly concentrated suspensions of oppositely charged model ceramic colloids: a numerical study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14:1431-1439, 2012 2012
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Wang, Z. W., Palmer, R. E.
Mass Spectrometry and Dynamics of Gold Adatoms Observed on the Surface of Size-Selected Au Nanoclusters
NANO LETTERS, 12:91-95, JAN 2012 2012
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Peng, Lili X., Yu, Lei, Howell, Stephen B., Gough, David A.
Effects of Solution Concentration on the Physicochemical Properties of a Polymeric Anticancer Therapeutic
MOLECULAR PHARMACEUTICS, 9:37-47, JAN 2012 2012
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Battisti, Anna, Tenenbaum, Alexander
Molecular dynamics simulation of intrinsically disordered proteins
MOLECULAR SIMULATION, 38:139-143, 2012 2012
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Wu, Xiaomin, Yang, Gang, Zu, Yuangang, Fu, Yujie, Zhou, Lijun, Yuan, Xiaohui
Molecular dynamics characterisations of the Trp-cage folding mechanisms: in the absence and presence of water solvents
MOLECULAR SIMULATION, 38:161-171, 2012 2012
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Chen, Wen Wen, Tay, Derrick Kok Sing, Leong, Susanna Su Jan, Kwak, Sang Kyu
Three-dimensional structure of human beta-defensin 28 via homology modelling and molecular dynamics
MOLECULAR SIMULATION, 38:90-101, 2012 2012
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Figueras, Luis, Faraudo, Jordi
Competition between hydrogen bonding and electric field in single-file transport of water in carbon nanotubes
MOLECULAR SIMULATION, 38:23-25, 2012 2012
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Sellis, Diamantis, Drosou, Victoria, Vlachakis, Dimitrios, Voukkalis, Nikolas, Giannakouros, Thomas, Vlassi, Metaxia
Phosphorylation of the arginine/serine repeats of lamin B receptor by SRPK1-Insights from molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1820:44-55, JAN 2012 2012
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Magalhaes de Souza, Cristina Alves, Nogueira Teixeira, Pedro Celso, Faria, Robson Xavier, Krylova, Oxana, Pohl, Peter, Alves, Luiz Anastacio
A consensus segment in the M2 domain of the hP2X(7) receptor shows ion channel activity in planar lipid bilayers and in biological membranes
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1818:64-71, JAN 2012 2012
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Shetty, Kartika N., Bhat, Ganapati G., Inamdar, Shashikala R., Swamy, Bale M., Suguna, K.
Crystal structure of a beta-prism II lectin from Remusatia vivipara
GLYCOBIOLOGY, 22:56-69, JAN 2012 2012
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Zhang, Yubo, Cui, Yubao, Chen, L. Y.
Mercury inhibits the L170C mutant of aquaporin Z by making waters clog the water channel
BIOPHYSICAL CHEMISTRY, 160:69-74, JAN 2012 2012
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Espinoza-Fonseca, L. Michel
Dynamic optimization of signal transduction via intrinsic disorder
MOLECULAR BIOSYSTEMS, 8:194-197, 2012 2012
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Espinoza-Fonseca, L. Michel
Aromatic residues link binding and function of intrinsically disordered proteins
MOLECULAR BIOSYSTEMS, 8:237-246, 2012 2012
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Frolov, Andrey I., Kirchner, Kathleen, Kirchner, Tom, Fedorov, Maxim V.
Molecular-scale insights into the mechanisms of ionic liquids interactions with carbon nanotubes
FARADAY DISCUSSIONS, 154:235-247, 2012 2012
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Sapay, Nicolas, Cabannes, Eric, Petitou, Maurice, Imberty, Anne
Molecular Model of Human Heparanase with Proposed Binding Mode of a Heparan Sulfate Oligosaccharide and Catalytic Amino Acids
BIOPOLYMERS, 97:21-34, JAN 2012 2012
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Zhu, Caizhen, Liu, Xiaofang, Yu, Xiaolan, Zhao, Ning, Liu, Jianhong, Xu, Jian
A small-angle X-ray scattering study and molecular dynamics simulation of microvoid evolution during the tensile deformation of carbon fibers
CARBON, 50:235-243, JAN 2012 2012
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Goel, Saurav, Luo, Xichun, Reuben, Robert L.
Molecular dynamics simulation model for the quantitative assessment of tool wear during single point diamond turning of cubic silicon carbide
COMPUTATIONAL MATERIALS SCIENCE, 51:402-408, JAN 2012 2012
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Nandi, Nilashis
CHIRALITY IN BIOLOGICAL NANOSPACES Reactions in Active Sites Introduction
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 1-46, 2012 2012
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Nandi, Nilashis
Influence of chirality on the hydrolysis reactions within the active site of hydrolases
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 107-116, 2012 2012
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Nandi, Nilashis
Chiral discrimination in the active site of ligases
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 123-163, 2012 2012
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Nandi, Nilashis
Chiral discrimination in the active site of oxidoreductases
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 47-64, 2012 2012
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Nandi, Nilashis
Transferases and chiral discrimination
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 65-105, 2012 2012
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Georgoulia, Panagiota S., Glykos, Nicholas M.
Using J-Coupling Constants for Force Field Validation: Application to Hepta-alanine
JOURNAL OF PHYSICAL CHEMISTRY B, 115:15221-15227, DEC 29 2011 2011
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Perez, Marta A. S., Sousa, Sergio F., Oliveira, Eduardo F. T., Fernandes, Pedro A., Ramos, Maria J.
Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis
JOURNAL OF PHYSICAL CHEMISTRY B, 115:15339-15354, DEC 29 2011 2011
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Gomes, Diego E. B., Lins, Roberto D., Pascutti, Pedro G., Lei, Chenghong, Soares, Thereza A.
Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding
JOURNAL OF PHYSICAL CHEMISTRY B, 115:15389-15398, DEC 29 2011 2011
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Shamay, Eric S., Johnson, Kevin E., Richmond, Geraldine L.
Dancing on Water: The Choreography of Sulfur Dioxide Adsorption to Aqueous Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 115:25304-25314, DEC 29 2011 2011
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Perez, Alejandro, Rubio, Angel
A molecular dynamics study of water nucleation using the TIP4P/2005 model
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 244505, DEC 28 2011 2011
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Zhao, Tongyang, Wang, Xiaogong
Phase behavior of lyotropic rigid-chain polymer liquid crystal studied by dissipative particle dynamics
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 244901, DEC 28 2011 2011
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Musgaard, Maria, Thogersen, Lea, Schiott, Birgit
Protonation States of Important Acidic Residues in the Central Ca(2+) Ion Binding Sites of the Ca(2+)-ATPase: A Molecular Modeling Study
BIOCHEMISTRY, 50:11109-11120, DEC 27 2011 2011
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Iacovella, Christopher R., Keys, Aaron S., Glotzer, Sharon C.
Self-assembly of soft-matter quasicrystals and their approximants
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:20935-20940, DEC 27 2011 2011
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Chapagain, Prem P., Regmi, Chola K., Castillo, William
Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 235101, DEC 21 2011 2011
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Patrick, Christopher E., Giustino, Feliciano
Structural and Electronic Properties of Semiconductor-Sensitized Solar-Cell Interfaces
ADVANCED FUNCTIONAL MATERIALS, 21:4663-4667, DEC 20 2011 2011
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Allison, Jane R., Bergeler, Maike, Hansen, Niels, van Gunsteren, Wilfred F.
Current Computer Modeling Cannot Explain Why Two Highly Similar Sequences Fold into Different Structures
BIOCHEMISTRY, 50:10965-10973, DEC 20 2011 2011
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Orsi, Mario, Essex, Jonathan W.
The ELBA Force Field for Coarse-Grain Modeling of Lipid Membranes
PLOS ONE, 6: Art. No. e28637, DEC 16 2011 2011
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Elizondo-Riojas, Miguel-Angel, Chamow, Steven M., Tuthill, Cynthia W., Gorenstein, David G., Volk, David E.
NMR structure of human thymosin alpha-1
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 416:356-361, DEC 16 2011 2011
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Florencia Lacaruso, Maria, Galli, Soledad, Marti, Marcelo, Ignacio Villalta, Jorge, Ariel Estrin, Dario, Andrea Jares-Erijman, Elizabeth, Isabel Pietrasanta, Lia
Structural Model for p75(NTR)-TrkA Intracellular Domain Interaction: A Combined FRET and Bioinformatics Study
JOURNAL OF MOLECULAR BIOLOGY, 414:681-698, DEC 16 2011 2011
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Ko, Jae Yoon, Heo, Sung Woo, Lee, Joon Ho, Oh, Han Bin, Kim, Hyungjun, Kim, Hugh I.
Host-Guest Chemistry in the Gas Phase: Complex Formation with 18-Crown-6 Enhances Helicity of Alanine-Based Peptides
JOURNAL OF PHYSICAL CHEMISTRY A, 115:14215-14220, DEC 15 2011 2011
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Kyrychenko, Alexander, Karpushina, Galina V., Bogatyrenko, Sergey I., Kryshtal, Alexander P., Doroshenko, Andrey O.
Preparation, structure, and a coarse-grained molecular dynamics model for dodecanethiol-stabilized gold nanoparticles
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 977:34-39, DEC 15 2011 2011
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Gannon, G., O'Dwyer, C., Larsson, J. A., Thompson, D.
Interdigitating Organic Bilayers Direct the Short Inter layer Spacing in Hybrid Organic-Inorganic Layered Vanadium Oxide Nanostructures
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14518-14525, DEC 15 2011 2011
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Wu, Jian, Albrecht, Laura, Boyd, Russell J.
Effect of Counterions on the Protonation State in a Poly(G)-Poly(C) Radical Cation
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14885-14890, DEC 15 2011 2011
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Kublbeck, Jenni, Laitinen, Tuomo, Jyrkkarinne, Johanna, Rousu, Timo, Tolonen, Ari, Abel, Tobias, Kortelainen, Tanja, Uusitalo, Jouko, Korjamo, Timo, Honkakoski, Paavo, Molnar, Ferdinand
Use of comprehensive screening methods to detect selective human CAR activators
BIOCHEMICAL PHARMACOLOGY, 82:1994-2007, DEC 15 2011 2011
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Huang, Baohua, Tang, Shengzhuang, Desai, Ankur, Lee, Kyung-Hoon, Leroueil, Pascale R., Baker, James R., Jr.
Novel (P)under-baroly((ET)under-barhylene(A)under-barmido(A)under-barmine) (PETAA) dendrimers produced through a unique and highly efficient synthesis
POLYMER, 52:5975-5984, DEC 13 2011 2011
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Shi, Dashuang, Li, Yongdong, Cabrera-Luque, Juan, Jin, Zhongmin, Yu, Xiaolin, Zhao, Gengxiang, Haskins, Nantaporn, Allewell, Norma M., Tuchman, Mendel
A Novel N-Acetylglutamate Synthase Architecture Revealed by the Crystal Structure of the Bifunctional Enzyme from Maricaulis maris
PLOS ONE, 6: Art. No. e28825, DEC 12 2011 2011
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Christelle, Bidouil, Eduardo, Basilio De Oliveira, Latifa, Chebil, Elaine-Rose, Maia, Bernard, Maigret, Evelyne, Ronat-Heidt, Mohamed, Ghoul, Jean-Marc, Engasser, Catherine, Humeau
Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation
JOURNAL OF BIOTECHNOLOGY, 156:203-210, DEC 10 2011 2011
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Goetz, Angela, Lanig, Harald, Gmeiner, Peter, Clark, Timothy
Molecular Dynamics Simulations of the Effect of the G-Protein and Diffusible Ligands on the beta 2-Adrenergic Receptor
JOURNAL OF MOLECULAR BIOLOGY, 414:611-623, DEC 9 2011 2011
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Navizet, Isabelle, Liu, Ya-Jun, Ferre, Nicolas, Roca-Sanjuan, Daniel, Lindh, Roland
The Chemistry of Bioluminescence: An Analysis of Chemical Functionalities
CHEMPHYSCHEM, 12:3064-3076, DEC 9 2011 2011
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Boereboom, Jelle M., van Hemert, Marc C., Neugebauer, Johannes
The Resonance Raman Spectra of Spheroidene Revisited with a First-Principles Approach
CHEMPHYSCHEM, 12:3157-3169, DEC 9 2011 2011
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Vargas, Ernesto, Bezanilla, Francisco, Roux, Benoit
In Search of a Consensus Model of the Resting State of a Voltage-Sensing Domain
NEURON, 72:713-720, DEC 8 2011 2011
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Callejas-Tovar, Rafael, Liao, Wenta, Mera, Hilda, Balbuena, Perla B.
Molecular Dynamics Simulations of Surface Oxidation on Pt and Pt/PtCo/Pt(3)Co Nanoparticles Supported over Carbon
JOURNAL OF PHYSICAL CHEMISTRY C, 115:23768-23777, DEC 8 2011 2011
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Pieraccini, Stefano, De Gonda, Riccardo, Sironi, Maurizio
Molecular modeling of the inhibition of protein-protein interactions with small molecules: The IL2-IL2R alpha case
CHEMICAL PHYSICS LETTERS, 517:217-222, DEC 7 2011 2011
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Joly, Laurent
Capillary filling with giant liquid/solid slip: Dynamics of water uptake by carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 214705, DEC 7 2011 2011
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Rasmussen, Christopher J., Vishnyakov, Aleksey, Neimark, Alexander V.
Calculation of chemical potentials of chain molecules by the incremental gauge cell method
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 214109, DEC 7 2011 2011
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Chakravorty, Dhruva K., Wang, Bing, Ucisik, Melek N., Merz, Kenneth M., Jr.
Insight into the Cation-pi Interaction at the Metal Binding Site of the Copper Metallochaperone CusF
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:19330-19333, DEC 7 2011 2011
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Chen, Rong, Robinson, Anna, Gordon, Dan, Chung, Shin-Ho
Modeling the Binding of Three Toxins to the Voltage-Gated Potassium Channel (Kv1.3)
BIOPHYSICAL JOURNAL, 101:2652-2660, DEC 7 2011 2011
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Gordon, Dan, Chung, Shin-Ho
Permeation and Block of the Kv1.2 Channel Examined Using Brownian and Molecular Dynamics
BIOPHYSICAL JOURNAL, 101:2671-2678, DEC 7 2011 2011
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Marcos, Enrique, Mestres, Pau, Crehuet, Ramon
Crowding Induces Differences in the Diffusion of Thermophilic and Mesophilic Proteins: A New Look at Neutron Scattering Results
BIOPHYSICAL JOURNAL, 101:2782-2789, DEC 7 2011 2011
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Boughton, Andrew P., Khoi Nguyen, Andricioaei, Ioan, Chen, Zhan
Interfacial Orientation and Secondary Structure Change in Tachyplesin I: Molecular Dynamics and Sum Frequency Generation Spectroscopy Studies
LANGMUIR, 27:14343-14351, DEC 6 2011 2011
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Seong, Joon-Kyung, Baek, Nakhoon, Kim, Ku-Jin
Real-time approximation of molecular interaction interfaces based on hierarchical space decomposition
COMPUTER-AIDED DESIGN, 43:1598-1605, DEC 2011 2011
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Moore, Emily, Corrales, L. Rene, Desai, Tapan, Devanathan, Ram
Molecular dynamics simulation of Xe bubble nucleation in nanocrystalline UO(2) nuclear fuel
JOURNAL OF NUCLEAR MATERIALS, 419:140-144, DEC 2011 2011
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Kiraly, Robert, Demeny, Mate A., Fesues, Laszlo
Protein transamidation by transglutaminase 2 in cells: a disputed Ca(2+)-dependent action of a multifunctional protein
FEBS JOURNAL, 278:4717-4739, DEC 2011 2011
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Boulet, Pascal, Record, Marie-Christine
Electronic properties of Zn(1-x)Cd(x)Sb solid solution investigated by density-functional theory
CALPHAD-COMPUTER COUPLING OF PHASE DIAGRAMS AND THERMOCHEMISTRY, 35:639-642, DEC 2011 2011
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Peng, Lili X., Yu, Lei, Howell, Stephen B., Gough, David A.
Aggregation Properties of a Polymeric Anticancer Therapeutic: A Coarse-Grained Modeling Study
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:3030-3035, DEC 2011 2011
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Nguyen Hoa My, Hirao, Hajime, Dang Ung Van, Morokuma, Keiji
Computational Studies of Bacterial Resistance to beta-Lactam Antibiotics: Mechanism of Covalent Inhibition of the Penicillin-Binding Protein 2a (PBP2a)
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:3226-3234, DEC 2011 2011
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Avdoshenko, Stas M., Ioffe, Ilya N., Cuniberti, Gianaurelio, Dunsch, Lothar, Popov, Alexey A.
Organometallic Complexes of Graphene: Toward Atomic Spintronics Using a Graphene Web
ACS NANO, 5:9939-9949, DEC 2011 2011
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Iyer, Lakshminarayan M., Zhang, Dapeng, Rogozin, Igor B., Aravind, L.
Evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems
NUCLEIC ACIDS RESEARCH, 39:9473-9497, DEC 2011 2011
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Mrinal, Nirotpal, Tomar, Archana, Nagaraju, Javaregowda
Role of sequence encoded kappa B DNA geometry in gene regulation by Dorsal
NUCLEIC ACIDS RESEARCH, 39:9574-9591, DEC 2011 2011
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Forbey, Jennifer Sorensen, Pu, Xinzhu, Xu, Dong, Kielland, Knut, Bryant, John
Inhibition of Snowshoe Hare Succinate Dehydrogenase Activity as a Mechanism of Deterrence for Papyriferic Acid in Birch
JOURNAL OF CHEMICAL ECOLOGY, 37:1285-1293, DEC 2011 2011
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Dubey, Kshatresh Dutta, Chaubey, Amit Kumar, Ojha, Rajendra Prasad
Role of pH on dimeric interactions for DENV envelope protein: An insight from molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:1796-1801, DEC 2011 2011
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Gussoni, Maristella, Scorciapino, Mariano Andrea, Vezzoli, Alessandra, Anedda, Roberto, Greco, Fulvia, Ceccarelli, Matteo, Casu, Mariano
Structural characterization of recombinant human myoglobin isoforms by (1)H and (129)Xe NMR and molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:1919-1929, DEC 2011 2011
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Kurkcuoglu, Zeynep, Ural, Gulgun, Akten, E. Demet, Doruker, Pemra
Blind Dockings of Benzothiazoles to Multiple Receptor Conformations of Triosephosphate Isomerase from Trypanosoma cruzi and Human
MOLECULAR INFORMATICS, 30:986-995, DEC 2011 2011
abstract, full text

Medeiros, Alessandra, Biagi, Diogo G., Sobreira, Tiago J. P., de Oliveira, Paulo Sergio L., Negrao, Carlos Eduardo, Mansur, Alfredo J., Krieger, Jose Eduardo, Brum, Patricia C., Pereira, Alexandre C.
Mutations in the human phospholamban gene in patients with heart failure
AMERICAN HEART JOURNAL, 162:1088-U184, DEC 2011 2011
abstract, full text

Meyer, Tim, Kieseritzky, Gernot, Knapp, Ernst-Walter
Electrostatic pK(a) computations in proteins: Role of internal cavities
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:3320-3332, DEC 2011 2011
abstract, full text

Polydorides, Savvas, Amara, Najette, Aubard, Caroline, Plateau, Pierre, Simonson, Thomas, Archontis, Georgios
Computational protein design with a generalized Born solvent model: Application to Asparaginyl-tRNA synthetase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:3448-3468, DEC 2011 2011
abstract, full text

Cymes, Gisela D., Grosman, Claudio
Estimating the pK(a) values of basic and acidic side chains in ion channels using electrophysiological recordings: A robust approach to an elusive problem
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:3485-3493, DEC 2011 2011
abstract, full text

Ensign, Daniel L., Webb, Lauren J.
Factors determining electrostatic fields in molecular dynamics simulations of the Ras/effector interface
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:3511-3524, DEC 2011 2011
abstract, full text

Kozachkova, A. N., Dudko, A. V., Tsaryk, N. V., Trachevskii, V. V., Rozhenko, A. B., Pekhnyo, V. I.
Different ways of coordination for aminoalkyldiphosphonic acids in palladium(II) complexes
RUSSIAN JOURNAL OF COORDINATION CHEMISTRY, 37:941-948, DEC 2011 2011
abstract, full text

Lorenzen, Winfried, Holst, Bastian, Redmer, Ronald
Metallization in hydrogen-helium mixtures
PHYSICAL REVIEW B, 84: Art. No. 235109, DEC 1 2011 2011
abstract, full text

Yang, Xiaodong, He, Pengfei, Gao, Huajian
Modeling frequency- and temperature-invariant dissipative behaviors of randomly entangled carbon nanotube networks under cyclic loading
NANO RESEARCH, 4:1191-1198, DEC 2011 2011
abstract, full text

Rosas-Trigueros, Jorge Luis, Correa-Basurto, Jose, Benitez-Cardoza, Claudia Guadalupe, Zamorano-Carrillo, Absalom
Insights into the structural stability of Bax from molecular dynamics simulations at high temperatures
PROTEIN SCIENCE, 20:2035-2046, DEC 2011 2011
abstract, full text

Kleinschroth, Thomas, Castellani, Michela, Trinh, Chi H., Morgner, Nina, Brutschy, Bernhard, Ludwig, Bernd, Hunte, Carola
X-ray structure of the dimeric cytochrome bc(1) complex from the soil bacterium Paracoccus denitrificans at 2.7-angstrom resolution
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:1606-1615, DEC 2011 2011
abstract, full text

Bondar, Ana-Nicoleta, Knapp-Mohammady, Michaela, Suhai, Sandor, Fischer, Stefan, Smith, Jeremy C.
Ground-state properties of the retinal molecule: from quantum mechanical to classical mechanical computations of retinal proteins
THEORETICAL CHEMISTRY ACCOUNTS, 130:1169-1183, DEC 2011 2011
abstract, full text

Stachowicz, Anna, Styrcz, Anna, Korchowiec, Jacek, Modaressi, Ali, Rogalski, Marek
DFT studies of cation binding by beta-cyclodextrin
THEORETICAL CHEMISTRY ACCOUNTS, 130:939-953, DEC 2011 2011
abstract, full text

Duan, Zhang-Qun, Du, Wei, Liu, De-Hua
The mechanism of solvent effect on the positional selectivity of Candida antarctica lipase B during 1,3-diolein synthesis by esterification
BIORESOURCE TECHNOLOGY, 102:11048-11050, DEC 2011 2011
abstract, full text

Weldon, John E., Pastan, Ira
A guide to taming a toxin - recombinant immunotoxins constructed from Pseudomonas exotoxin A for the treatment of cancer
FEBS JOURNAL, 278:4683-4700, DEC 2011 2011
abstract, full text

Schmidtke, Peter, Bidon-Chanal, Axel, Javier Luque, F., Barril, Xavier
MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories
BIOINFORMATICS, 27:3276-3285, DEC 1 2011 2011
abstract, full text

Qi, Dongdong, Jiang, Jianzhuang
Toward Panchromatic Organic Functional Molecules: Density Functional Theory Study on the Electronic Absorption Spectra of Substituted Tetraanthracenylporphyrins
JOURNAL OF PHYSICAL CHEMISTRY A, 115:13811-13820, DEC 1 2011 2011
abstract, full text

Ghalib, Raza Murad, Hashim, Rokiah, Silva, P. S. Pereira, Sulaiman, Othman
Synthesis, Crystal Structure and ab Initio Studies of 5-Phenylamino-3-phenylimino-3H[1,2]dithiole-4-carboxylic acid ethyl ester
JOURNAL OF CHEMICAL CRYSTALLOGRAPHY, 41:1889-1893, DEC 2011 2011
abstract, full text

Garcia-Heredia, Jose M., Diaz-Quintana, Antonio, Salzano, Maria, Orzaez, Mar, Perez-Paya, Enrique, Teixeira, Miguel, De la Rosa, Miguel A., Diaz-Moreno, Irene
Tyrosine phosphorylation turns alkaline transition into a biologically relevant process and makes human cytochrome c behave as an anti-apoptotic switch
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 16:1155-1168, DEC 2011 2011
abstract, full text

Liu, Yuli, Burger, Steven K., Ayers, Paul W., Voehringer-Martinez, Esteban
Computational Study of the Binding Modes of Caffeine to the Adenosine A(2A) Receptor
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13880-13890, DEC 1 2011 2011
abstract, full text

Du, Huailiang, Li, Jingyuan, Zhang, Jing, Su, Gang, Li, Xiaoyi, Zhao, Yuliang
Separation of Hydrogen and Nitrogen Gases with Porous Graphene Membrane
JOURNAL OF PHYSICAL CHEMISTRY C, 115:23261-23266, DEC 1 2011 2011
abstract, full text

Lin, Ying-Wu, Liao, Li-Fu
Probing interactions between uranyl ions and lipid membrane by molecular dynamics simulation
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 976:130-134, DEC 1 2011 2011
abstract, full text

Pagano, Bruno, Del Vecchio, Pompea, Mattia, Carlo A., Graziano, Giuseppe
Molecular dynamics study of the conformational stability of esterase 2 from Alicyclobacillus acidocaldarius
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 49:1072-1077, DEC 1 2011 2011
abstract, full text

Pozzo, Monica, Alfe, Dario
Dehydrogenation of pure and Ti-doped Na(3)AlH(6) surfaces from first principles calculations
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY, 36:15632-15641, DEC 2011 2011
abstract, full text

Lombardi, Alessio, Gianese, Giulio, Arcangeli, Caterina, Galeffi, Patrizia, Sperandei, Maria
Bacterial Cytoplasm Production of an EGFP-Labeled Single-Chain Fv Antibody Specific for the HER2 Human Receptor
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:425-439, DEC 2011 2011
abstract, full text

Bairagya, Hridoy R., Mukhopadhyay, Bishnu P., Bera, Asim K.
Role of Salt Bridge Dynamics in Inter Domain Recognition of Human IMPDH Isoforms: An Insight to Inhibitor Topology for Isoform-II
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:441-462, DEC 2011 2011
abstract, full text

Kitagawa, Yuya, Matsuda, Kenji, Hasegawa, Jun-ya
Theoretical study of the excited states of the photosynthetic reaction center in photosystem II: Electronic structure, interactions, and their origin
BIOPHYSICAL CHEMISTRY, 159:227-236, DEC 2011 2011
abstract, full text

Renthal, Robert, Brancaleon, Lorenzo, Pena, Isaac, Silva, Frances, Chen, Liao Y.
Interaction of a two-transmembrane-helix peptide with lipid bilayers and dodecyl sulfate micelles
BIOPHYSICAL CHEMISTRY, 159:321-327, DEC 2011 2011
abstract, full text

Soontrapa, C., Chen, Y.
Molecular dynamics potentials in magnetite (Fe(3)O(4)) modeling
COMPUTATIONAL MATERIALS SCIENCE, 50:3271-3281, DEC 2011 2011
abstract, full text

Ayatollahi, Abdul Majid, Ghanadian, Mustafa, Afsharypuor, Suleiman, Mesaik, M. Ahmad, Abdalla, Omer Mohamed, Shahlaei, Mohsen, Farzandi, Gholamhossein, Mostafavi, Hamid
Cycloartanes from Euphorbia aellenii Rech. f. and their Antiproliferative Activity
IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH, 10:105-111, WIN 2011 2011
abstract, full text

Liu, Wanfei, Huang, Dawei, Liu, Kan, Hu, Songnian, Yu, Jun, Gao, Gang, Song, Shuhui
Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae
Genomics Proteomics & Bioinformatics, 8:229-237, DEC 2010 2010
abstract, full text

Kaila, Ville R. I., Hummer, Gerhard
Energetics of Direct and Water-Mediated Proton-Coupled Electron Transfer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:19040-19043, NOV 30 2011 2011
abstract, full text

Joshi, Harshad, Cheluvaraja, Srinath, Somogyi, Endre, Brown, Darron R., Ortoleva, Peter
A molecular dynamics study of loop fluctuation in human papillomavirus type 16 virus-like particles: A possible indicator of immunogenicity
VACCINE, 29:9423-9430, NOV 28 2011 2011
abstract, full text

Friedman, Ran, Caflisch, Amedeo
Surfactant Effects on Amyloid Aggregation Kinetics
JOURNAL OF MOLECULAR BIOLOGY, 414:303-312, NOV 25 2011 2011
abstract, full text

Liu, Jin, Nussinov, Ruth
Flexible Cullins in Cullin-RING E3 Ligases Allosterically Regulate Ubiquitination
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:40934-40942, NOV 25 2011 2011
abstract, full text

Payne, Christina M., Bomble, Yannicki, Taylor, Courtney B., McCabe, Clare, Himmel, Michael E., Crowley, Michael F., Beckham, Gregg T.
Multiple Functions of Aromatic-Carbohydrate Interactions in a Processive Cellulase Examined with Molecular Simulation
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:41028-41035, NOV 25 2011 2011
abstract, full text

Tavernelli, Ivano, Curchod, Basile F. E., Rothlisberger, Ursula
Nonadiabatic molecular dynamics with solvent effects: A LR-TDDFT QM/MM study of ruthenium (II) tris (bipyridine) in water
CHEMICAL PHYSICS, 391:101-109, NOV 24 2011 2011
abstract, full text

Wu, Hong-Zhang, Zhao, Shi-Jin
Molecular Dynamics Study of the Response of Nanostructured Al/Ni Clad Particles System under Thermal Loading
JOURNAL OF PHYSICAL CHEMISTRY A, 115:13605-13610, NOV 24 2011 2011
abstract, full text

Orlowski, Adam, St-Pierre, Jean-Francois, Magarkar, Aniket, Bunker, Alex, Pasenkiewicz-Gierula, Marta, Vattulainen, Ilpo, Rog, Tomasz
Properties of the Membrane Binding Component of Catechol-O-methyltransferase Revealed by Atomistic Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13541-13550, NOV 24 2011 2011
abstract, full text

Yuzlenko, Olga, Lazandis, Themis
Interactions between Ionizable Amino Acid Side Chains at a Lipid Bilayer-Water Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13674-13684, NOV 24 2011 2011
abstract, full text

Wostenberg, Christopher, Kumar, Sushant, Noid, William G., Showalter, Scott A.
Atomistic Simulations Reveal Structural Disorder in the RAP74-FCP1 Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13731-13739, NOV 24 2011 2011
abstract, full text

Kuehhorn, Julia, Goetz, Angela, Huebner, Harald, Thompson, Dawn, Whistler, Jennifer, Gmeiner, Peter
Development of a Bivalent Dopamine D(2) Receptor Agonist
JOURNAL OF MEDICINAL CHEMISTRY, 54:7911-7919, NOV 24 2011 2011
abstract, full text

Cranford, Steven W., Buehler, Markus J.
Packing efficiency and accessible surface area of crumpled graphene
PHYSICAL REVIEW B, 84: Art. No. 205451, NOV 22 2011 2011
abstract, full text

Cino, Elio A., Wong-ekkabut, Jirasak, Karttunen, Mikko, Choy, Wing-Yiu
Microsecond Molecular Dynamics Simulations of Intrinsically Disordered Proteins Involved in the Oxidative Stress Response
PLOS ONE, 6: Art. No. e27371, NOV 18 2011 2011
abstract, full text

Yung-Hung, Roy Lee, Ismail, Asma, Lim, Theam Soon, Choong, Yee Siew
A 35 kDa antigenic protein from Shigella flexneri: In silico structural and functional studies
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 415:229-234, NOV 18 2011 2011
abstract, full text

Ganim, Ziad, Tokmakoff, Andrei, Vaziri, Alipasha
Vibrational excitons in ionophores: experimental probes for quantum coherence-assisted ion transport and selectivity in ion channels
NEW JOURNAL OF PHYSICS, 13: Art. No. 113030, NOV 18 2011 2011
abstract, full text

Placzek, William J., Sturlese, Mattia, Wu, Bainan, Cellitti, Jason F., Wei, Jun, Pellecchia, Maurizio
Identification of a Novel Mcl-1 Protein Binding Motif
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:39829-39835, NOV 18 2011 2011
abstract, full text

Buin, Andrei, Consta, Styliani, Sham, Tsun-Kong
Mechanisms of Phase Transformations of TiO(2) Nanotubes and Nanorods
JOURNAL OF PHYSICAL CHEMISTRY C, 115:22257-22264, NOV 17 2011 2011
abstract, full text

Dai, Zheng-Wei, Wan, Ling-Shu, Huang, Xiao-Jun, Ling, Jun, Xu, Zhi-Kang
Selective Adsorption of Isopropyl Alcohol Aqueous Solution on Polypropylene Surfaces: A Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY C, 115:22415-22421, NOV 17 2011 2011
abstract, full text

Sun, Sheng, Wong, Joseph T. Y., Zhang, Tong-Yi
Atomistic Simulations of Electroporation in Water Preembedded Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:13355-13359, NOV 17 2011 2011
abstract, full text

Mirau, Peter A., Naik, Rajesh R., Gehring, Patricia
Structure of Peptides on Metal Oxide Surfaces Probed by NMR
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:18243-18248, NOV 16 2011 2011
abstract, full text

Heinzelmann, Germano, Bastug, Turgut, Kuyucak, Serdar
Free Energy Simulations of Ligand Binding to the Aspartate Transporter Glt(Ph)
BIOPHYSICAL JOURNAL, 101:2380-2388, NOV 16 2011 2011
abstract, full text

Ahlstrom, Logan S., Miyashita, Osamu
Molecular Simulation Uncovers the Conformational Space of the lambda Cro Dimer in Solution
BIOPHYSICAL JOURNAL, 101:2516-2524, NOV 16 2011 2011
abstract, full text

Ganoth, Assaf, Alhadeff, Raphael, Kohen, Dovrat, Arkin, Isaiah T.
Characterization of the Na(+)/H(+) Antiporter from Yersinia pestis
PLOS ONE, 6: Art. No. e26115, NOV 15 2011 2011
abstract, full text

Mills, Matthew J. L., Popelier, Paul L. A.
Intramolecular polarisable multipolar electrostatics from the machine learning method Kriging
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 975:42-51, NOV 15 2011 2011
abstract, full text

Bonanata, Jenner N., Signorelli, Santiago, Laura Coitino, E.
Increasing complexity models for describing the generation of substrate radicals at the active site of ethanolamine ammonia-lyase/B(12)
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 975:52-60, NOV 15 2011 2011
abstract, full text

Garate, Jose-Antonio, English, Niall J., Singh, Ajay, Ryan, Kevin M., Mooney, Damian A., MacElroy, J. M. D.
Electrophoretic Deposition of Poly(3-decylthiophene) onto Gold-Mounted Cadmium Selenide Nanorods
LANGMUIR, 27:13506-13513, NOV 15 2011 2011
abstract, full text

Mendez, Manuel A., Nazemi, Zahra, Uyanik, Ibrahim, Lu, Yu, Girault, Hubert H.
Melittin Adsorption and Lipid Monolayer Disruption at Liquid-Liquid Interfaces
LANGMUIR, 27:13918-13924, NOV 15 2011 2011
abstract, full text

Mane, Rajendra S., Ghosh, Sougata, Singh, Shailza, Chopade, Balu A., Dhavale, Dilip D.
Synthesis of anomeric 1,5-anhydrosugars as conformationally locked selective alpha-mannosidase inhibitors
BIOORGANIC & MEDICINAL CHEMISTRY, 19:6720-6725, NOV 15 2011 2011
abstract, full text

Chu, John J., Steeves, Craig A.
Thermal expansion and recrystallization of amorphous Al and Ti: A molecular dynamics study
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:3765-3773, NOV 15 2011 2011
abstract, full text

Ichikawa, Kazuhide, Ikeda, Yuji, Wagatsuma, Ayumu, Watanabe, Kouhei, Szarek, Pawel, Tachibana, Akitomo
Theoretical Study of Hydrogenated Tetrahedral Aluminum Clusters
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:3548-3555, NOV 15 2011 2011
abstract, full text

Ahmad, Kareem M., Oh, Seung Soo, Kim, Seon, McClellen, Forrest M., Xiao, Yi, Soh, H. Tom
Probing the Limits of Aptamer Affinity with a Microfluidic SELEX Platform
PLOS ONE, 6: Art. No. e27051, NOV 14 2011 2011
abstract, full text

Goel, Saurav, Luo, Xichun, Reuben, Robert L., Bin Rashid, Waleed
Annealing of gold nanostructures sputtered on polytetrafluoroethylene
NANOSCALE RESEARCH LETTERS, 6:1-9, NOV 11 2011 2011
abstract, full text

Ferrer, Tania, Cordero-Morales, Julio F., Arias, Marcelo, Ficker, Eckhard, Medovoy, David, Perozo, Eduardo, Tristani-Firouzi, Martin
Molecular Coupling in the Human ether-a-go-go-related gene-1 (hERG1) K(+) Channel Inactivation Pathway
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:39091-39099, NOV 11 2011 2011
abstract, full text

Zanzoni, Serena, Assfalg, Michael, Giorgetti, Alejandro, D'Onofrio, Mariapina, Molinari, Henriette
Structural Requirements for Cooperativity in Ileal Bile Acid-binding Proteins
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:39307-39317, NOV 11 2011 2011
abstract, full text

Karena, Ekaterini, Frillingos, Stathis
The Role of Transmembrane Segment TM3 in the Xanthine Permease XanQ of Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:39595-39605, NOV 11 2011 2011
abstract, full text

He, Chunmao, Neya, Saburo, Knipp, Markus
Breaking the Proximal Fe(II)-N(His) Bond in Heme Proteins through Local Structural Tension: Lessons from the Heme b Proteins Nitrophorin 4, Nitrophorin 7, and Related Site-Directed Mutant Proteins
BIOCHEMISTRY, 50:8559-8575, NOV 11 2011 2011
abstract, full text

Li, Minghui, Zheng, Wenjun
Probing the Structural and Energetic Basis of Kinesin-Microtubule Binding Using Computational Alanine-Scanning Mutagenesis
BIOCHEMISTRY, 50:8645-8655, NOV 11 2011 2011
abstract, full text

Lim, Kok Hong, Huang, Heng, Pralle, Arnd, Park, Sheldon
Engineered Streptavidin Monomer and Dimer with Improved Stability and Function
BIOCHEMISTRY, 50:8682-8691, NOV 11 2011 2011
abstract, full text

Almeida, Joao A. S., Faneca, Henrique, Carvalho, Rui A., Marques, Eduardo F., Pais, Alberto A. C. C.
Dicationic Alkylammonium Bromide Gemini Surfactants. Membrane Perturbation and Skin Irritation
PLOS ONE, 6: Art. No. e26965, NOV 10 2011 2011
abstract, full text

Gang, Hong-Ze, Liu, Jin-Feng, Mu, Bo-Zhong
Molecular Dynamics Study of Surfactin Monolayer at the Air/Water Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12770-12777, NOV 10 2011 2011
abstract, full text

Lee, Hwankyu, Choi, Joon Sig, Larson, Ronald G.
Molecular Dynamics Studies of the Size and Internal Structure of the PAMAM Dendrimer Grafted with Arginine and Histidine
MACROMOLECULES, 44:8681-8686, NOV 8 2011 2011
abstract, full text

Bonomi, Francesco, Iametti, Stefania, Morleo, Anna, Ta, Dennis, Vickery, Larry E.
Facilitated Transfer of IscU-[2Fe2S] Clusters by Chaperone-Mediated Ligand Exchange
BIOCHEMISTRY, 50:9641-9650, NOV 8 2011 2011
abstract, full text

D'Antonio, Edward L., D'Antonio, Jennifer, de Serrano, Vesna, Gracz, Hanna, Thompson, Matthew K., Ghiladi, Reza A., Bowden, Edmond F., Franzen, Stefan
Functional Consequences of the Creation of an Asp-His-Fe Triad in a 3/3 Globin
BIOCHEMISTRY, 50:9664-9680, NOV 8 2011 2011
abstract, full text

Sempombe, Joseph, Stein, Benjamin, Kirk, Martin L.
Spectroscopic and Electronic Structure Studies Probing Covalency Contributions to C-H Bond Activation and Transition-State Stabilization in Xanthine Oxidase
INORGANIC CHEMISTRY, 50:10919-10928, NOV 7 2011 2011
abstract, full text

Hartley, C. Scott
Excited-State Behavior of ortho-Phenylenes
JOURNAL OF ORGANIC CHEMISTRY, 76:9188-9191, NOV 4 2011 2011
abstract, full text

Karachevtsev, Victor A., Stepanian, Stepan G., Glamazda, Alexander Yu., Karachevtsev, Maksym V., Eremenko, Victor V., Lytvyn, Oksana S., Adamowicz, Ludwik
Noncovalent Interaction of Single-Walled Carbon Nanotubes with 1-Pyrenebutanoic Acid Succinimide Ester and Glucoseoxidase
JOURNAL OF PHYSICAL CHEMISTRY C, 115:21072-21082, NOV 3 2011 2011
abstract, full text

von Hansen, Yann, Sedlmeier, Felix, Hinczewski, Michael, Netz, Roland R.
Friction contribution to water-bond breakage kinetics
PHYSICAL REVIEW E, 84: Art. No. 051501, NOV 2 2011 2011
abstract, full text

Li, Huiyu, Luo, Yin, Derreumaux, Philippe, Wei, Guanghong
Carbon Nanotube Inhibits the Formation of beta-Sheet-Rich Oligomers of the Alzheimer's Amyloid-beta(16-22) Peptide
BIOPHYSICAL JOURNAL, 101:2267-2276, NOV 2 2011 2011
abstract, full text

Kublbeck, Jenni, Jyrkkarinne, Johanna, Molnar, Ferdinand, Kuningas, Tiina, Patel, Jayendra, Windshugel, Bjorn, Nevalainen, Tapio, Laitinen, Tuomo, Sippl, Wolfgang, Poso, Antti, Honkakoski, Paavo
New in Vitro Tools to Study Human Constitutive Androstane Receptor (CAR) Biology: Discovery and Comparison of Human CAR Inverse Agonists
MOLECULAR PHARMACEUTICS, 8:2424-2433, NOV-DEC 2011 2011
abstract, full text

Schaefer, Benjamin, Kisker, Caroline, Sotriffer, Christoph A.
Molecular dynamics of Mycobacterium tuberculosis KasA: implications for inhibitor and substrate binding and consequences for drug design
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:1053-1069, NOV 2011 2011
abstract, full text

Anisimov, Victor M., Ziemys, Arturas, Kizhake, Smitha, Yuan, Ziyan, Natarajan, Amarnath, Cavasotto, Claudio N.
Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:1071-1084, NOV 2011 2011
abstract, full text

Dutta, Suman, Bhaduri, Nipa, Upadhayaya, Ram Shankar, Rastogi, Neha, Chandel, Sunita G., Vandavasi, Jaya Kishore, Plashkevych, Oleksandr, Kardile, Ramakant A., Chattopadhyaya, Jyoti
The R-diastereomer of 6 '-O-toluoyl-carba-LNA modification in the core region of siRNA leads to 24-times improved RNA silencing potency against the HIV-1 compared to its S-counterpart
MEDCHEMCOMM, 2:1110-1119, NOV 2011 2011
abstract, full text

Kovalenko, Andriy, Blinov, Nikolay
Multiscale methods for nanochemistry and biophysics in solution
JOURNAL OF MOLECULAR LIQUIDS, 164:101-112, NOV 1 2011 2011
abstract, full text

Sindhikara, Daniel J., Yoshida, Norio, Kataoka, Mikio, Hirata, Fumio
Solvent penetration in photoactive yellow protein R52Q mutant: A theoretical study
JOURNAL OF MOLECULAR LIQUIDS, 164:120-122, NOV 1 2011 2011
abstract, full text

Narayanan, Arjun, LeClaire, Lawrence L., I.I.I., Barber, Diane L., Jacobson, Matthew P.
Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002226, NOV 2011 2011
abstract, full text

Caballero, Julio, Alzate-Morales, Jans H., Vergara-Jaque, Ariela
Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-Based De Novo Design: Study of Binding Mode of Diastereomer Compounds
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2920-2931, NOV 2011 2011
abstract, full text

Chavent, Matthieu, Levy, Bruno, Krone, Michael, Bidmon, Katrin, Nomine, Jean-Philippe, Ertl, Thomas, Baaden, Marc
GPU-powered tools boost molecular visualization
BRIEFINGS IN BIOINFORMATICS, 12:689-701, NOV 2011 2011
abstract, full text

Ghalib, Raza Murad, Hashim, Rokiah, Pereira Silva, P. S., Mehdi, Sayed Hasan, Sulaiman, Othman, Silva, Manuela Ramos
Synthesis, Crystal Structure, Ab Initio Studies and Fingerprint Plots of 2-Chloro-1,3-dioxo-2,3-dihydro-1H-inden-2-yl acetate
JOURNAL OF CHEMICAL CRYSTALLOGRAPHY, 41:1688-1693, NOV 2011 2011
abstract, full text

Elder, Robert M., Emrick, Todd, Jayaraman, Arthi
Understanding the Effect of Polylysine Architecture on DNA Binding Using Molecular Dynamics Simulations
BIOMACROMOLECULES, 12:3870-3879, NOV 2011 2011
abstract, full text

Morshed, A. K. M. M., Paul, Taitan C., Khan, Jamil A.
Effect of nanostructures on evaporation and explosive boiling of thin liquid films: a molecular dynamics study
APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING, 105:445-451, NOV 2011 2011
abstract, full text

Sathe, Chaitanya, Zou, Xueqing, Leburton, Jean-Pierre, Schulten, Klaus
Computational Investigation of DNA Detection Using Graphene Nanopores
ACS NANO, 5:8842-8851, NOV 2011 2011
abstract, full text

Dopieralski, Przemyslaw, Perrin, Charles L., Latajka, Zdzislaw
On the Intramolecular Hydrogen Bond in Solution: Car-Parrinello and Path Integral Molecular Dynamics Perspective
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3505-3513, NOV 2011 2011
abstract, full text

Huggins, David J., Marsh, May, Payne, Mike C.
Thermodynamic Properties of Water Molecules at a Protein Protein Interaction Surface
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3514-3522, NOV 2011 2011
abstract, full text

Kale, Seyit, Herzfeld, Judith
Pairwise Long-Range Compensation for Strongly Ionic Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3620-3624, NOV 2011 2011
abstract, full text

Tanner, David E., Chan, Kwok-Yan, Phillips, James C., Schulten, Klaus
Parallel Generalized Born Implicit Solvent Calculations with NAMD
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3635-3642, NOV 2011 2011
abstract, full text

Codorniu-Hernandez, Edelsys, Kusalik, Peter G.
Insights into the Solvation and Mobility of the Hydroxyl Radical in Aqueous Solution
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3725-3732, NOV 2011 2011
abstract, full text

Wu, Zhe, Cui, Qiang, Yethiraj, Arun
A New Coarse-Grained Force Field for Membrane-Peptide Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3793-3802, NOV 2011 2011
abstract, full text

Gilman-Politi, Regina, Harries, Daniel
Unraveling the Molecular Mechanism of Enthalpy Driven Peptide Folding by Polyol Osmolytes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3816-3828, NOV 2011 2011
abstract, full text

Durrant, Jacob D., McCammon, J. Andrew
HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 31:5-9, NOV 2011 2011
abstract, full text

Garstka, Malgorzata Anna, Fritzsche, Susanne, Lenart, Izabela, Hein, Zeynep, Jankevicius, Gytis, Boyle, Louise H., Elliott, Tim, Trowsdale, John, Antoniou, Antony N., Zacharias, Martin, Springer, Sebastian
Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibility
FASEB JOURNAL, 25:3989-3998, NOV 2011 2011
abstract, full text

Kuei, Chester, Yu, Jingxue, Zhu, Jessica, Wu, Jiejun, Zhang, Li, Shih, Amy, Mirzadegan, Taraneh, Lovenberg, Timothy, Liu, Changlu
Study of GPR81, the Lactate Receptor, from Distant Species Identifies Residues and Motifs Critical for GPR81 Functions
MOLECULAR PHARMACOLOGY, 80:848-858, NOV 2011 2011
abstract, full text

Weissgraeber, Stephanie, Hoffgaard, Franziska, Hamacher, Kay
Structure-based, biophysical annotation of molecular coevolution of acetylcholinesterase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:3144-3154, NOV 2011 2011
abstract, full text

Singh, Shailza, Joshi, Priyanka, Chopade, Balu A.
Pathway Analysis of Acinetobacter baylyi: A Combined Bioinformatic and Genomics Approach
CHEMICAL BIOLOGY & DRUG DESIGN, 78:893-905, NOV 2011 2011
abstract, full text

Kleczkowski, Leszek A., Geisler, Matt, Fitzek, Elisabeth, Wilczynska, Malgorzata
A common structural blueprint for plant UDP-sugar-producing pyrophosphorylases
BIOCHEMICAL JOURNAL, 439:375-379, NOV 1 2011 2011
abstract, full text

Mishra, Sabyashachi, Caflisch, Amedeo
Dynamics in the Active Site of beta-Secretase: A Network Analysis of Atomistic Simulations
BIOCHEMISTRY, 50:9328-9339, NOV 1 2011 2011
abstract, full text

Holloway, Daniel E., Singh, Umesh P., Shogen, Kuslima, Acharya, K. Ravi
Crystal structure of Onconase at 1.1 angstrom resolution - insights into substrate binding and collective motion
FEBS JOURNAL, 278:4136-4149, NOV 2011 2011
abstract, full text

Utesch, Tillmann, Daminelli, Grazia, Mroginski, Maria Andrea
Molecular Dynamics Simulations of the Adsorption of Bone Morphogenetic Protein-2 on Surfaces with Medical Relevance
LANGMUIR, 27:13144-13153, NOV 1 2011 2011
abstract, full text

Schwardt, Oliver, Rabbani, Said, Hartmann, Margrit, Abgottspon, Daniela, Wittwer, Matthias, Kleeb, Simon, Zalewski, Adam, Smiesko, Martin, Cutting, Brian, Ernst, Beat
Design, synthesis and biological evaluation of mannosyl triazoles as FimH antagonists
BIOORGANIC & MEDICINAL CHEMISTRY, 19:6454-6473, NOV 1 2011 2011
abstract, full text

Wu, Qing-Yun, Jin, Kai-Zhou, Li, Feng, Hu, Zhi-Qian, Wang, Xiao-Yun
Impact of intra-subunit interactions on the dimeric arginine kinase activity and structural stability
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, 49:822-831, NOV 1 2011 2011
abstract, full text

Severin, Philip M. D., Zou, Xueqing, Gaub, Hermann E., Schulten, Klaus
Cytosine methylation alters DNA mechanical properties
NUCLEIC ACIDS RESEARCH, 39:8740-8751, NOV 2011 2011
abstract, full text

Barata, Teresa S., Brocchini, Steve, Teo, Ian, Shaunak, Sunil, Zloh, Mire
From sequence to 3D structure of hyperbranched molecules: application to surface modified PAMAM dendrimers
JOURNAL OF MOLECULAR MODELING, 17:2741-2749, NOV 2011 2011
abstract, full text

Koonammackal, Mathew Varghese, Nellipparambil, Unnikrishnan Viswambharan Nair, Sudarsanakumar, Chellappanpillai
Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin
JOURNAL OF MOLECULAR MODELING, 17:2805-2816, NOV 2011 2011
abstract, full text

Sorkin, Viacheslav, Zhang, Yong Wei
Graphene-based pressure nano-sensors
JOURNAL OF MOLECULAR MODELING, 17:2825-2830, NOV 2011 2011
abstract, full text

Guimaraes, Ana P., Oliveira, Aline A., da Cunha, Elaine F. F., Ramalho, Teodorico C., Franco, Tanos C. C.
Analysis of Bacillus anthracis nucleoside hydrolase via in silico docking with inhibitors and molecular dynamics simulation
JOURNAL OF MOLECULAR MODELING, 17:2939-2951, NOV 2011 2011
abstract, full text

Sadasivan, Vatsala D., Narpala, Sandeep R., Budil, David E., Sacco, Albert, Jr., Carrier, Rebecca L.
Modeling the human intestinal Mucin (MUC2) C-terminal cystine knot dimer
JOURNAL OF MOLECULAR MODELING, 17:2953-2963, NOV 2011 2011
abstract, full text

Peng, Lili X., Das, Sanjib K., Yu, Lei, Howell, Stephen B., Gough, David A.
Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(gamma-glutamyl-glutamate) paclitaxel conjugates
JOURNAL OF MOLECULAR MODELING, 17:2973-2987, NOV 2011 2011
abstract, full text

Durlak, Piotr, Berski, Sawomir, Latajka, Zdzisaw
Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the acetic acid dimer in the gas phase
JOURNAL OF MOLECULAR MODELING, 17:2995-3004, NOV 2011 2011
abstract, full text

Contreras-Torres, Flavio F., Martinez-Loran, Erick
DNA insertion in and wrapping around carbon nanotubes
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 1:902-919, NOV-DEC 2011 2011
abstract, full text

Habenstein, Birgit, Wasmer, Christian, Bousset, Luc, Sourigues, Yannick, Schuetz, Anne, Loquet, Antoine, Meier, Beat H., Melki, Ronald, Boeckmann, Anja
Extensive de novo solid-state NMR assignments of the 33 kDa C-terminal domain of the Ure2 prion
JOURNAL OF BIOMOLECULAR NMR, 51:235-243, NOV 2011 2011
abstract, full text

Mukherjee, Dibyendu, Vaughn, Michael, Khomami, Bamin, Bruce, Barry D.
Modulation of cyanobacterial photosystem I deposition properties on alkanethiolate Au substrate by various experimental conditions
COLLOIDS AND SURFACES B-BIOINTERFACES, 88:181-190, NOV 1 2011 2011
abstract, full text

Caulfield, Thomas, Medina-Franco, Jose L.
Molecular dynamics simulations of human DNA methyltransferase 3B with selective inhibitor nanaomycin A
JOURNAL OF STRUCTURAL BIOLOGY, 176:185-191, NOV 2011 2011
abstract, full text

Schlodder, Eberhard, Hussels, Martin, Cetin, Marianne, Karapetyan, Navassard V., Brecht, Marc
Fluorescence of the various red antenna states in photosystem I complexes from cyanobacteria is affected differently by the redox state of P700
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:1423-1431, NOV 2011 2011
abstract, full text

Gorham, Ronald D., Jr., Kieslich, Chris A., Nichols, Aaron, Sausman, Noriko U., Foronda, Marisse, Morikis, Dimitrios
An Evaluation of Poisson-Boltzmann Electrostatic Free Energy Calculations through Comparison with Experimental Mutagenesis Data
BIOPOLYMERS, 95:746-754, NOV 2011 2011
abstract, full text

Patel, Mayank M., Tzul, Franco, Makhatadze, George I.
Equilibrium and kinetic studies of protein cooperativity using urea-induced folding/unfolding of a Ubq-UIM fusion protein
BIOPHYSICAL CHEMISTRY, 159:58-65, NOV 2011 2011
abstract, full text

Cranford, Steven W., Buehler, Markus J.
Mechanical properties of graphyne
CARBON, 49:4111-4121, NOV 2011 2011
abstract, full text

Trung Dac Nguyen, Phillips, Carolyn L., Anderson, Joshua A., Glotzer, Sharon C.
Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units
COMPUTER PHYSICS COMMUNICATIONS, 182:2307-2313, NOV 2011 2011
abstract, full text

Lu Tian, Chen Feiwu
Calculation of Molecular Orbital Composition
ACTA CHIMICA SINICA, 69:2393-2406, OCT 28 2011 2011
abstract, full text

Ghosh, Amit, Sakaguchi, Reiko, Liu, Cuiping, Vishveshwara, Saraswathi, Hou, Ya-Ming
Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:37721-37731, OCT 28 2011 2011
abstract, full text

Hezaveh, Samira, Samanta, Susruta, Milano, Giuseppe, Roccatano, Danilo
Structure and dynamics of 1,2-dimethoxyethane and 1,2-dimethoxypropane in aqueous and non-aqueous solutions: A molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 164501, OCT 28 2011 2011
abstract, full text

Flores, Samuel C., Gerstein, Mark B.
Predicting protein ligand binding motions with the conformation explorer
BMC BIOINFORMATICS, 12: Art. No. 417, OCT 27 2011 2011
abstract, full text

Espinoza-Fonseca, L. Michel, Thomas, David D.
Atomic-Level Characterization of the Activation Mechanism of SERCA by Calcium
PLOS ONE, 6: Art. No. e26936, OCT 27 2011 2011
abstract, full text

Kulkarni, Chidambar, Reddy, Sandeep Kumar, George, Subi J., Balasubramanian, Sundaram
Cooperativity in the stacking of benzene-1,3,5-tricarboxamide: The role of dispersion
CHEMICAL PHYSICS LETTERS, 515:226-230, OCT 27 2011 2011
abstract, full text

Zhao, Li Na, Chiu, See-Wing, Benoit, Jerome, Chew, Lock Yue, Mu, Yuguang
Amyloid beta Peptides Aggregation in a Mixed Membrane Bilayer: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 115:12247-12256, OCT 27 2011 2011
abstract, full text

Zhang, Zhiyong, Sanbonmatsu, Karissa Y., Voth, Gregory A.
Key Intermolecular Interactions in the E. coli 70S Ribosome Revealed by Coarse-Grained Analysis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:16828-16838, OCT 26 2011 2011
abstract, full text

Lee, Hyun Ju, Gennis, Robert B., Adelroth, Pia
Entrance of the proton pathway in cbb(3)-type heme-copper oxidases
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:17661-17666, OCT 25 2011 2011
abstract, full text

Atilgan, Ali Rana, Aykut, Ayse Ozlem, Atilgan, Canan
Subtle pH differences trigger single residue motions for moderating conformations of calmodulin
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 155102, OCT 21 2011 2011
abstract, full text

Kapoor, Abhijeet, Shandilya, Manish, Kundu, Suman
Structural Insight of Dopamine beta-Hydroxylase, a Drug Target for Complex Traits, and Functional Significance of Exonic Single Nucleotide Polymorphisms
PLOS ONE, 6: Art. No. e26509, OCT 20 2011 2011
abstract, full text

Liu, Yuemin, Gallo, August A., Xu, Wu, Bajpai, Rakesh, Florian, Jan
CH center dot center dot center dot pi Interactions Do Not Contribute to Hydrogen Transfer Catalysis by Glycerol Dehydratase
JOURNAL OF PHYSICAL CHEMISTRY A, 115:11162-11166, OCT 20 2011 2011
abstract, full text

Garzon, Beatriz, Oeste, Clara L., Diez-Dacal, Beatriz, Perez-Sala, Dolores
Proteomic studies on protein modification by cyclopentenone prostaglandins: Expanding our view on electrophile actions
JOURNAL OF PROTEOMICS, 74:2243-2263, OCT 19 2011 2011
abstract, full text

Bharatham, Nagakumar, Chi, Seung-Wook, Yoon, Ho Sup
Molecular Basis of Bcl-X(L)-p53 Interaction: Insights from Molecular Dynamics Simulations
PLOS ONE, 6: Art. No. e26014, OCT 19 2011 2011
abstract, full text

Hargreaves, Rowan, Bowron, Daniel T., Edler, Karen
Atomistic Structure of a Micelle in Solution Determined by Wide Q-Range Neutron Diffraction
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:16524-16536, OCT 19 2011 2011
abstract, full text

Lin, Yuchun, Silvestre-Ryan, Jordi, Himmel, Michael E., Crowley, Michael F., Beckham, Gregg T., Chu, Jhih-Wei
Protein Allostery at the Solid-Liquid Interface: Endoglucanase Attachment to Cellulose Affects Glucan Clenching in the Binding Cleft
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:16617-16624, OCT 19 2011 2011
abstract, full text

Willenbring, Dan, Liu, Lu Tian, Mowrey, David, Xu, Yan, Tang, Pei
Isoflurane Alters the Structure and Dynamics of GLIC
BIOPHYSICAL JOURNAL, 101:1905-1912, OCT 19 2011 2011
abstract, full text

Prakash, Anupam, Janosi, Lorant, Doxastakis, Manolis
GxxxG Motifs, Phenylalanine, and Cholesterol Guide the Self-Association of Transmembrane Domains of ErbB2 Receptors
BIOPHYSICAL JOURNAL, 101:1949-1958, OCT 19 2011 2011
abstract, full text

Ma, Cheng-Wei, Xiu, Zhi-Long, Zeng, An-Ping
A New Concept to Reveal Protein Dynamics Based on Energy Dissipation
PLOS ONE, 6: Art. No. e26453, OCT 17 2011 2011
abstract, full text

Wu, Xiaomin, Yang, Gang, Zu, Yuangang, Fu, Yujie, Zhou, Lijun, Yuan, Xiaohui
The Trp-cage miniprotein with single-site mutations: Studies of stability and dynamics using molecular dynamics
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 973:1-8, OCT 15 2011 2011
abstract, full text

Saunders, Marissa G., Voth, Gregory A.
Water Molecules in the Nucleotide Binding Cleft of Actin: Effects on Subunit Conformation and Implications for ATP Hydrolysis
JOURNAL OF MOLECULAR BIOLOGY, 413:279-291, OCT 14 2011 2011
abstract, full text

Wong, Diana Y., Sept, David
The Interaction of Cofilin with the Actin Filament
JOURNAL OF MOLECULAR BIOLOGY, 413:97-105, OCT 14 2011 2011
abstract, full text

Chen, Xuehui, Sun, Yunxiang, An, Xiongbo, Ming, Dengming
Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 144108, OCT 14 2011 2011
abstract, full text

Du, Wei-Na, Marino, Kristen A., Bolhuis, Peter G.
Multiple state transition interface sampling of alanine dipeptide in explicit solvent
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 145102, OCT 14 2011 2011
abstract, full text

Eken, A. E., Tozzi, E. J., Klingenberg, D. J., Bauhofer, W.
A simulation study on the effects of shear flow on the microstructure and electrical properties of carbon nanotube/polymer composites
POLYMER, 52:5178-5185, OCT 13 2011 2011
abstract, full text

Gomaa, Mohamed S., Bridgens, Caroline E., Veal, Gareth J., Redfern, Christopher P. F., Brancale, Andrea, Armstrong, Jane L., Simons, Claire
Synthesis and Biological Evaluation of 3-(1H-Imidazol- and Triazol-1-yl)-2,2-dimethyl-3-[4-(naphthalen-2-ylamino)phenyl]propyl Derivatives as Small Molecule Inhibitors of Retinoic Acid 4-Hydroxylase (CYP26)
JOURNAL OF MEDICINAL CHEMISTRY, 54:6803-6811, OCT 13 2011 2011
abstract, full text

Benitez, J. J., San-Miguel, M. A., Dominguez-Meister, S., Heredia-Guerrero, J. A., Salmeron, M.
Structure and Chemical State of Octadecylamine Self-Assembled Monolayers on Mica
JOURNAL OF PHYSICAL CHEMISTRY C, 115:19716-19723, OCT 13 2011 2011
abstract, full text

Webb, Melanie B., Garofalini, Stephen H., Scherer, George W.
Molecular Dynamics Investigation of Solution Structure between NaCl and Quartz Crystals
JOURNAL OF PHYSICAL CHEMISTRY C, 115:19724-19732, OCT 13 2011 2011
abstract, full text

Alberti, M., Lago, N. Faginas, Pirani, F.
Ar Solvation Shells in K(+)-HFBz: From Cluster Rearrangement to Solvation Dynamics
JOURNAL OF PHYSICAL CHEMISTRY A, 115:10871-10879, OCT 13 2011 2011
abstract, full text

Alhadeff, Raphael, Ganoth, Assaf, Krugliak, Miriam, Arkin, Isaiah T.
Promiscuous Binding in a Selective Protein: The Bacterial Na(+)/H(+) Antiporter
PLOS ONE, 6: Art. No. e25182, OCT 12 2011 2011
abstract, full text

Sheena, Aswathy, Mohan, Suma S., Haridas, Nidhina Pachakkil A., Anilkumar, Gopalakrishnapillai
Elucidation of the Glucose Transport Pathway in Glucose Transporter 4 via Steered Molecular Dynamics Simulations
PLOS ONE, 6: Art. No. e25747, OCT 12 2011 2011
abstract, full text

Kalli, Antreas C., Hall, Benjamin A., Campbell, Iain D., Sansom, Mark S. P.
A Helix Heterodimer in a Lipid Bilayer: Prediction of the Structure of an Integrin Transmembrane Domain via Multiscale Simulations
STRUCTURE, 19:1477-1484, OCT 12 2011 2011
abstract, full text

Wang, Kairong, Yan, Jiexi, Liu, Xin, Zhang, Jindao, Chen, Ru, Zhang, Bangzhi, Dang, Wen, Zhang, Wei, Kai, Ming, Song, Jingjing, Wang, Rui
Novel cytotoxity exhibition mode of polybia-CP, a novel antimicrobial peptide from the venom of the social wasp Polybia paulista
TOXICOLOGY, 288:27-33, OCT 9 2011 2011
abstract, full text

Souza, Paulo C. T., Barra, Gustavo B., Velasco, Lara F. R., Ribeiro, Isabel C. J., Simeoni, Luiz A., Togashi, Marie, Webb, Paul, Neves, Francisco A. R., Skaf, Munir S., Martinez, Leandro, Polikarpov, Igor
Helix 12 Dynamics and Thyroid Hormone Receptor Activity: Experimental and Molecular Dynamics Studies of Ile280 Mutants
JOURNAL OF MOLECULAR BIOLOGY, 412:882-893, OCT 7 2011 2011
abstract, full text

Marchenko, Anatolyi, Koidan, Heorgii, Hurieva, Anastasiya, Merkulov, Anatolyi, Pinchuk, Aleksandr, Yurchenko, Aleksandr, Rozhenko, Alexander B., Jones, Peter G., Thoennessen, Holger, Kostyuk, Aleksandr
Cyclization of C-phosphorylated (P(III)) arylformamidines to 3H-1,3-benzazaphospholes
TETRAHEDRON, 67:7748-7758, OCT 7 2011 2011
abstract, full text

Frederix, Pim W. J. M., Ulijn, Rein V., Hunt, Neil T., Tuttle, Tell
Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2380-2384, OCT 6 2011 2011
abstract, full text

Sorensen, Jesper, Periole, Xavier, Skeby, Katrine K., Marrink, S.i.e.w.e.r.t.-.J., Schiott, Birgit
Protofibrillar Assembly Toward the Formation of Amyloid Fibrils
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2385-2390, OCT 6 2011 2011
abstract, full text

Dixit, Anshuman, Verkhivker, Gennady M.
The Energy Landscape Analysis of Cancer Mutations in Protein Kinases
PLOS ONE, 6: Art. No. e26071, OCT 6 2011 2011
abstract, full text

England, Alice H., Duffin, Andrew M., Schwartz, Craig P., Uejio, Janel S., Prendergast, David, Saykally, Richard J.
On the hydration and hydrolysis of carbon dioxide
CHEMICAL PHYSICS LETTERS, 514:187-195, OCT 6 2011 2011
abstract, full text

Lv, Wenping
The adsorption of DNA bases on neutral and charged (8,8) carbon-nanotubes
CHEMICAL PHYSICS LETTERS, 514:311-316, OCT 6 2011 2011
abstract, full text

Oakley, Mark T., Wales, David J., Johnston, Roy L.
Energy Landscape and Global Optimization for a Frustrated Model Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11525-11529, OCT 6 2011 2011
abstract, full text

Goldsmith, Jacob, Hinds, Bruce J.
Simulation of Steady-State Methanol Flux through a Model Carbon Nanotube Catalyst Support
JOURNAL OF PHYSICAL CHEMISTRY C, 115:19158-19164, OCT 6 2011 2011
abstract, full text

Sarkar, Anindya, Zhou, Crystal, Meklemburg, Robert, Wintrode, Patrick L.
Local Conformational Flexibility Provides a Basis for Facile Polymer Formation in Human Neuroserpin
BIOPHYSICAL JOURNAL, 101:1758-1765, OCT 5 2011 2011
abstract, full text

Patapati, Kalliopi K., Glykos, Nicholas M.
Three Force Fields' Views of the 3(10) Helix
BIOPHYSICAL JOURNAL, 101:1766-1771, OCT 5 2011 2011
abstract, full text

Kunisada, Y., Escano, M. C., Kasai, H.
Surface magnetism in O(2) dissociation-from basics to application
JOURNAL OF PHYSICS-CONDENSED MATTER, 23: Art. No. 394207, OCT 5 2011 2011
abstract, full text

Zhang, Xu, Ramirez, Benjamin E., Liao, Xiubei, Diekwisch, Thomas G. H.
Amelogenin Supramolecular Assembly in Nanospheres Defined by a Complex Helix-Coil-PPII Helix 3D-Structure
PLOS ONE, 6: Art. No. e24952, OCT 3 2011 2011
abstract, full text

Angyan, Janos G.
Linear Response and Measures of Electron Delocalization in Molecules
CURRENT ORGANIC CHEMISTRY, 15:3609-3618, OCT 2011 2011
abstract, full text

DeMarco, Mari L., Woods, Robert J.
From agonist to antagonist: Structure and dynamics of innate immune glycoprotein MD-2 upon recognition of variably acylated bacterial endotoxins
MOLECULAR IMMUNOLOGY, 49:124-133, OCT-NOV 2011 2011
abstract, full text

Soriano-Ursua, M. A., Mancilla-Percino, T., Correa-Basurto, J., Querejeta, E., Trujillo-Ferrara, J. G.
Give Boron a Chance: Boron Containing Compounds Reach Ionotropic and Metabotropic Transmembrane Receptors
MINI-REVIEWS IN MEDICINAL CHEMISTRY, 11:1031-1038, OCT 2011 2011
abstract, full text

Koldso, Heidi, Noer, Pernille, Grouleff, Julie, Autzen, Henriette Elisabeth, Sinning, Steffen, Schiott, Birgit
Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na(+) Ion Release
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002246, OCT 2011 2011
abstract, full text

Skillman, Kristen M., Diraviyam, Karthikeyan, Khan, Asis, Tang, Keliang, Sept, David, Sibley, L. David
Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites
PLOS PATHOGENS, 7: Art. No. e1002280, OCT 2011 2011
abstract, full text

Friedrichs, Wenke, Ohler, Bastian, Langel, Walter, Monti, Susanna, Koeppen, Susan
Adsorption of Collagen Nanofibrils on Rough TiO(2): A Molecular Dynamics Study
ADVANCED ENGINEERING MATERIALS, 13:B334-B342, OCT 2011 2011
abstract, full text

Li, X., Cao, X.
Nature of M-Ng interaction in the MNg (4) (2+) (M = Cu, Ag and Au; Ng = He and Ne) molecules: ab initio calculations
EUROPEAN PHYSICAL JOURNAL D, 64:221-225, OCT 2011 2011
abstract, full text

Wymore, Troy, Chen, Brian Y., Nicholas, Hugh B., Jr., Ropelewski, Alexander J., Brooks, Charles L., I.I.I.
A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function
MOLECULAR INFORMATICS, 30:896-906, OCT 2011 2011
abstract, full text

Tisler, Julia, Reuter, Rolf, Laemmle, Anke, Jelezko, Fedor, Balasubramanian, Gopalakrishnan, Hemmer, Philip R., Reinhard, Friedemann, Wrachtrup, Joerg
Highly Efficient FRET from a Single Nitrogen-Vacancy Center in Nanodiamonds to a Single Organic Molecule
ACS NANO, 5:7893-7898, OCT 2011 2011
abstract, full text

Kannan, Srinivasaraghavan, Zacharias, Martin
Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations
NUCLEIC ACIDS RESEARCH, 39:8271-8280, OCT 2011 2011
abstract, full text

Szott, Luisa Mayorga, Horbett, Thomas A.
Protein interactions with surfaces: Computational approaches and repellency
CURRENT OPINION IN CHEMICAL BIOLOGY, 15:683-689, OCT 2011 2011
abstract, full text

Vassiliev, Serguei, Mahboob, Abdullah, Bruce, Doug
Calculation of chromophore excited state energy shifts in response to molecular dynamics of pigment-protein complexes
PHOTOSYNTHESIS RESEARCH, 110:25-38, OCT 2011 2011
abstract, full text

Wang, Yi, Markwick, Phineus R. L., de Oliveira, Cesar Augusto F., McCammon, J. Andrew
Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3199-3207, OCT 2011 2011
abstract, full text

Nayar, Divya, Agarwal, Manish, Chakravarty, Charusita
Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3354-3367, OCT 2011 2011
abstract, full text

Patel, Jagdish Suresh, Branduardi, Davide, Masetti, Matteo, Rocchia, Walter, Cavalli, Andrea
Insights into Ligand-Protein Binding from Local Mechanical Response
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:3368-3378, OCT 2011 2011
abstract, full text

Borosky, Gabriela L., Lin, Susana
Computational Modeling of the Catalytic Mechanism of Human Placental Alkaline Phosphatase (PLAP)
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2538-2548, OCT 2011 2011
abstract, full text

Cappel, Daniel, Wahlstroem, Rickard, Brenk, Ruth, Sotriffer, Christoph A.
Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2581-2594, OCT 2011 2011
abstract, full text

Wright, David W., Coveney, Peter V.
Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2636-2649, OCT 2011 2011
abstract, full text

Shahlaei, Mohsen, Madadkar-Sobhani, Armin, Fassihi, Afshin, Saghaie, Lotfollah
Exploring a Model of a Chemokine Receptor/Ligand Complex in an Explicit Membrane Environment by Molecular Dynamics Simulation: The Human CCR1 Receptor
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2717-2730, OCT 2011 2011
abstract, full text

Wang, Ningyu, Rokhlin, S. I., Farson, D. F.
Ultrafast laser melting of Au nanoparticles: atomistic simulations
JOURNAL OF NANOPARTICLE RESEARCH, 13:4491-4509, OCT 2011 2011
abstract, full text

Freedman, Holly, Luchko, Tyler, Luduena, Richard F., Tuszynski, Jack A.
Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2968-2982, OCT 2011 2011
abstract, full text

Yuan, Peng, Meng, Kun, Luo, Huiying, Shi, Pengjun, Huang, Huoqing, Bai, Yingguo, Yang, Peilong, Yao, Bin
A novel low-temperature active alkaline pectate lyase from Klebsiella sp Y1 with potential in textile industry
PROCESS BIOCHEMISTRY, 46:1921-1926, OCT 2011 2011
abstract, full text

Berhanu, Workalemahu Mikre, Masunov, Artem E.
Can molecular dynamics simulations assist in design of specific inhibitors and imaging agents of amyloid aggregation? Structure, stability and free energy predictions for amyloid oligomers of VQIVYK, MVGGVV and LYQLEN
JOURNAL OF MOLECULAR MODELING, 17:2423-2442, OCT 2011 2011
abstract, full text

Soriano-Ursua, Marvin A., Correa-Basurto, Jose, Trujillo-Ferrara, Jose G., Kaumann, Alberto J.
Homology model and docking studies on porcine beta(2) adrenoceptor: description of two binding sites
JOURNAL OF MOLECULAR MODELING, 17:2525-2538, OCT 2011 2011
abstract, full text

Jojart, Balazs, Szori, Milan, Izsak, Robert, Marsi, Istvan, Aranka Laszlo, Csizmadia, Imre G., Viskolcz, Bela
The effect of a Pro(28)Thr point mutation on the local structure and stability of human galactokinase enzyme-a theoretical study
JOURNAL OF MOLECULAR MODELING, 17:2639-2649, OCT 2011 2011
abstract, full text

Sun, Chongbo, T'ang, Tian, Uludag, Hasan
Molecular Dynamics Simulations of PEI Mediated DNA Aggregation
BIOMACROMOLECULES, 12:3698-3707, OCT 2011 2011
abstract, full text

Zhou, Junpei, Zhang, Rui, Shi, Pengjun, Huang, Huoqing, Meng, Kun, Yuan, Tiezheng, Yang, Peilong, Yao, Bin
A novel low-temperature-active beta-glucosidase from symbiotic Serratia sp TN49 reveals four essential positions for substrate accommodation
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 92:305-315, OCT 2011 2011
abstract, full text

Abe, Tetsuya, Oka, Toshihiko, Nakagome, Atsushi, Tsukada, Yoshihiro, Yasunaga, Takuo, Yohda, Masafumi
StHsp14.0, a small heat shock protein of Sulfolobus tokodaii strain 7, protects denatured proteins from aggregation in the partially dissociated conformation
JOURNAL OF BIOCHEMISTRY, 150:403-409, OCT 2011 2011
abstract, full text

Khao, Jonathan, Arce-Lopera, Jaime, Sturgis, James N., Duneau, Jean-Pierre
Structure of a protein-detergent complex: the balance between detergent cohesion and binding
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:1143-1155, OCT 2011 2011
abstract, full text

Spolnik, Pawel, Krol, Marcin, Stopa, Barbara, Konieczny, Leszek, Piekarska, Barbara, Rybarska, Janina, Zemanek, Grzegorz, Jagusiak, Anna, Piwowar, Piotr, Szoniec, Grzegorz, Roterman, Irena
Influence of the electric field on supramolecular structure and properties of amyloid-specific reagent Congo red
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:1187-1196, OCT 2011 2011
abstract, full text

Blasco, Benjamin, Stenta, Marco, Alonso-Sarduy, Livan, Dietler, Giovanni, Dal Peraro, Matteo, Cole, Stewart T., Pojer, Florence
Atypical DNA recognition mechanism used by the EspR virulence regulator of Mycobacterium tuberculosis
MOLECULAR MICROBIOLOGY, 82:251-264, OCT 2011 2011
abstract, full text

McArthur, J. R., Singh, G., McMaster, D., Winkfein, R., Tieleman, D. P., French, R. J.
Interactions of Key Charged Residues Contributing to Selective Block of Neuronal Sodium Channels by mu-Conotoxin KIIIA
MOLECULAR PHARMACOLOGY, 80:573-584, OCT 2011 2011
abstract, full text

Hawver, Lisa A., Gillooly, Caitlin A., Beuning, Penny J.
Characterization of Escherichia coli UmuC Active-Site Loops Identifies Variants That Confer UV Hypersensitivity
JOURNAL OF BACTERIOLOGY, 193:5400-5411, OCT 2011 2011
abstract, full text

Warshaviak, Dora Toledo, Muellner, Michael J., Chachisvilis, Mirianas
Effect of membrane tension on the electric field and dipole potential of lipid bilayer membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2608-2617, OCT 2011 2011
abstract, full text

Li, Ping, Liu, Ming, Tan, Jian Jun, Zhang, Xiao Yi, Chen, Wei Zu, Wang, Cun Xin
Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:311-323, OCT 2011 2011
abstract, full text

Oliveira, Aline A., Renno, Magdalena N., de Matos, Cesar A. S., Bertuzzi, Morena D., Ramalho, Teodorico C., Fraga, Carlos A. M., Franca, Tanos C. C.
Molecular Modeling Studies of Yersinia pestis Dihydrofolate Reductase
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:351-367, OCT 2011 2011
abstract, full text

Gong, Zhou, Zhao, Yunjie, Chen, Changjun, Xiao, Yi
Role of Ligand Binding in Structural Organization of Add A-riboswitch Aptamer: A Molecular Dynamics Simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:403-416, OCT 2011 2011
abstract, full text

Uenal, Can, Schwedhelm, Kai F., Thiele, Alexandra, Weiwad, Matthias, Schweimer, Kristian, Frese, Frederike, Fischer, Gunter, Hacker, Joerg, Faber, Cornelius, Steinert, Michael
Collagen IV-derived peptide binds hydrophobic cavity of Legionella pneumophila Mip and interferes with bacterial epithelial transmigration
CELLULAR MICROBIOLOGY, 13:1558-1572, OCT 2011 2011
abstract, full text

Liu, Yingzhe, Chipot, Christophe, Shao, Xueguang, Cai, Wensheng
The effects of 7-dehydrocholesterol on the structural properties of membranes
PHYSICAL BIOLOGY, 8: Art. No. 056005, OCT 2011 2011
abstract, full text

Szarecka, Agnieszka, Lesnock, Kimberly R., Ramirez-Mondragon, Carlos A., Nicholas, Hugh B., Jr., Wymore, Troy
The Class D beta-lactamase family: residues governing the maintenance and diversity of function
PROTEIN ENGINEERING DESIGN & SELECTION, 24:801-809, OCT 2011 2011
abstract, full text

Lepeshkevich, Sergei V., Biziuk, Sergey A., Lemeza, Alexander M., Dzhagarov, Boris M.
The kinetics of molecular oxygen migration in the isolated a chains of human hemoglobin as revealed by molecular dynamics simulations and laser kinetic spectroscopy
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:1279-1288, OCT 2011 2011
abstract, full text

Wikstrom, Marten, Verkhovsky, Michael I.
The D-channel of cytochrome oxidase: An alternative view
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:1273-1278, OCT 2011 2011
abstract, full text

Wan, Shunzhou, Coveney, Peter V.
Molecular Dynamics Simulation Reveals Structural and Thermodynamic Features of Kinase Activation by Cancer Mutations Within the Epidermal Growth Factor Receptor
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2843-2852, OCT 2011 2011
abstract, full text

Artemova, Svetlana, Grudinin, Sergei, Redon, Stephane
A Comparison of Neighbor Search Algorithms for Large Rigid Molecules
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2865-2877, OCT 2011 2011
abstract, full text

Chavent, Matthieu, Vanel, Antoine, Tek, Alex, Levy, Bruno, Robert, Sophie, Raffin, Bruno, Baaden, Marc
GPU-Accelerated Atom and Dynamic Bond Visualization Using Hyperballs: A Unified Algorithm for Balls, Sticks, and Hyperboloids
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2924-2935, OCT 2011 2011
abstract, full text

Jacob, Reed B., Bullock, Casey W., Andersen, Tim, McDougal, Owen M.
DockoMatic: Automated Peptide Analog Creation for High Throughput Virtual Screening
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2936-2941, OCT 2011 2011
abstract, full text

Cosden, Ian A., Lukes, Jennifer R.
Effect of Cutoff Radius on the Surface Tension of Nanoscale Bubbles
JOURNAL OF HEAT TRANSFER-TRANSACTIONS OF THE ASME, 133: Art. No. 101501, OCT 2011 2011
abstract, full text

Wang, Bin, Puzyrev, Yevgeniy, Pantelides, Sokrates T.
Strain enhanced defect reactivity at grain boundaries in polycrystalline graphene
CARBON, 49:3983-3988, OCT 2011 2011
abstract, full text

Ji, Xiang-Ying, Feng, Xi-Qiao
Coarse-grained mechanochemical model for simulating the dynamic behavior of microtubules
PHYSICAL REVIEW E, 84: Art. No. 031933, SEP 30 2011 2011
abstract, full text

Lee, Kuo Hao, Miller, Craig R., Nagel, Anna C., Wichman, Holly A., Joyce, Paul, Ytreberg, F. Marty
First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus
PLOS ONE, 6: Art. No. e25640, SEP 29 2011 2011
abstract, full text

Yang, Zaixing, Shi, Biyun, Lu, Hangjun, Xiu, Peng, Zhou, Ruhong
Dewetting Transitions in the Self-Assembly of Two Amyloidogenic beta-Sheets and the Importance of Matching Surfaces
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11137-11144, SEP 29 2011 2011
abstract, full text

Rieff, Benjamin, Bauer, Sebastian, Mathias, Gerald, Tavan, Paul
DFT/MM Description of Flavin IR Spectra in BLUF Domains
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11239-11253, SEP 29 2011 2011
abstract, full text

Hirao, Hajime
The Effects of Protein Environment and Dispersion on the Formation of Ferric-Superoxide Species in myo-Inositol Oxygenase (MIOX): A Combined ONIOM(DFT:MM) and Energy Decomposition Analysis
JOURNAL OF PHYSICAL CHEMISTRY B, 115:11278-11285, SEP 29 2011 2011
abstract, full text

Vehvilainen, T. T., Ganchenkova, M. G., Nieminen, R. M.
Nanoporous carbon structures based on C(20)
PHYSICAL REVIEW B, 84: Art. No. 125444, SEP 28 2011 2011
abstract, full text

Solovyeva, Vita, Cmyrev, Anastasia, Sachser, Roland, Reith, Heiko, Huth, Michael
Influence of irradiation-induced disorder on the Peierls transition in TTF-TCNQ microdomains
JOURNAL OF PHYSICS D-APPLIED PHYSICS, 44: Art. No. 385301, SEP 28 2011 2011
abstract, full text

Torres, Rodrigo, Swift, Robert V., Chim, Nicholas, Wheatley, Nicole, Lan, Benson, Atwood, Brian R., Pujol, Celine, Sankaran, Banu, Bliska, James B., Amaro, Rommie E., Goulding, Celia W.
Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis
PLOS ONE, 6: Art. No. e25084, SEP 26 2011 2011
abstract, full text

Wang, Mingcong, Kapralov, Maxim V., Anisimova, Maria
Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco
BMC EVOLUTIONARY BIOLOGY, 11: Art. No. 266, SEP 23 2011 2011
abstract, full text

Favia, Angelo D., Masetti, Matteo, Recanatini, Maurizio, Cavalli, Andrea
Substrate Binding Process and Mechanistic Functioning of Type 1 11 beta-Hydroxysteroid Dehydrogenase from Enhanced Sampling Methods
PLOS ONE, 6: Art. No. e25375, SEP 23 2011 2011
abstract, full text

Mann, Bernward A. F., Kremer, Kurt, Lenz, Olaf, Holm, Christian
Hydrogels in Poor Solvents: A Molecular Dynamics Study
MACROMOLECULAR THEORY AND SIMULATIONS, 20:721-734, SEP 23 2011 2011
abstract, full text

Shim, Joong-Youn, Bertalovitz, Alexander C., Kendall, Debra A.
Identification of Essential Cannabinoid-binding Domains STRUCTURAL INSIGHTS INTO EARLY DYNAMIC EVENTS IN RECEPTOR ACTIVATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:33422-33435, SEP 23 2011 2011
abstract, full text

Tavagnacco, Letizia, Schnupf, Udo, Mason, Philip E., Saboungi, Marie-Louise, Cesaro, Attilio, Brady, John W.
Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10957-10966, SEP 22 2011 2011
abstract, full text

Rahane, Amol B., Deshpande, Mrinalini D., Kumar, Vijay
Structural and Electronic Properties of (Al(2)O(3))(n) Clusters with n=1-10 from First Principles Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 115:18111-18121, SEP 22 2011 2011
abstract, full text

Jaervi, Tommi T., van Duin, Adri C. T., Nordlund, Kai, Goddard, William A., I.I.I.
Development of Interatomic ReaxFF Potentials for Au-S-C-H Systems
JOURNAL OF PHYSICAL CHEMISTRY A, 115:10315-10322, SEP 22 2011 2011
abstract, full text

Miao, Yinglong, Baudry, Jerome
Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process
BIOPHYSICAL JOURNAL, 101:1493-1503, SEP 21 2011 2011
abstract, full text

Lintz, Mario J., Oinuma, Ken-Ichi, Wysoczynski, Christina L., Greenberg, Everett Peter, Churchill, Mair E. A.
Crystal structure of QscR, a Pseudomonas aeruginosa quorum sensing signal receptor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:15763-15768, SEP 20 2011 2011
abstract, full text

Frost, Denzil S., Dai, Lenore L.
Molecular Dynamics Simulations of Nanoparticle Self-Assembly at Ionic Liquid-Water and Ionic Liquid-Oil Interfaces
LANGMUIR, 27:11339-11346, SEP 20 2011 2011
abstract, full text

King, Dylan T., Warren, Dallas B., Pouton, Colin W., Chalmers, David K.
Using Molecular Dynamics to Study Liquid Phase Behavior: Simulations of the Ternary Sodium Laurate/Sodium Oleate/Water System
LANGMUIR, 27:11381-11393, SEP 20 2011 2011
abstract, full text

Barr, Daniel, Oashi, Taiji, Burkhard, Kimberly, Lucius, Sarah, Samadani, Ramin, Zhang, Jun, Shapiro, Paul, MacKerell, Alexander D., Jr., van der Vaart, Arjan
Importance of Domain Closure for the Autoactivation of ERK2
BIOCHEMISTRY, 50:8038-8048, SEP 20 2011 2011
abstract, full text

Ruiz, Jose, Rodriguez, Venancio, Cutillas, Natalia, Espinosa, Arturo, Hannon, Michael J.
A Potent Ruthenium(II) Antitumor Complex Bearing a Lipophilic Levonorgestrel Group
INORGANIC CHEMISTRY, 50:9164-9171, SEP 19 2011 2011
abstract, full text

Ilhan, Mehmet A., Spohr, Eckhard
Hydrogen bonding in narrow protonated polymer electrolyte pores
JOURNAL OF ELECTROANALYTICAL CHEMISTRY, 660:347-351, SEP 15 2011 2011
abstract, full text

Friedman, Ran
Aggregation of amyloids in a cellular context: modelling and experiment
BIOCHEMICAL JOURNAL, 438:415-426, SEP 15 2011 2011
abstract, full text

Modi, Niraj, Singh, Pratik Raj, Mahendran, Kozhinjampara R., Schulz, Robert, Winterhalter, Mathias, Kleinekathoefer, Ulrich
Probing the Transport of Ionic Liquids in Aqueous Solution through Nanopores
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:2331-2336, SEP 15 2011 2011
abstract, full text

Primo, Maria E., Jakoncic, Jean, Noguera, Martin E., Risso, Valeria A., Sosa, Laura, Sica, Mauricio P., Solimena, Michele, Poskus, Edgardo, Ermacora, Mario R.
Protein-Protein Interactions in Crystals of the Human Receptor-Type Protein Tyrosine Phosphatase ICA512 Ectodomain
PLOS ONE, 6: Art. No. e24191, SEP 15 2011 2011
abstract, full text

Singleton, Belinda K., Lau, Winnie, Fairweather, Victoria S. S., Burton, Nicholas M., Wilson, Marieangela C., Parsons, Steve F., Richardson, Ben M., Trakarnsanga, Kongtana, Brady, R. Leo, Anstee, David J., Frayne, Jan
Mutations in the second zinc finger of human EKLF reduce promoter affinity but give rise to benign and disease phenotypes
BLOOD, 118:3137-3145, SEP 15 2011 2011
abstract, full text

Liang, Xiao, Montoya, Alejandro, Haynes, Brian S.
Local Site Selectivity and Conformational Structures in the Glycosidic Bond Scission of Cellobiose
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10682-10691, SEP 15 2011 2011
abstract, full text

Rosenthal, Joel, Nepomnyashchii, Alexander B., Kozhukh, Julia, Bard, Allen J., Lippard, Stephen J.
Synthesis, Photophysics, Electrochemistry, and Electrogenerated Chemiluminescence of a Homologous Set of BODIPY-Appended Bipyridine Derivatives
JOURNAL OF PHYSICAL CHEMISTRY C, 115:17993-18001, SEP 15 2011 2011
abstract, full text

Andersson, Ida E., Batsalova, Tsvetelina, Haag, Sabrina, Dzhambazov, Balik, Holmdahl, Rikard, Kihberg, Jan, Linusson, Anna
(E)-Alkene and Ethylene Isosteres Substantially Alter the Hydrogen-Bonding Network in Class II MHC A(q)/Glycopeptide Complexes and Affect T-Cell Recognition
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:14368-14378, SEP 14 2011 2011
abstract, full text

Panek, Jaroslaw J., Jezierska-Mazzarello, Aneta, Koll, Aleksander, Dovbeshko, Galina, Fesenko, Olena
p-Nitrobenzoic Acid Adsorption on Nanostructured Gold Surfaces Investigated by Combined Experimental and Computational Approaches
CHEMPHYSCHEM, 12:2484-2494, SEP 12 2011 2011
abstract, full text

Cui, Yubao, Bastien, David A.
Water transport in human aquaporin-4: Molecular dynamics (MD) simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 412:654-659, SEP 9 2011 2011
abstract, full text

Lawrence, Scott A., Hackett, John C., Moran, Richard G.
Tetrahydrofolate Recognition by the Mitochondrial Folate Transporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:31480-31489, SEP 9 2011 2011
abstract, full text

Bhargava, B. L., Klein, Michael L.
Nanoscale Organization in Aqueous Dicationic Ionic Liquid Solutions
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10439-10446, SEP 8 2011 2011
abstract, full text

Chan, Kwok-Yan, Gumbart, James, McGreevy, Ryan, Watermeyer, Jean M., Sewell, B. Trevor, Schulten, Klaus
Symmetry-Restrained Flexible Fitting for Symmetric EM Maps
STRUCTURE, 19:1211-1218, SEP 7 2011 2011
abstract, full text

Berski, Slawomir, Gordon, Agnieszka J.
Comparative density functional theory and post-Hartree-Fock (CCSD, CASSCF) studies on the electronic structure of halogen nitrites ClONO and BrONO using quantum chemical topology
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 094303, SEP 7 2011 2011
abstract, full text

Wang, Zilu, He, Xuehao
Phase transition of a single star polymer: A Wang-Landau sampling study
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 094902, SEP 7 2011 2011
abstract, full text

Lakkaraju, Sirish Kaushik, Hwang, Wonmuk
Hysteresis-Based Mechanism for the Directed Motility of the Ncd Motor
BIOPHYSICAL JOURNAL, 101:1105-1113, SEP 7 2011 2011
abstract, full text

Beierlein, Frank R., Kneale, G. Geoff, Clark, Timothy
Predicting the Effects of Basepair Mutations in DNA-Protein Complexes by Thermodynamic Integration
BIOPHYSICAL JOURNAL, 101:1130-1138, SEP 7 2011 2011
abstract, full text

Javkhlantugs, Namsrai, Naito, Akira, Ueda, Kazuyoshi
Molecular Dynamics Simulation of Bombolitin II in the Dipalmitoylphosphatidylcholine Membrane Bilayer
BIOPHYSICAL JOURNAL, 101:1212-1220, SEP 7 2011 2011
abstract, full text

Zhang, Jiapu, Gao, David Y., Yearwood, John
A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling
JOURNAL OF THEORETICAL BIOLOGY, 284:149-157, SEP 7 2011 2011
abstract, full text

Perlmutter, Jason D., Drasler, William J., I.I., Xie, Wangshen, Gao, Jiali, Popot, Jean-Luc, Sachs, Jonathan N.
All-Atom and Coarse-Grained Molecular Dynamics Simulations of a Membrane Protein Stabilizing Polymer
LANGMUIR, 27:10523-10537, SEP 6 2011 2011
abstract, full text

Leow, Wee Wen, Hwang, Wonmuk
Epitaxially Guided Assembly of Collagen Layers on Mica Surfaces
LANGMUIR, 27:10907-10913, SEP 6 2011 2011
abstract, full text

Romero, Tomas, Orenes, Raul A., Espinosa, Arturo, Tarraga, Alberto, Molina, Pedro
Synthesis, Structural Charaterization, and Electrochemical and Optical Properties of Ferrocene-Triazole-Pyridine Triads
INORGANIC CHEMISTRY, 50:8214-8224, SEP 5 2011 2011
abstract, full text

Wang, Hai Ming, Wenz, Gerhard
Solubilization of Polycyclic Aromatics in Water by gamma-Cyclodextrin Derivatives
CHEMISTRY-AN ASIAN JOURNAL, 6:2390-2399, SEP 5 2011 2011
abstract, full text

Simunovic, Mijo, Zagrovic, Bojan, Tomic, Sanja
Mechanism and thermodynamics of ligand binding to auxin amidohydrolase
JOURNAL OF MOLECULAR RECOGNITION, 24:854-861, SEP-OCT 2011 2011
abstract, full text

Windshugel, Bjorn, Poso, Antti
Constitutive activity and ligand-dependent activation of the nuclear receptor CAR-insights from molecular dynamics simulations
JOURNAL OF MOLECULAR RECOGNITION, 24:875-882, SEP-OCT 2011 2011
abstract, full text

Wang, Jinhu, Hou, Qianqian, Dong, Lihua, Liu, Yongjun, Liu, Chengbu
QM/MM studies on the glycosylation mechanism of rice BGlu1 beta-glucosidase
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 30:148-152, SEP 2011 2011
abstract, full text

Kelly, Evan B., Tuszynski, Jack A., Klobukowski, M.
QM and QM/MD simulations of the Vinca alkaloids docked to tubulin
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 30:54-66, SEP 2011 2011
abstract, full text

Farber, Robert M.
Topical perspective on massive threading and parallelism
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 30:82-89, SEP 2011 2011
abstract, full text

Negri, Matthias, Recanatini, Maurizio, Hartmann, Rolf W.
Computational investigation of the binding mode of bis(hydroxylphenyl)arenes in 17 beta-HSD1: molecular dynamics simulations, MM-PBSA free energy calculations, and molecular electrostatic potential maps
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:795-811, SEP 2011 2011
abstract, full text

Potamitis, C., Matsoukas, M. -T., Tselios, T., Mavromoustakos, T., Grdadolnik, S. Golic
Conformational analysis of the LBQ(83-99) (Phe(91)) and LBQ(83-99) (Tyr(91)) peptide analogues and study of their interactions with the HLA-DR2 and human TCR receptors by using Molecular Dynamics
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:837-853, SEP 2011 2011
abstract, full text

Tomasic, Tihomir, Kovac, Andreja, Simcic, Mihael, Blanot, Didier, Grdadolnik, Simona Golic, Gobec, Stanislav, Kikelj, Danijel, Masic, Lucija Peterlin
Novel 2-thioxothiazolidin-4-one inhibitors of bacterial MurD ligase targeting D-Glu- and diphosphate-binding sites
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 46:3964-3975, SEP 2011 2011
abstract, full text

Cichero, Elena, Ligresti, Alessia, Allara, Marco, di Marzo, Vincenzo, Lazzati, Zelda, D'Ursi, Pasqualina, Marabotti, Anna, Milanesi, Luciano, Spallarossa, Andrea, Ranise, Angelo, Fossa, Paola
Homology modeling in tandem with 3D-QSAR analyses: A computational approach to depict the agonist binding site of the human CB2 receptor
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 46:4489-4505, SEP 2011 2011
abstract, full text

Wang, Yeng-Tseng, Su, Zhi-Yuan
Free energies and folding mechanics between human prion fragment alpha-2 domain and beta-2 domain under steered molecular dynamics simulations
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS, 42:719-723, SEP 2011 2011
abstract, full text

Wang, Yeng-Tseng, Lee, Wen-Jay, Su, Zhi-Yuan, Chen, Cheng-Lung
Carbon-nanotube-based artificial peptide channel: Transportation of small peptide under external electric field force
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS, 42:724-726, SEP 2011 2011
abstract, full text

Ferrario, Valerio, Ebert, Cynthia, Knapic, Lorena, Fattor, Diana, Basso, Alessandra, Spizzo, Patrizia, Gardossi, Lucia
Conformational Changes of Lipases in Aqueous Media: A Comparative Computational Study and Experimental Implications
ADVANCED SYNTHESIS & CATALYSIS, 353:2466-2480, SEP 2011 2011
abstract, full text

Serebryakova, Marina V., Kordyukova, Larisa V., Semashko, Tatiana A., Ksenofontov, Alexander L., Rudneva, Irina A., Kropotkina, Ekaterina A., Filippova, Irina Yu., Veit, Michael, Baratova, Lyudmila A.
Influenza virus hemagglutinin spike neck architectures and interaction with model enzymes evaluated by MALDI-TOF mass spectrometry and bioinformatics tools
VIRUS RESEARCH, 160:294-304, SEP 2011 2011
abstract, full text

Marcos, Enrique, Crehuet, Ramon, Bahar, Ivet
Changes in Dynamics upon Oligomerization Regulate Substrate Binding and Allostery in Amino Acid Kinase Family Members
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002201, SEP 2011 2011
abstract, full text

Hu, Guang, Michielssens, Servaas, Moors, Samuel L. C., Ceulemans, Arnout
Normal Mode Analysis of Trp RNA Binding Attenuation Protein: Structure and Collective Motions
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2361-2371, SEP 2011 2011
abstract, full text

Chou, H., Tam, M. F., Lee, S. -S., Tang, R. -B., Lin, T. -H., Tai, H. -Y., Chen, Y. -S., Shen, H. -D.
Asp159 is a critical core amino acid of an IgE-binding and cross-reactive epitope of a dust mite allergen Der f 7
MOLECULAR IMMUNOLOGY, 48:2130-2134, SEP 2011 2011
abstract, full text

Kim, Hansung, Tomar, Vikas
Nanometer to micron scale mechanics of [100] silicon nanowires using atomistic simulations at accelerated time steps
PHYSICA STATUS SOLIDI A-APPLICATIONS AND MATERIALS SCIENCE, 208:2115-2123, SEP 2011 2011
abstract, full text

Ierano, Teresa, Nurisso, Alessandra, Lanzetta, Rosa, Parrilli, Michelangelo, Silipo, Alba, Imberty, Anne, Molinaro, Antonio
Molecular Modeling Study of the Carbohydrate Region of the Endotoxin from Burkholderia cenocepacia ET-12
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 26, 5114-5122, SEP 2011 2011
abstract, full text

Kushwaha, Hemant R., Kumar, Gautam, Verma, Praveen K., Singla-Pareek, Sneh L., Pareek, Ashwani
Analysis of a salinity induced BjSOS3 protein from Brassica indicate it to be structurally and functionally related to its ortholog from Arabidopsis
PLANT PHYSIOLOGY AND BIOCHEMISTRY, 49:996-1004, SEP 2011 2011
abstract, full text

Mi, Changwen, Buttry, Daniel A., Sharma, Pradeep, Kouris, Demitris A.
Atomistic insights into dislocation-based mechanisms of void growth and coalescence
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS, 59:1858-1871, SEP 2011 2011
abstract, full text

Paluch, Andrew S., Mobley, David L., Maginn, Edward J.
Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2910-2918, SEP 2011 2011
abstract, full text

Mares, Jiri, Liimatainen, Helmi, Laasonen, Kari, Vaara, Juha
Solvation Structure and Dynamics of Ni(2+)(aq) from First Principles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2937-2946, SEP 2011 2011
abstract, full text

Sklenovsky, Petr, Florova, Petra, Banas, Pavel, Reblova, Kamila, Lankas, Filip, Otyepka, Michal, Sponer, Jiri
Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2963-2980, SEP 2011 2011
abstract, full text

Rosenthal, Joel, Nepomnyashchii, Alexander B., Kozhukh, Julia, Bard, Allen J., Lippard, Stephen J.
Synthesis, Photophysics, Electrochemistry, and Electrogenerated Chemiluminescence of a Homologous Set of BODIPY-Appended Bipyridine Derivatives
JOURNAL OF PHYSICAL CHEMISTRY C, 115:17175-17183, SEP 1 2011 2011
abstract, full text

Monteiro Torres, Pedro Henrique, Soares Costa Sousa, Gabriel Limaverde, Pascutti, Pedro Geraldo
Structural analysis of the N-terminal fragment of the antiangiogenic protein endostatin: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2684-2692, SEP 2011 2011
abstract, full text

Pol-Fachin, Laercio, Becker, Camila Franco, Guimaraes, Jorge Almeida, Verli, Hugo
Effects of glycosylation on heparin binding and antithrombin activation by heparin
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2735-2745, SEP 2011 2011
abstract, full text

Kramer, Markus, Kleinpeter, Erich
A conformational study of N-acetyl glucosamine derivatives utilizing residual dipolar couplings
JOURNAL OF MAGNETIC RESONANCE, 212:174-185, SEP 2011 2011
abstract, full text

Durlak, Piotr, Latajka, Zdzislaw
Proton transfer dynamics in the propionic acid dimer from path integral molecular dynamics calculations
JOURNAL OF MOLECULAR MODELING, 17:2159-2168, SEP 2011 2011
abstract, full text

Moldovan, Clara, Thompson, Damien
Molecular dynamics of the "hydrophobic patch" that immobilizes hydrophobin protein HFBII on silicon
JOURNAL OF MOLECULAR MODELING, 17:2227-2235, SEP 2011 2011
abstract, full text

Mikulska, Karolina, Peplowski, Lukasz, Nowak, Wieslaw
Nanomechanics of Ig-like domains of human contactin (BIG-2)
JOURNAL OF MOLECULAR MODELING, 17:2313-2323, SEP 2011 2011
abstract, full text

Masella, Michel, Borgis, Daniel, Cuniasse, Philippe
Combining a Polarizable Force-Field and a Coarse-Grained Polarizable Solvent Model. II. Accounting for Hydrophobic Effects
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2664-2678, SEP 2011 2011
abstract, full text

Dlugosz, Maciej, Zielinski, Pawel, Trylska, Joanna
Software News and Updates Brownian Dynamics Simulations on CPU and GPU with BD_BOX
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2734-2744, SEP 2011 2011
abstract, full text

Bertini, Ivano, Case, David A., Ferella, Lucio, Giachetti, Andrea, Rosato, Antonio
A Grid-enabled web portal for NMR structure refinement with AMBER
BIOINFORMATICS, 27:2384-2390, SEP 1 2011 2011
abstract, full text

La Penna, Giovanni, Furlan, Sara, Sola, Miquel
Measuring electron sharing between atoms in first-principle simulations
THEORETICAL CHEMISTRY ACCOUNTS, 130:27-36, SEP 2011 2011
abstract, full text

Balaeff, Alexander, Craig, Stephen L., Beratan, David N.
B-DNA to Zip-DNA: Simulating a DNA Transition to a Novel Structure with Enhanced Charge-Transport Characteristics
JOURNAL OF PHYSICAL CHEMISTRY A, 115:9377-9391, SEP 1 2011 2011
abstract, full text

Ullmann, R. Thomas, Ullmann, G. Matthias
Coupling of Protonation, Reduction, and Conformational Change in azurin from Pseudomonas aeruginosa Investigated with Free Energy Measures of Cooperativity
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10346-10359, SEP 1 2011 2011
abstract, full text

Sezer, Murat, Frielingsdorf, Stefan, Millo, Diego, Heidary, Nina, Utesch, Tillman, Mroginski, Maria-Andrea, Friedrich, Baerbel, Hildebrandt, Peter, Zebger, Ingo, Weidinger, Inez M.
Role of the HoxZ Subunit in the Electron Transfer Pathway of the Membrane-Bound [NiFe]-Hydrogenase from Ralstonia eutropha Immobilized on Electrodes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10368-10374, SEP 1 2011 2011
abstract, full text

Tang, Haili, Robinson, James E., Gnanakaran, S., Li, Ming, Rosenberg, Eric S., Perez, Lautaro G., Haynes, Barton F., Liao, Hua-Xin, LaBranche, Celia C., Korber, Bette T., Montefiori, David C.
Epitopes Immediately below the Base of the V3 Loop of gp120 as Targets for the Initial Autologous Neutralizing Antibody Response in Two HIV-1 Subtype B-Infected Individuals
JOURNAL OF VIROLOGY, 85:9286-9299, SEP 2011 2011
abstract, full text

Kostyuchenko, Victor A., Jakana, Joanita, Liu, Xiangan, Haddow, Andrew D., Aung, Myint, Weaver, Scott C., Chiu, Wah, Lok, Shee-Mei
The Structure of Barmah Forest Virus as Revealed by Cryo-Electron Microscopy at a 6-Angstrom Resolution Has Detailed Transmembrane Protein Architecture and Interactions
JOURNAL OF VIROLOGY, 85:9327-9333, SEP 2011 2011
abstract, full text

Park, Jae Hyun, Aluru, N. R.
Self-assembly of graphenes
SURFACE SCIENCE, 605:1616-1620, SEP 2011 2011
abstract, full text

Sapay, Nicolas, Cabannes, Eric, Petitou, Maurice, Imberty, Anne
Molecular modeling of the interaction between heparan sulfate and cellular growth factors: Bringing pieces together
GLYCOBIOLOGY, 21:1181-1193, SEP 2011 2011
abstract, full text

Garcia-Ortega, Lucia, Alegre-Cebollada, Jorge, Garcia-Linares, Sara, Bruix, Marta, Martinez-del-Pozo, Alvaro, Gavilanes, Jose G.
The behavior of sea anemone actinoporins at the water-membrane interface
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2275-2288, SEP 2011 2011
abstract, full text

Banik, S. Dutta, Nandi, N.
Influence of the conserved active site residues of histidyl tRNA synthetase on the mechanism of aminoacylation reaction
BIOPHYSICAL CHEMISTRY, 158:61-72, SEP 2011 2011
abstract, full text

Berhanu, Workalemahu M., Masunov, Artem E.
Molecular Dynamic Simulation of Wild Type and Mutants of the Polymorphic Amyloid NNQNTF Segments of Elk Prion: Structural Stability and Thermodynamic of Association
BIOPOLYMERS, 95:573-590, SEP 2011 2011
abstract, full text

Kormos, Bethany L., Pieniazek, Susan N., Beveridge, David L., Baranger, Anne M.
U1A Protein-Stem Loop 2 RNA Recognition: Prediction of Structural Differences from Protein Mutations
BIOPOLYMERS, 95:591-606, SEP 2011 2011
abstract, full text

Dlugosz, Maciej, Huber, Gary A., McCammon, J. Andrew, Trylska, Joanna
Brownian Dynamics Study of the Association Between the 70S Ribosome and Elongation Factor G
BIOPOLYMERS, 95:616-627, SEP 2011 2011
abstract, full text

Caroli Rezende, Marcos, Mascayano, Carolina, Briones, Luis, Aliaga, Carolina
Sensing different micellar microenvironments with solvatochromic dyes of variable lipophilicity
DYES AND PIGMENTS, 90:219-224, SEP 2011 2011
abstract, full text

Vukovic, Lela, Khatib, Fatima A., Drake, Stephanie P., Madriaga, Antonett, Brandenburg, Kenneth S., Kral, Petr, Onyuksel, Hayat
Structure and Dynamics of Highly PEG-ylated Sterically Stabilized Micelles in Aqueous Media
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13481-13488, AUG 31 2011 2011
abstract, full text

Roxbury, Daniel, Jagota, Anand, Mittal, Jeetain
Sequence-Specific Self-Stitching Motif of Short Single-Stranded DNA on a Single-Walled Carbon Nanotube
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13545-13550, AUG 31 2011 2011
abstract, full text

Nishima, Wataru, Kanamaru, Shuji, Arisaka, Fumio, Kitao, Akio
Screw Motion Regulates Multiple Functions of T4 Phage Protein Gene Product 5 during Cell Puncturing
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:13571-13576, AUG 31 2011 2011
abstract, full text

Brown, Christopher J., Dastidar, Shubhra G., Quah, Soo T., Lim, Annie, Chia, Brian, Verma, Chandra S.
C-Terminal Substitution of MDM2 Interacting Peptides Modulates Binding Affinity by Distinctive Mechanisms
PLOS ONE, 6: Art. No. e24122, AUG 31 2011 2011
abstract, full text

Mao, Debin, Lu, Shouqin, Li, Ning, Zhang, Yan, Long, Mian
Conformational Stability Analyses of Alpha Subunit I Domain of LFA-1 and Mac-1
PLOS ONE, 6: Art. No. e24188, AUG 31 2011 2011
abstract, full text

Patrick, Christopher E., Giustino, Feliciano
O 1s core-level shifts at the anatase TiO(2)(101)/N3 photovoltaic interface: Signature of H-bonded supramolecular assembly
PHYSICAL REVIEW B, 84: Art. No. 085330, AUG 31 2011 2011
abstract, full text

Manning, Edward P., Tardiff, Jil C., Schwartz, Steven D.
A Model of Calcium Activation of the Cardiac Thin Filament
BIOCHEMISTRY, 50:7405-7413, AUG 30 2011 2011
abstract, full text

Ucisik, Melek N., Dashti, Danial S., Faver, John C., Merz, Kenneth M., Jr.
Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 085101, AUG 28 2011 2011
abstract, full text

Hult, Ekaterina F., Tobe, Stephen S., Chang, Belinda S. W.
Molecular Evolution of Ultraspiracle Protein (USP/RXR) in Insects
PLOS ONE, 6: Art. No. e23416, AUG 25 2011 2011
abstract, full text

Legrand, Baptiste, Giudice, Emmanuel, Nicolas, Aurelie, Delalande, Olivier, Le Rumeur, Elisabeth
Computational Study of the Human Dystrophin Repeats: Interaction Properties and Molecular Dynamics
PLOS ONE, 6: Art. No. e23819, AUG 25 2011 2011
abstract, full text

Ellis, Christopher R., Rudzinski, Joseph F., Noid, William G.
Generalized-Yvon-Born-Green Model of Toluene
MACROMOLECULAR THEORY AND SIMULATIONS, 20:478-495, AUG 25 2011 2011
abstract, full text

Liyana-Arachchi, Thilanga P., Valsaraj, Kalliat T., Hung, Francisco R.
Molecular Simulation Study of the Adsorption of Naphthalene and Ozone on Atmospheric Air/Ice Interfaces
JOURNAL OF PHYSICAL CHEMISTRY A, 115:9226-9236, AUG 25 2011 2011
abstract, full text

Hirao, Hajime
Which DFT Functional Performs Well in the Calculation of Methylcobalamin? Comparison of the B3LYP and BP86 Functionals and Evaluation of the Impact of Empirical Dispersion Correction
JOURNAL OF PHYSICAL CHEMISTRY A, 115:9308-9313, AUG 25 2011 2011
abstract, full text

van Hoof, Bram, Markvoort, Albert J., van Santen, Rutger A., Hilbers, Peter A. J.
The CUMULUS Coarse Graining Method: Transferable Potentials for Water and Solutes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10001-10012, AUG 25 2011 2011
abstract, full text

Duan, Li, Zhmurov, Artem, Barsegov, Valeri, Dima, Ruxandra I.
Exploring the Mechanical Stability of the C2 Domains in Human Synaptotagmin 1
JOURNAL OF PHYSICAL CHEMISTRY B, 115:10133-10146, AUG 25 2011 2011
abstract, full text

Anzini, Maurizio, Valenti, Salvatore, Braile, Carlo, Cappelli, Andrea, Vomero, Salvatore, Acaro, Stefano, Ortuso, Francesco, Marinelli, Luciana, Limongelli, Vittorio, Novellino, Ettore, Betti, Laura, Giannaccini, Gino, Lucacchini, Antonio, Daniele, Simona, Martini, Claudia, Ghelardini, Carla, Mannelli, Lorenzo Di Cesare, Giorgi, Gianluca, Mascia, Maria Paola, Biggio, Giovanni
New Insight into the Central Benzodiazepine Receptor-Ligand Interactions: Design, Synthesis, Biological Evaluation, and Molecular Modeling of 3-Substituted 6-Phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and Related Compounds
JOURNAL OF MEDICINAL CHEMISTRY, 54:5694-5711, AUG 25 2011 2011
abstract, full text

Isaksson, Johan, Brandsdal, Bjorn O., Engqvist, Magnus, Flaten, Goril Eide, Svendsen, John S. Mjoen, Stensen, Wenche
A Synthetic Antimicrobial Peptidomimetic (LTX 109): Stereochemical Impact on Membrane Disruption
JOURNAL OF MEDICINAL CHEMISTRY, 54:5786-5795, AUG 25 2011 2011
abstract, full text

Yetukuri, Laxman, Huopaniemi, Ilkka, Koivuniemi, Artturi, Maranghi, Marianna, Hiukka, Anne, Nygren, Heli, Kaski, Samuel, Taskinen, Marja-Riitta, Vattulainen, Ilpo, Jauhiainen, Matti, Oresic, Matej
High Density Lipoprotein Structural Changes and Drug Response in Lipidomic Profiles following the Long-Term Fenofibrate Therapy in the FIELD Substudy
PLOS ONE, 6: Art. No. e23589, AUG 24 2011 2011
abstract, full text

Nunez-Villanueva, Diego, Angeles Bonache, M., Infantes, Lourdes, Teresa Garcia-Lopez, M., Martin-Martinez, Mercedes, Gonzalez-Muniz, Rosario
Quaternary alpha,alpha-2-Oxoazepane alpha-Amino Acids: Synthesis from Ornithine-Derived beta-Lactams and Incorporation into Model Dipeptides
JOURNAL OF ORGANIC CHEMISTRY, 76:6592-6603, AUG 19 2011 2011
abstract, full text

Aci-Seche, Samia, Genest, Monique, Garnier, Norbert
Ligand entry pathways in the ligand binding domain of PPAR gamma receptor
FEBS LETTERS, 585:2599-2603, AUG 19 2011 2011
abstract, full text

Rossetti, Giulia, Cong, Xiaojing, Caliandro, Rocco, Legname, Giuseppe, Carloni, Paolo
Common Structural Traits across Pathogenic Mutants of the Human Prion Protein and Their Implications for Familial Prion Diseases
JOURNAL OF MOLECULAR BIOLOGY, 411:700-712, AUG 19 2011 2011
abstract, full text

Qiu, Liming, Buie, Creighton, Reay, Andrew, Vaughn, Mark W., Cheng, Kwan Hon
Molecular Dynamics Simulations Reveal the Protective Role of Cholesterol in beta-Amyloid Protein-Induced Membrane Disruptions in Neuronal Membrane Mimics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9795-9812, AUG 18 2011 2011
abstract, full text

Ou, Luchun, Luo, Yin, Wei, Guanghong
Atomic-Level Study of Adsorption, Conformational Change, and Dimerization of an alpha-Helical Peptide at Graphene Surface
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9813-9822, AUG 18 2011 2011
abstract, full text

Woiczikowski, Paul Benjamin, Steinbrecher, Thomas, Kubar, Tomas, Elstner, Marcus
Nonadiabatic QM/MM Simulations of Fast Charge Transfer in Escherichia coli DNA Photolyase
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9846-9863, AUG 18 2011 2011
abstract, full text

Raghuraman, Arjun, Ko, Eunhwa, Perez, Lisa M., Ioerger, Thomas R., Burgess, Kevin
Pyrrolinone-Pyrrolidine Oligomers as Universal Peptidomimetics
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12350-12353, AUG 17 2011 2011
abstract, full text

Pham, Van-Thai, Penfold, Thomas J., van der Veen, Renske M., Lima, Frederico, El Nahhas, Amal, Johnson, Steve L., Beaud, Paul, Abela, Rafael, Bressler, Christian, Tavernelli, Ivano, Milne, Christopher J., Chergui, Majed
Probing the Transition from Hydrophilic to Hydrophobic Solvation with Atomic Scale Resolution
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:12740-12748, AUG 17 2011 2011
abstract, full text

Lee, Tai-Sung, Kantarjian, Hagop, Ma, Wanlong, Yeh, Chen-Hsiung, Giles, Francis, Albitar, Maher
Effects of Clinically Relevant MPL Mutations in the Transmembrane Domain Revealed at the Atomic Level through Computational Modeling
PLOS ONE, 6: Art. No. e23396, AUG 17 2011 2011
abstract, full text

Haddadian, Esmael J., Gong, Haipeng, Jha, Abhishek K., Yang, Xiaojing, DeBartolo, Joe, Hinshaw, James R., Rice, Phoebe A., Sosnick, Tobin R., Freed, Karl F.
Automated Real-Space Refinement of Protein Structures Using a Realistic Backbone Move Set
BIOPHYSICAL JOURNAL, 101:899-909, AUG 17 2011 2011
abstract, full text

Barnaby, Omar S., Cerny, Ronald L., Clarke, William, Hage, David S.
Quantitative analysis of glycation patterns in human serum albumin using (16)O/(18)O-labeling and MALDI-TOF MS
CLINICA CHIMICA ACTA, 412:1606-1615, AUG 17 2011 2011
abstract, full text

Baugh, Evan H., Lyskov, Sergey, Weitzner, Brian D., Gray, Jeffrey J.
Real-Time PyMOL Visualization for Rosetta and PyRosetta
PLOS ONE, 6: Art. No. e21931, AUG 16 2011 2011
abstract, full text

Hassan, Natalia, Ruso, Juan M., Pineiro, Angel
Hydrogenated/Fluorinated Catanionic Surfactants as Potential Templates for Nanostructure Design
LANGMUIR, 27:9719-9728, AUG 16 2011 2011
abstract, full text

Brown, Steven D., Guss, Adam M., Karpinets, Tatiana V., Parks, Jerry M., Smolin, Nikolai, Yang, Shihui, Land, Miriam L., Klingeman, Dawn M., Bhandiwad, Ashwini, Rodriguez, Miguel, Jr., Raman, Babu, Shao, Xiongjun, Mielenz, Jonathan R., Smith, Jeremy C., Keller, Martin, Lynd, Lee R.
Mutant alcohol dehydrogenase leads to improved ethanol tolerance in Clostridium thermocellum
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:13752-13757, AUG 16 2011 2011
abstract, full text

Losasso, Valeria, Pietropaolo, Adriana, Zannoni, Claudio, Gustincich, Stefano, Carloni, Paolo
Structural Role of Compensatory Amino Acid Replacements in the alpha-Synuclein Protein
BIOCHEMISTRY, 50:6994-7001, AUG 16 2011 2011
abstract, full text

Klvana, Martin, Jerabek, Petr, Goodman, Myron F., Florian, Jan
An Abridged Transition State Model To Derive Structure, Dynamics, and Energy Components of DNA Polymerase beta Fidelity
BIOCHEMISTRY, 50:7023-7032, AUG 16 2011 2011
abstract, full text

Chen, Wen-Jie, Zhai, Hua-Jin, Huang, Xin, Wang, Lai-Sheng
On the electronic structure of mono-rhenium oxide clusters: ReO(n)(-) and ReO(n) (n=3, 4)
CHEMICAL PHYSICS LETTERS, 512:49-53, AUG 16 2011 2011
abstract, full text

Lokstein, Heiko, Krikunova, Maria, Teuchner, Klaus, Voigt, Bernd
Elucidation of structure-function relationships in photosynthetic light-harvesting antenna complexes by non-linear polarization spectroscopy in the frequency domain (NLPF)
JOURNAL OF PLANT PHYSIOLOGY, 168:1488-1496, AUG 15 2011 2011
abstract, full text

Jensen, Bjornar, Kuznetsova, Tatiana, Kvamme, Bjorn, Oterhals, Age
Molecular dynamics study of selective adsorption of PCB on activated carbon
FLUID PHASE EQUILIBRIA, 307:58-65, AUG 15 2011 2011
abstract, full text

Kim, Seonghoon, Chang, Rakwoo, Teunissen, Charlotte, Gebremichael, Yeshitila, Petzold, Axel
Neurofilament stoichiometry simulations during neurodegeneration suggest a remarkable self-sufficient and stable in vivo protein structure
JOURNAL OF THE NEUROLOGICAL SCIENCES, 307:132-138, AUG 15 2011 2011
abstract, full text

Yip, Kevin Y., Utz, Lukas, Sitwell, Simon, Hu, Xihao, Sidhu, Sachdev S., Turk, Benjamin E., Gerstein, Mark, Kim, Philip M.
Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps
BMC BIOLOGY, 9: Art. No. 53, AUG 11 2011 2011
abstract, full text

Cueva, Juan Pablo, Gallardo-Godoy, Alejandra, Juncosa, Jose I., Jr., Vidi, Pierre A., Lill, Markus A., Watts, Val J., Nichols, David E.
Probing the Steric Space at the Floor of the D(1) Dopamine Receptor Orthosteric Binding Domain: 7 alpha-, 7 beta-, 8 alpha-, and 8 beta-Methyl Substituted Dihydrexidine Analogues
JOURNAL OF MEDICINAL CHEMISTRY, 54:5508-5521, AUG 11 2011 2011
abstract, full text

Klein, Tobias, Henn, Claudia, Negri, Matthias, Frotscher, Martin
Structural Basis for Species Specific Inhibition of 17 beta-Hydroxysteroid Dehydrogenase Type 1 (17 beta-HSD1): Computational Study and Biological Validation
PLOS ONE, 6: Art. No. e22990, AUG 9 2011 2011
abstract, full text

Hadizadeh, Shirin, Linhananta, Apichart, Plotkin, Steven S.
Improved Measures for the Shape of a Disordered Polymer To Test a Mean-Field Theory of Collapse
MACROMOLECULES, 44:6182-6197, AUG 9 2011 2011
abstract, full text

Blundell, S. A., Haldar, Soumyajyoti, Kanhere, D. G.
Metallic clusters on a model surface: Quantum versus geometric effects
PHYSICAL REVIEW B, 84: Art. No. 075430, AUG 8 2011 2011
abstract, full text

Wan, Shunzhou, Coveney, Peter V.
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 8:1114-1127, AUG 7 2011 2011
abstract, full text

Shi, Ning, Zeng, Weizhong, Ye, Sheng, Li, Yang, Jiang, Youxing
Crucial Points within the Pore as Determinants of K(+) Channel Conductance and Gating
JOURNAL OF MOLECULAR BIOLOGY, 411:27-35, AUG 5 2011 2011
abstract, full text

Kuzmanic, Antonija, Kruschel, Daniela, van Gunsteren, Wilfred F., Pannu, Navraj S., Zagrovic, Bojan
Dynamics May Significantly Influence the Estimation of Interatomic Distances in Biomolecular X-ray Structures
JOURNAL OF MOLECULAR BIOLOGY, 411:286-297, AUG 5 2011 2011
abstract, full text

Louet, Maxime, Perahia, David, Martinez, Jean, Floquet, Nicolas
A Concerted Mechanism for Opening the GDP Binding Pocket and Release of the Nucleotide in Hetero-Trimeric G-Proteins
JOURNAL OF MOLECULAR BIOLOGY, 411:298-312, AUG 5 2011 2011
abstract, full text

Steckbeck, Jonathan D., Craigo, Jodi K., Barnes, Christopher O., Montelaro, Ronald C.
Highly Conserved Structural Properties of the C-terminal Tail of HIV-1 gp41 Protein Despite Substantial Sequence Variation among Diverse Clades IMPLICATIONS FOR FUNCTIONS IN VIRAL REPLICATION
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:27156-27166, AUG 5 2011 2011
abstract, full text

Achbergerova, Lucia, Nahalka, Jozef
Polyphosphate - an ancient energy source and active metabolic regulator
MICROBIAL CELL FACTORIES, 10: Art. No. 63, AUG 4 2011 2011
abstract, full text

Sorkin, Anastassia, Tay, Bengkang, Su, Haibin
Three-Stage Transformation Pathway from Nanodiamonds to Fullerenes
JOURNAL OF PHYSICAL CHEMISTRY A, 115:8327-8334, AUG 4 2011 2011
abstract, full text

Jonsson, E. O., Thygesen, K. S., Ulstrup, J., Jacobsen, K. W.
Ab Initio Calculations of the Electronic Properties of Polypyridine Transition Metal Complexes and Their Adsorption on Metal Surfaces in the Presence of Solvent and Counterions
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9410-9416, AUG 4 2011 2011
abstract, full text

Manji, Shehnaaz S. M., Miller, Kerry A., Williams, Louise H., Andreasen, Lotte, Siboe, Maria, Rose, Elizabeth, Bahlo, Melanie, Kuiper, Michael, Dahl, Hans-Henrik M.
An ENU-Induced Mutation of Cdh23 Causes Congenital Hearing Loss, but No Vestibular Dysfunction, in Mice
AMERICAN JOURNAL OF PATHOLOGY, 179:903-914, AUG 2011 2011
abstract, full text

Dolenc, Jozica, Riniker, Sereina, Gaspari, Roberto, Daura, Xavier, van Gunsteren, Wilfred F.
Free energy calculations offer insights into the influence of receptor flexibility on ligand-receptor binding affinities
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:709-716, AUG 2011 2011
abstract, full text

Butala, Matej, Klose, Daniel, Hodnik, Vesna, Rems, Ana, Podlesek, Zdravko, Klare, Johann P., Anderluh, Gregor, Busby, Stephen J. W., Steinhoff, Heinz-Juergen, Zgur-Bertok, Darja
Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response
NUCLEIC ACIDS RESEARCH, 39:6546-6557, AUG 2011 2011
abstract, full text

Kunisada, Yuji, Nakanishi, Hiroshi, Kasai, Hideaki
A First Principles Study of O(2)/Ag(111) -Adsorption and Magnetic Properties-
JOURNAL OF THE PHYSICAL SOCIETY OF JAPAN, 80: Art. No. 084605, AUG 2011 2011
abstract, full text

Pietra, Francesco
On the Egress of Carbon Monoxide from Myoglobin
CHEMISTRY & BIODIVERSITY, 8:1410-1421, AUG 2011 2011
abstract, full text

Perez, Alejandro, von Lilienfeld, O. Anatole
Path Integral Computation of Quantum Free Energy Differences Due to Alchemical Transformations Involving Mass and Potential
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2358-2369, AUG 2011 2011
abstract, full text

Cojocaru, Vlad, Balali-Mood, Kia, Sansom, Mark S. P., Wade, Rebecca C.
Structure and Dynamics of the Membrane-Bound Cytochrome P450 2C9
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002152, AUG 2011 2011
abstract, full text

Dourado, Eduardo M. A., Herdes, Carmelo, Van Tassel, Paul R., Sarkisov, Lev
Molecular Recognition Effects in Atomistic Models of Imprinted Polymers
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 12:4781-4804, AUG 2011 2011
abstract, full text

Yasi, Joseph A., Hector, Louis G., Jr., Trinkle, Dallas R.
Prediction of thermal cross-slip stress in magnesium alloys from direct first-principles data
ACTA MATERIALIA, 59:5652-5660, AUG 2011 2011
abstract, full text

Felts, Anthony K., LaBarge, Krystal, Bauman, Joseph D., Patel, Dishaben V., Himmel, Daniel M., Arnold, Eddy, Parniak, Michael A., Levy, Ronald M.
Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1986-1998, AUG 2011 2011
abstract, full text

Brehm, Martin, Kirchner, Barbara
TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:2007-2023, AUG 2011 2011
abstract, full text

Haider, Shozeb M., Autiero, Ida, Neidle, Stephen
Surface area accessibility and the preferred topology of telomeric DNA quadruplex-ligand complexes
BIOCHIMIE, 93:1275-1279, AUG 2011 2011
abstract, full text

Petraccone, Luigi, Fotticchia, Iolanda, Cummaro, Annunziata, Pagano, Bruno, Ginnari-Satriani, Luca, Haider, Shozeb, Randazzo, Antonio, Novellino, Ettore, Neidle, Stephen, Giancola, Concetta
The triazatruxene derivative azatrux binds to the parallel form of the human telomeric G-quadruplex under molecular crowding conditions: Biophysical and molecular modeling studies
BIOCHIMIE, 93:1318-1327, AUG 2011 2011
abstract, full text

Calderon, Cristian, Abuin, Elsa, Lissi, Eduardo, Montecinos, Rodrigo
Effect of Human Serum Albumin on the Kinetics of 4-Methylumbelliferyl-beta-D-N-N '-N '' Triacetylchitotrioside Hydrolysis Catalyzed by Hen Egg White Lysozyme
PROTEIN JOURNAL, 30:367-373, AUG 2011 2011
abstract, full text

Khan, Hanif Muhammad, Kim, Sung-Gaun
On the wear mechanism of thin nickel film during AFM-based scratching process using molecular dynamics
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 25:2111-2120, AUG 2011 2011
abstract, full text

Cuesta-Lopez, Santiago, Perlado, J. M.
NANOSCALE VIEW OF SHOCK WAVE PROPAGATION IN SINGLE CRYSTAL FE,W, AND TA FOR NUCLEAR FUSION TECHNOLOGY
FUSION SCIENCE AND TECHNOLOGY, 60:590-594, AUG 2011 2011
abstract, full text

Glykos, Nicholas M.
On the application of structure-specific bulk-solvent models
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 67:739-741, AUG 2011 2011
abstract, full text

Du, Hongbo, Qian, Xianghong
Molecular Dynamics Simulations of PNIPAM-co-PEGMA Copolymer Hydrophilic to Hydrophobic Transition in NaCl Solution
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 49:1112-1122, AUG 1 2011 2011
abstract, full text

Ganoth, Assaf, Alhadeff, Raphael, Arkin, Isaiah T.
Computational study of the Na(+)/H(+) antiporter from Vibrio parahaemolyticus
JOURNAL OF MOLECULAR MODELING, 17:1877-1890, AUG 2011 2011
abstract, full text

Meiselbach, Heike, Sticht, Heinrich
Effect of the SH3-SH2 domain linker sequence on the structure of Hck kinase
JOURNAL OF MOLECULAR MODELING, 17:1927-1934, AUG 2011 2011
abstract, full text

Barata, Teresa Silva, Shaunak, Sunil, Teo, Ian, Zloh, Mire, Brocchini, Steve
Structural studies of biologically active glycosylated polyamidoamine (PAMAM) dendrimers
JOURNAL OF MOLECULAR MODELING, 17:2051-2060, AUG 2011 2011
abstract, full text

Zhu, Haimei, Briggs, James M.
Mechanistic role of NS4A and substrate in the activation of HCV NS3 protease
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2428-2443, AUG 2011 2011
abstract, full text

McArthur, J. R., Singh, G., O'Mara, M. L., McMaster, D., Ostroumov, V., Tieleman, D. P., French, R. J.
Orientation of mu-Conotoxin PIIIA in a Sodium Channel Vestibule, Based on Voltage Dependence of Its Binding
MOLECULAR PHARMACOLOGY, 80:219-227, AUG 2011 2011
abstract, full text

Wu, Qing-Yun, Li, Feng, Wang, Xiao-Yun, Chen, Zheng Jun
Impact of inter-subunit interactions on the dimeric arginine kinase activity and structural stability
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 512:61-68, AUG 1 2011 2011
abstract, full text

Woofter, Ricky T., Maurer, Muriel C.
Role of calcium in the conformational dynamics of factor XIII activation examined by hydrogen-deuterium exchange coupled with MALDI-TOF MS
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 512:87-95, AUG 1 2011 2011
abstract, full text

Purohit, Rituraj, Rajendran, Vidya, Sethumadhavan, Rao
Studies on Adaptability of Binding Residues and Flap Region of TMC-114 Resistance HIV-1 Protease Mutants
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:137-152, AUG 2011 2011
abstract, full text

Cortopassi, Wilian A., Oliveira, Aline A., Guimaraes, Ana P., Renno, Magdalena N., Krettli, Antoniana U., Franca, Tanos C. C.
Docking Studies on the Binding of Quinoline Derivatives and Hematin to Plasmodium Falciparum Lactate Dehydrogenase
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:207-218, AUG 2011 2011
abstract, full text

Chakraborty, Joydeep, Dutta, Tapan K.
From Lipid Transport to Oxygenation of Aromatic Compounds: Evolution within the Bet v1-like Superfamily
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 29:67-78, AUG 2011 2011
abstract, full text

Romo, Tod D., Bradney, Laura A., Greathouse, Denise V., Grossfield, Alan
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:2019-2030, AUG 2011 2011
abstract, full text

Michaud-Agrawal, Naveen, Denning, Elizabeth J., Woolf, Thomas B., Beckstein, Oliver
Software News and Updates MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2319-2327, JUL 30 2011 2011
abstract, full text

Mollaamin, F., Layali, I., Ilkhani, A. R., Monajjemi, M.
Nanomolecular simulation of the voltage-gated potassium channel protein by gyration radius study
AFRICAN JOURNAL OF MICROBIOLOGY RESEARCH, 4:2795-2803, DEC 18 2010 2010
abstract, full text

Yamasaki, Kazuo, Daiho, Takashi, Danko, Stefania, Suzuki, Hiroshi
Ca(2+) Release to Lumen from ADP-sensitive Phosphoenzyme E1PCa(2) without Bound K(+) of Sarcoplasmic Reticulum Ca(2+)-ATPase
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:38674-38683, DEC 3 2010 2010
abstract, full text

Elrad, Oren M., Hagan, Michael F.
Encapsulation of a polymer by an icosahedral virus
PHYSICAL BIOLOGY, 7: Art. No. 045003, DEC 2010 2010
abstract, full text

Armache, Jean-Paul, Jarasch, Alexander, Anger, Andreas M., Villa, Elizabeth, Becker, Thomas, Bhushan, Shashi, Jossinet, Fabrice, Habeck, Michael, Dindar, Guelcin, Franckenberg, Sibylle, Marquez, Viter, Mielke, Thorsten, Thomm, Michael, Berninghausen, Otto, Beatrix, Birgitta, Soeding, Johannes, Westhof, Eric, Wilson, Daniel N., Beckmann, Roland
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-angstrom resolution
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:19748-19753, NOV 16 2010 2010
abstract, full text

Armache, Jean-Paul, Jarasch, Alexander, Anger, Andreas M., Villa, Elizabeth, Becker, Thomas, Bhushan, Shashi, Jossinet, Fabrice, Habeck, Michael, Dindar, Guelcin, Franckenberg, Sibylle, Marquez, Viter, Mielke, Thorsten, Thomm, Michael, Berninghausen, Otto, Beatrix, Birgitta, Soeding, Johannes, Westhof, Eric, Wilson, Daniel N., Beckmann, Roland
Localization of eukaryote-specific ribosomal proteins in a 5.5-angstrom cryo-EM map of the 80S eukaryotic ribosome
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:19754-19759, NOV 16 2010 2010
abstract, full text

Mullinax, J. W., Noid, W. G.
Recovering physical potentials from a model protein databank
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:19867-19872, NOV 16 2010 2010
abstract, full text

Lipfert, Jan, Klijnhout, Sven, Dekker, Nynke H.
Torsional sensing of small-molecule binding using magnetic tweezers
NUCLEIC ACIDS RESEARCH, 38:7122-7132, NOV 2010 2010
abstract, full text

Zhuang, Shulin, Linhananta, Apichart, Li, Hongbin
Phenotypic effects of Ehlers-Danlos syndrome-associated mutation on the FnIIII domain of tenascin-X
PROTEIN SCIENCE, 19:2231-2239, NOV 2010 2010
abstract, full text

Cox, Dermot, Brennan, Marian, Moran, Niamh
Integrins as therapeutic targets: lessons and opportunities
NATURE REVIEWS DRUG DISCOVERY, 9:804-820, OCT 2010 2010
abstract, full text

McDaniel, Allison, Fuchs, Erica, Liu, Ying, Ford, Clark
Directed evolution of Aspergillus niger glucoamylase to increase thermostability
MICROBIAL BIOTECHNOLOGY, 1:523-531, NOV 2008 2008
abstract, full text

Jacob, Christoph R., Beyhan, S. Maya, Bulo, Rosa E., Gomes, Andre Severo Pereira, Goetz, Andreas W., Kiewisch, Karin, Sikkema, Jetze, Visscher, Lucas
Software News and Updates PyADF - A Scripting Framework for Multiscale Quantum Chemistry
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:2328-2338, JUL 30 2011 2011
abstract, full text

Pentikainen, Ulla, Jiang, Pengju, Takala, Heikki, Ruskamo, Salla, Campbell, Iain D., Ylanne, Jari
Assembly of a Filamin Four-domain Fragment and the Influence of Splicing Variant-1 on the Structure
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:26921-26930, JUL 29 2011 2011
abstract, full text

Bihani, Subhash C., Das, Amit, Nilgiriwala, Kayzad S., Prashar, Vishal, Pirocchi, Michel, Apte, Shree Kumar, Ferrer, Jean-Luc, Hosur, Madhusoodan V.
X-Ray Structure Reveals a New Class and Provides Insight into Evolution of Alkaline Phosphatases
PLOS ONE, 6: Art. No. e22767, JUL 28 2011 2011
abstract, full text

Chen, Jianhan, Zolkiewska, Anna
Force-Induced Unfolding Simulations of the Human Notch1 Negative Regulatory Region: Possible Roles of the Heterodimerization Domain in Mechanosensing
PLOS ONE, 6: Art. No. e22837, JUL 28 2011 2011
abstract, full text

Wang, Qiang, Werstiuk, Nick H., Kramer, James R., Bell, Russell A.
Effects of Cu Ions and Explicit Water Molecules on the Copper Binding Domain of Amyloid Precursor Protein APP(131-189): A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9224-9235, JUL 28 2011 2011
abstract, full text

Karachevtsev, Maxim V., Karachevtsev, Victor A.
Peculiarities of Homooligonucleotides Wrapping around Carbon Nanotubes: Molecular Dynamics Modeling
JOURNAL OF PHYSICAL CHEMISTRY B, 115:9271-9279, JUL 28 2011 2011
abstract, full text

Baviskar, Ashish T., Madaan, Chetna, Preet, Ranjan, Mohapatra, Purusottam, Jain, Vaibhav, Agarwal, Amit, Guchhait, Sankar K., Kundu, Chanakya N., Banerjee, Uttam C., Bharatam, Prasad V.
N-Fused Imidazoles As Novel Anticancer Agents That Inhibit Catalytic Activity of Topoisomerase II alpha and Induce Apoptosis in G1/S Phase
JOURNAL OF MEDICINAL CHEMISTRY, 54:5013-5030, JUL 28 2011 2011
abstract, full text

Ryng, Stanislaw, Zimecki, Michal, Jezierska-Mazzarello, Aneta, Panek, Jaroslaw J., Maczynski, Marcin, Glowiak, Tadeusz, Sawka-Dobrowolska, Wanda, Koll, Aleksander
A complex study of 5-amino-3-methyl-4-[2-(5-amino-1,3,4-oxadiazolo)]-isoxazole monohydrate: A new low-molecular-weight immune response modifier
JOURNAL OF MOLECULAR STRUCTURE, 999:60-67, JUL 27 2011 2011
abstract, full text

Liu, Bo, Ha, Matthew, Meng, Xuan-Yu, Kaur, Tanno, Khaleduzzaman, Mohammed, Zhang, Zhe, Jiang, Peihua, Li, Xia, Cui, Meng
Molecular Mechanism of Species-Dependent Sweet Taste toward Artificial Sweeteners
JOURNAL OF NEUROSCIENCE, 31:11070-11076, JUL 27 2011 2011
abstract, full text

He, Yuhui, Scheicher, Ralph H., Grigoriev, Anton, Ahuja, Rajeev, Long, Shibing, Huo, ZongLiang, Liu, Ming
Enhanced DNA Sequencing Performance Through Edge-Hydrogenation of Graphene Electrodes
ADVANCED FUNCTIONAL MATERIALS, 21:2674-2679, JUL 22 2011 2011
abstract, full text

Oezen, Ayseguel, Haliloglu, Turkan, Schiffer, Celia A.
Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope
JOURNAL OF MOLECULAR BIOLOGY, 410:726-744, JUL 22 2011 2011
abstract, full text

Dubovskii, Peter V., Vassilevski, Alexander A., Slavokhotova, Anna A., Odintsova, Tatyana I., Grishin, Eugene V., Egorov, Tsezi A., Arseniev, Alexander S.
Solution structure of a defense peptide from wheat with a 10-cysteine motif
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 411:14-18, JUL 22 2011 2011
abstract, full text

Wu, Henry H., Trinkle, Dallas R.
Direct Diffusion through Interpenetrating Networks: Oxygen in Titanium
PHYSICAL REVIEW LETTERS, 107: Art. No. 045504, JUL 22 2011 2011
abstract, full text

Bortolotti, Carlo Augusto, Siwko, Magdalena E., Castellini, Elena, Ranieri, Antonio, Sola, Marco, Corni, Stefano
The Reorganization Energy in Cytochrome c is Controlled by the Accessibility of the Heme to the Solvent
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1761-1765, JUL 21 2011 2011
abstract, full text

Baez, Mauricio, Wilson, Christian A. M., Babul, Jorge
Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: A homodimeric enzyme with a complex domain organization
FEBS LETTERS, 585:2158-2164, JUL 21 2011 2011
abstract, full text

Flechsig, Holger, Popp, Denny, Mikhailov, Alexander S.
In Silico Investigation of Conformational Motions in Superfamily 2 Helicase Proteins
PLOS ONE, 6: Art. No. e21809, JUL 19 2011 2011
abstract, full text

Kalli, Antreas C., Campbell, Iain D., Sansom, Mark S. P.
Multiscale simulations suggest a mechanism for integrin inside-out activation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:11890-11895, JUL 19 2011 2011
abstract, full text

Howard, Rebecca J., Murail, Samuel, Ondricek, Kathryn E., Corringer, Pierre-Jean, Lindahl, Erik, Trudell, James R., Harris, R. Adron
Structural basis for alcohol modulation of a pentameric ligand-gated ion channel
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:12149-12154, JUL 19 2011 2011
abstract, full text

Hirao, Hajime, Li, Feifei, Que, Lawrence, Jr., Morokuma, Keiji
Theoretical Study of the Mechanism of Oxoiron(IV) Formation from H(2)O(2) and a Nonheme Iron(II) Complex: O-O Cleavage Involving Proton-Coupled Electron Transfer
INORGANIC CHEMISTRY, 50:6637-6648, JUL 18 2011 2011
abstract, full text

Dowdle, William E., Robinson, Jon F., Kneist, Andreas, Salome Sirerol-Piquer, M., Frints, Suzanna G. M., Corbit, Kevin C., Zaghloul, Norran A., van Lijnschoten, Gesina, Mulders, Leon, Verver, Dideke E., Zerres, Klaus, Reed, Randall R., Attie-Bitach, Tania, Johnson, Colin A., Manuel Garcia-Verdugo, Jose, Katsanis, Nicholas, Bergmann, Carsten, Reiter, Jeremy E.
Disruption of a Ciliary B9 Protein Complex Causes Meckel Syndrome
AMERICAN JOURNAL OF HUMAN GENETICS, 89:94-110, JUL 15 2011 2011
abstract, full text

Tomaszewski, Jeanne E., Schwarzenbach, Rene P., Sander, Michael
Protein Encapsulation by Humic Substances
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 45:6003-6010, JUL 15 2011 2011
abstract, full text

Reyes, Anibal M., Hugo, Martin, Trostchansky, Andres, Capece, Luciana, Radi, Rafael, Trujillo, Madia
Oxidizing substrate specificity of Mycobacterium tuberculosis alkyl hydroperoxide reductase E: kinetics and mechanisms of oxidation and overoxidation
FREE RADICAL BIOLOGY AND MEDICINE, 51:464-473, JUL 15 2011 2011
abstract, full text

Heyes, D. M., Smith, E. R., Dini, D., Zaki, T. A.
The equivalence between volume averaging and method of planes definitions of the pressure tensor at a plane
JOURNAL OF CHEMICAL PHYSICS, 135: Art. No. 024512, JUL 14 2011 2011
abstract, full text

Andersson, Magnus, Freites, J. Alfredo, Tobias, Douglas J., White, Stephen H.
Structural Dynamics of the S4 Voltage-Sensor Helix in Lipid Bilayers Lacking Phosphate Groups
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8732-8738, JUL 14 2011 2011
abstract, full text

Yassin, Aymen S., Agrawal, Rajendra K., Banavali, Nilesh K.
Computational Exploration of Structural Hypotheses for an Additional Sequence in a Mammalian Mitochondrial Protein
PLOS ONE, 6: Art. No. e21871, JUL 11 2011 2011
abstract, full text

Banerjee, Rajat, Reynolds, Noah M., Yadavalli, Srujana S., Rice, Cory, Roy, Herve, Banerjee, Papri, Alexander, Rebecca W., Ibba, Michael
Mitochondrial Aminoacyl-tRNA Synthetase Single-Nucleotide Polymorphisms That Lead to Defects in Refolding but Not Aminoacylation
JOURNAL OF MOLECULAR BIOLOGY, 410:280-293, JUL 8 2011 2011
abstract, full text

Urbanc, B., Betnel, M., Cruz, L., Li, H., Fradinger, E. A., Monien, B. H., Bitan, G.
Structural Basis for A beta(1-42) Toxicity Inhibition by A beta C-Terminal Fragments: Discrete Molecular Dynamics Study
JOURNAL OF MOLECULAR BIOLOGY, 410:316-328, JUL 8 2011 2011
abstract, full text

Schurmann, Kathrin, Anton, Monika, Ivanov, Igor, Richter, Constanze, Kuhn, Hartmut, Walther, Matthias
Molecular Basis for the Reduced Catalytic Activity of the Naturally Occurring T560M Mutant of Human 12/15-Lipoxygenase That Has Been Implicated in Coronary Artery Disease
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:23920-23927, JUL 8 2011 2011
abstract, full text

Watson, Aleksandra A., Lebedev, Andrey A., Hall, Benjamin A., Fenton-May, Angharad E., Vagin, Alexei A., Dejnirattisai, Wanwisa, Felce, James, Mongkolsapaya, Juthathip, Palma, Angelina S., Liu, Yan, Feizi, Ten, Screaton, Gavin R., Murshudov, Garib N., O'Callaghan, Christopher A.
Structural Flexibility of the Macrophage Dengue Virus Receptor CLEC5A IMPLICATIONS FOR LIGAND BINDING AND SIGNALING
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:24208-24218, JUL 8 2011 2011
abstract, full text

Hamacher, Kay
Free energy of contact formation in proteins: Efficient computation in the elastic network approximation
PHYSICAL REVIEW E, 84: Art. No. 016703, JUL 7 2011 2011
abstract, full text

Hughto, J., Schneider, A. S., Horowitz, C. J., Berry, D. K.
Diffusion in Coulomb crystals
PHYSICAL REVIEW E, 84: Art. No. 016401, JUL 7 2011 2011
abstract, full text

Payne, Christina M., Himmel, Michael E., Crowley, Michael F., Beckham, Gregg T.
Decrystallization of Oligosaccharides from the Cellulose I beta Surface with Molecular Simulation
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1546-1550, JUL 7 2011 2011
abstract, full text

Lin, Bin, Wong, Ka-Yiu, Hu, Char, Kokubo, Hironori, Pettitt, B. Montgomery
Fast Calculations of Electrostatic Solvation Free Energy from Reconstructed Solvent Density Using Proximal Radial Distribution Functions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2:1626-1632, JUL 7 2011 2011
abstract, full text

Mohammed, Omar F., Luber, Sandra, Batista, Victor S., Nibbering, Erik T. J.
Ultrafast Branching of Reaction Pathways in 2-(2 '-Hydroxyphenyl)benzothiazole in Polar Acetonitrile Solution
JOURNAL OF PHYSICAL CHEMISTRY A, 115:7550-7558, JUL 7 2011 2011
abstract, full text

Restrepo, Oscar A., Delcorte, Arnaud
Au(400) Sputtering of a Polymer with Adsorbed Metal Nanoparticles: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY C, 115:12751-12759, JUL 7 2011 2011
abstract, full text

Garrec, J., Sautet, P., Fleurat-Lessard, P.
Understanding the HIV-1 Protease Reactivity with DFT: What Do We Gain from Recent Functionals?
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8545-8558, JUL 7 2011 2011
abstract, full text

Olbrich, Carsten, Jansen, Thomas L. C., Liebers, Joerg, Aghtar, Mortaza, Struempfer, Johan, Schulten, Klaus, Knoester, Jasper, Kleinekathoefer, Ulrich
From Atomistic Modeling to Excitation Transfer and Two-Dimensional Spectra of the FMO Light-Harvesting Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8609-8621, JUL 7 2011 2011
abstract, full text

Rommel, Judith B., Kaestner, Johannes
The Fragmentation-Recombination Mechanism of the Enzyme Glutamate Mutase Studied by QM/MM Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:10195-10203, JUL 6 2011 2011
abstract, full text

Gamini, Ramya, Sotomayor, Marcos, Chipot, Christophe, Schulten, Klaus
Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance
BIOPHYSICAL JOURNAL, 101:80-89, JUL 6 2011 2011
abstract, full text

Kanudia, Pavitra, Mittal, Monica, Kumaran, Sangaralingam, Chakraborti, Pradip K.
Amino-terminal extension present in the methionine aminopeptidase type 1c of Mycobacterium tuberculosis is indispensible for its activity
BMC BIOCHEMISTRY, 12: Art. No. 35, JUL 5 2011 2011
abstract, full text

Cristiani, Andrea, Costa, Giorgio, Cozza, Giorgio, Meggio, Flavio, Scapozza, Leonardo, Moro, Stefano
The Role of the N-Terminal Domain in the Regulation of the "Constitutively Active" Conformation of Protein Kinase CK2 alpha: Insight from a Molecular Dynamics Investigation
CHEMMEDCHEM, 6:1207-1216, JUL 4 2011 2011
abstract, full text

Santo, Kolattukudy P., Berjanskii, Mark, Wishart, David S., Stepanova, Maria
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins
PRION, 5:188-200, JUL-SEP 2011 2011
abstract, full text

Kralikova, Sarka, Budesinsky, Milos, Barvik, Ivan, Masojidkova, Milena, Tocik, Zdenek, Rosenberg, Ivan
SYNTHESIS AND PROPERTIES OF ApA ANALOGUES WITH SHORTENED PHOSPHONATE INTERNUCLEOTIDE LINKAGE
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 30:524-543, JUL-SEP 2011 2011
abstract, full text

Amarasinghe, Priyanthi M., Anandarajah, A.
Influence of fabric variables on clay-water-air capillary meniscus
CANADIAN GEOTECHNICAL JOURNAL, 48:987-995, JUL 2011 2011
abstract, full text

Amaro, Rommie E., Swift, Robert V., Votapka, Lane, Li, Wilfred W., Walker, Ross C., Bush, Robin M.
Mechanism of 150-cavity formation in influenza neuraminidase
NATURE COMMUNICATIONS, 2: Art. No. 388, JUL 2011 2011
abstract, full text

Kuan, Chee Sian, Wong, Mun Teng, Choi, Sy Bing, Chang, Ching Ching, Yee, Yoke Hiang, Wahab, Habibah A., Normi, Yahaya Mohd, Ling, Wei Cun See Too, Few, Ling Ling
Klebsiella pneumoniae yggG Gene Product: A Zinc-Dependent Metalloprotease
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 12:4441-4455, JUL 2011 2011
abstract, full text

Schmid, Nathan, Eichenberger, Andreas P., Choutko, Alexandra, Riniker, Sereina, Winger, Moritz, Mark, Alan E., van Gunsteren, Wilfred F.
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:843-856, JUL 2011 2011
abstract, full text

Baio, J. E., Weidner, T., Interlandi, G., Mendoza-Barrera, C., Canavan, H. E., Michel, R., Castner, D. G.
Probing albumin adsorption onto calcium phosphates by x-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry
JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B, 29: Art. No. 04D113, JUL 2011 2011
abstract, full text

Romanowska, Julia, McCammon, J. Andrew, Trylska, Joanna
Understanding the Origins of Bacterial Resistance to Aminoglycosides through Molecular Dynamics Mutational Study of the Ribosomal A-Site
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002099, JUL 2011 2011
abstract, full text

Wang, Qian, Liang, Kao-Chen, Czader, Arkadiusz, Waxham, M. Neal, Cheung, Margaret S.
The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002114, JUL 2011 2011
abstract, full text

Pellequer, Jean-Luc, Chen, Shu-wen W., Saboulard, Didier, Delcourt, Marc, Negrier, Claude, Plantier, Jean-Luc
Functional mapping of factor VIII C2 domain
THROMBOSIS AND HAEMOSTASIS, 106:121-131, JUL 2011 2011
abstract, full text

Iacovache, Ioan, Degiacomi, Matteo T., Pernot, Lucile, Ho, Sylvia, Schiltz, Marc, Dal Peraro, Matteo, van der Goot, F. Gisou
Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
PLOS PATHOGENS, 7: Art. No. e1002135, JUL 2011 2011
abstract, full text

Lashkov, A. A., Zhukhlistova, N. E., Seregina, T. A., Gabdulkhakov, A. G., Mikhailov, A. M.
Uridine phosphorylase in biomedical, structural, and functional aspects: A review
CRYSTALLOGRAPHY REPORTS, 56:560-589, JUL 2011 2011
abstract, full text

Dumit, Veronica I., Cortez, Nestor, Ullmann, G. Matthias
Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2076-2085, JUL 2011 2011
abstract, full text

Chng, Choon-Peng, Tan, Suet-Mien
Leukocyte integrin alpha L beta 2 transmembrane association dynamics revealed by coarse-grained molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2203-2213, JUL 2011 2011
abstract, full text

Spronk, Steven A., Carlson, Heather A.
The role of tyrosine 71 in modulating the flap conformations of BACE1
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2247-2259, JUL 2011 2011
abstract, full text

Janosi, Lorant, Keer, Harindar, Cogdell, Richard J., Ritz, Thorsten, Kosztin, Ioan
In silico predictions of LH2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:2306-2315, JUL 2011 2011
abstract, full text

Thaulow, Christian, Schieffer, Stella V., Vatne, Inga R., Sen, Dipanjan, Ostby, Erling
Crack Tip Opening Displacement in atomistic modeling of fracture of silicon
COMPUTATIONAL MATERIALS SCIENCE, 50:2621-2627, JUL 2011 2011
abstract, full text

Soriano-Ursua, Marvin A., Ocampo-Lopez, Jorge O., Ocampo-Mendoza, Karina, Trujillo-Ferrara, Jose G., Correa-Basurto, Jose
Theoretical study of 3-D molecular similarity and ligand binding modes of orthologous human and rat D(2) dopamine receptors
COMPUTERS IN BIOLOGY AND MEDICINE, 41:537-545, JUL 2011 2011
abstract, full text

Wong, Kin-Yiu, Gao, Jiali
Insight into the phosphodiesterase mechanism from combined QM/MM free energy simulations
FEBS JOURNAL, 278:2579-2595, JUL 2011 2011
abstract, full text

Helmann, John D.
New dimensions at Molecular Microbiology: 3D graphics and the Wiley Online Library
MOLECULAR MICROBIOLOGY, 81:295-296, JUL 2011 2011
full text

Tseng, Chih-Yuan, Ashrafuzzaman, Md, Mane, Jonathan Y., Kapty, Janice, Mercer, John R., Tuszynski, Jack A.
Entropic Fragment-Based Approach to Aptamer Design
CHEMICAL BIOLOGY & DRUG DESIGN, 78:1-13, JUL 2011 2011
abstract, full text

Jacobson, Leif D., Herbert, John M.
A Simple Algorithm for Determining Orthogonal, Self-Consistent Excited-State Wave Functions for a State-Specific Hamiltonian: Application to the Optical Spectrum of the Aqueous Electron
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2085-2093, JUL 2011 2011
abstract, full text

Sondergaard, Chresten R., Olsson, Mats H. M., Rostkowski, Michal, Jensen, Jan H.
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pK(a) Values
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:2284-2295, JUL 2011 2011
abstract, full text

Catoire, Laurent J., Damian, Marjorie, Baaden, Marc, Guittet, Eric, Baneres, Jean-Louis
Electrostatically-driven fast association and perdeuteration allow detection of transferred cross-relaxation for G protein-coupled receptor ligands with equilibrium dissociation constants in the high-to-low nanomolar range
JOURNAL OF BIOMOLECULAR NMR, 50:191-195, JUL 2011 2011
abstract, full text

Talavera, Ariel, Mackenzie, Jenny, Garrido, Greta, Friemann, Rosmarie, Lopez-Requena, Alejandro, Moreno, Ernesto, Krengel, Ute
Structure of the Fab fragment of the anti-murine EGFR antibody 7A7 and exploration of its receptor binding site
MOLECULAR IMMUNOLOGY, 48:1578-1585, JUL 2011 2011
abstract, full text

Martinez, Ronny, Schwaneberg, Ulrich, Roccatano, Danilo
Temperature effects on structure and dynamics of the psychrophilic protease subtilisin S41 and its thermostable mutants in solution
PROTEIN ENGINEERING DESIGN & SELECTION, 24:533-544, JUL 2011 2011
abstract, full text

Perez-Siles, Gonzalo, Morreale, Antonio, Leo-Macias, Alejandra, Pita, Guillermo, Ortiz, Angel R., Aragon, Carmen, Lopez-Corcuera, Beatriz
Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2
JOURNAL OF NEUROCHEMISTRY, 118:195-204, JUL 2011 2011
abstract, full text

Hidalgo, Alvaro, Carvajal, Ana, Vester, Birte, Pringle, Marit, Naharro, German, Rubio, Pedro
Trends towards Lower Antimicrobial Susceptibility and Characterization of Acquired Resistance among Clinical Isolates of Brachyspira hyodysenteriae in Spain
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 55:3330-3337, JUL 2011 2011
abstract, full text

Nair, A. K., Cranford, S. W., Buehler, M. J.
The minimal nanowire: Mechanical properties of carbyne
EPL, 95: Art. No. 16002, JUL 2011 2011
abstract, full text

Jevnikar, Zala, Obermajer, Natasa, Doljak, Bojan, Turk, Samo, Gobec, Stanislav, Svajger, Urban, Hailfinger, Stephan, Thome, Margot, Kos, Janko
Cathepsin X cleavage of the beta(2) integrin regulates talin-binding and LFA-1 affinity in T cells
JOURNAL OF LEUKOCYTE BIOLOGY, 90:99-109, JUL 2011 2011
abstract, full text

Strunk, Timo, Hamacher, Kay, Hoffgaard, Franziska, Engelhardt, Harald, Zillig, Martina Daniela, Faist, Karin, Wenzel, Wolfgang, Pfeifer, Felicitas
Structural model of the gas vesicle protein GvpA and analysis of GvpA mutants in vivo
MOLECULAR MICROBIOLOGY, 81:56-68, JUL 2011 2011
abstract, full text

Coluzza, Ivan
A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding
PLOS ONE, 6: Art. No. e20853, JUL 1 2011 2011
abstract, full text

Fujiwara, Shin-ichi, Amisaki, Takashi
Steric and Allosteric Effects of Fatty Acids on the Binding of Warfarin to Human Serum Albumin Revealed by Molecular Dynamics and Free Energy Calculations
CHEMICAL & PHARMACEUTICAL BULLETIN, 59:860-867, JUL 2011 2011
abstract, full text

Blanchet, Christophe, Pasi, Marco, Zakrzewska, Krystyna, Lavery, Richard
CURVES plus web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures
NUCLEIC ACIDS RESEARCH, 39:W68-W73, JUL 2011 2011
abstract, full text

Tavoosi, Narjes, Davis-Harrison, Rebecca L., Pogorelov, Taras V., Ohkubo, Y. Zenmei, Arcario, Mark J., Clay, Mary C., Rienstra, Chad M., Tajkhorshid, Emad, Morrissey, James H.
Molecular Determinants of Phospholipid Synergy in Blood Clotting
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:23247-23253, JUL 1 2011 2011
abstract, full text

Credali, Alfredo, Diaz-Quintana, Antonio, Garcia-Calderon, Margarita, De la Rosa, Miguel A., Marquez, Antonio J., Vega, Jose M.
Structural analysis of K(+) dependence in l-asparaginases from Lotus japonicus
PLANTA, 234:109-122, JUL 2011 2011
abstract, full text

Ohnuma, Takayuki, Numata, Tomoyuki, Osawa, Takuo, Mizuhara, Mamiko, Lampela, Outi, Juffer, Andre H., Skriver, Karen, Fukamizo, Tamo
A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis
PLANTA, 234:123-137, JUL 2011 2011
abstract, full text

Araujo-Alvarez, Juan M., Trujillo-Ferrara, Jose G., Ponce-Franco, Daniel, Correa-Basurto, Jose, Delgado, Alfonso, Querejeta, Enrique
(+)-(S)-Trujillon, (+)-(S)-4-(2,2-Diphenyl-1,3,2-oxazabolidin-5-oxo)propionic acid, a Novel Glutamatergic Analog, Modifies the Activity of Globus Pallidus Neurons by Selective NMDA Receptor Activation
CHIRALITY, 23:429-437, JUL 2011 2011
abstract, full text

Mayo, Daniel, Zhou, Andy, Sahu, Indra, McCarrick, Robert, Walton, Parker, Ring, Adam, Troxel, Kaylee, Coey, Aaron, Hawn, Jaclyn, Emwas, Abdul-Hamid, Lorigan, Gary A.
Probing the structure of membrane proteins with electron spin echo envelope modulation spectroscopy
PROTEIN SCIENCE, 20:1100-1104, JUL 2011 2011
abstract, full text

Cranford, Steven, Buehler, Markus J.
Twisted and coiled ultralong multilayer graphene ribbons
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, 19: Art. No. 054003, JUL 2011 2011
abstract, full text

Sokkar, Pandian, Mohandass, Shylajanaciyar, Ramachandran, Murugesan
Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking
JOURNAL OF MOLECULAR MODELING, 17:1565-1577, JUL 2011 2011
abstract, full text

Khrenova, Maria, Domratcheva, Tatiana, Grigorenko, Bella, Nemukhin, Alexander
Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1
JOURNAL OF MOLECULAR MODELING, 17:1579-1586, JUL 2011 2011
abstract, full text

Lee, Angelina Noviani, Hartono, Yossa Dwi, Sun, Tiedong, Leow, Min Li, Liu, Xue-wei, Huang, Xuri, Zhang, Dawei
Molecular dynamics studies of human receptor molecule in hemagglutinin of 1918 and 2009 H1N1 influenza viruses
JOURNAL OF MOLECULAR MODELING, 17:1635-1641, JUL 2011 2011
abstract, full text

Hu, Mingwen, Kim, Byung
Flexibility of the exportins Cse1p and Xpot depicted by elastic network model
JOURNAL OF MOLECULAR MODELING, 17:1735-1741, JUL 2011 2011
abstract, full text

Stavrakoudis, Athanassios, Tsoulos, Ioannis G., Uray, Katalin, Ferenc, Hudecz, Apostolopoulos, Vasso
Homology modeling and molecular dynamics simulations of MUC1-9/H-2K(b) complex suggest novel binding interactions
JOURNAL OF MOLECULAR MODELING, 17:1817-1829, JUL 2011 2011
abstract, full text

Weston, Chris J., Adams, David H.
Hepatic consequences of vascular adhesion protein-1 expression
JOURNAL OF NEURAL TRANSMISSION, 118:1055-1064, JUL 2011 2011
abstract, full text

Rawat, Manmeet, Vijay, Sonam, Gupta, Yash, Dixit, Rajnikant, Tiwari, P. K., Sharma, Arun
Sequence homology and structural analysis of plasmepsin 4 isolated from Indian Plasmodium vivax isolates
INFECTION GENETICS AND EVOLUTION, 11:924-933, JUL 2011 2011
abstract, full text

Stavrakoudis, Athanassios
Insights into the structure of the LC13 TCR/HLA-B8-EBV peptide complex with molecular dynamics simulations
CELL BIOCHEMISTRY AND BIOPHYSICS, 60:283-295, JUL 2011 2011
abstract, full text

Raliou, Mariam, Grauso, Marta, Hoffmann, Brice, Schlegel-Le-Poupon, Claire, Nespoulous, Claude, Debat, Helene, Belloir, Christine, Wiencis, Anna, Sigoillot, Maud, Bano, Singh Preet, Trotier, Didier, Pernollet, Jean-Claude, Montmayeur, Jean-Pierre, Faurion, Annick, Briand, Loic
Human Genetic Polymorphisms in T1R1 and T1R3 Taste Receptor Subunits Affect Their Function
CHEMICAL SENSES, 36:527-537, JUL 2011 2011
abstract, full text

Mitson, Matthew, Kelley, Lawrence A., Sternberg, Michael J. E., Higgs, Douglas R., Gibbons, Richard J.
Functional significance of mutations in the Snf2 domain of ATRX
HUMAN MOLECULAR GENETICS, 20:2603-2610, JUL 1 2011 2011
abstract, full text

Kaila, Ville R. I., Oksanen, Esko, Goldman, Adrian, Bloch, Dmitry A., Verkhovsky, Michael I., Sundholm, Dage, Wikstrom, Marten
A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:769-778, JUL 2011 2011
abstract, full text

Sharma, Vivek, Wikstrom, Marten, Kaila, Ville R. I.
Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb(3)
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:813-818, JUL 2011 2011
abstract, full text

Lee, Kyung-Hoon, Kuczera, Krzysztof, Holl, Mark M. Banaszak
Effect of osteogenesis imperfecta mutations on free energy of collagen model peptides: A molecular dynamics simulation
BIOPHYSICAL CHEMISTRY, 156:146-152, JUL 2011 2011
abstract, full text

Bueyuekoeztuerk, Oral, Buehler, Markus J., Lau, Denvid, Tuakta, Chakrapan
Structural solution using molecular dynamics: Fundamentals and a case study of epoxy-silica interface
INTERNATIONAL JOURNAL OF SOLIDS AND STRUCTURES, 48:2131-2140, JUL 2011 2011
abstract, full text

Sicca, Federico, Imbrici, Paola, D'Adamo, Maria Cristina, Moro, Francesca, Bonatti, Fabrizia, Brovedani, Paola, Grottesi, Alessandro, Guerrini, Renzo, Masi, Gabriele, Santorelli, Filippo Maria, Pessia, Mauro
Autism with Seizures and Intellectual Disability: Possible Causative Role of Gain-of-function of the Inwardly-Rectifying K(+) Channel Kir4.1
NEUROBIOLOGY OF DISEASE, 43:239-247, JUL 2011 2011
abstract, full text

Narayanan, Sai Shyam, Sokkar, Pandian, Ramachandran, Murugesan, Nampoothiri, Kesavan Madhavan
Glycine in the conserved motif III modulates the thermostability and oxidative stress resistance of peptide deformylase in Mycobacterium tuberculosis
FEMS MICROBIOLOGY LETTERS, 320:40-47, JUL 2011 2011
abstract, full text

Kleinekathoefer, Ulrich, Isralewitz, Barry, Dittrich, Markus, Schulten, Klaus
Domain Motion of Individual F(1)-ATPase beta-Subunits during Unbiased Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 115:7267-7274, JUN 30 2011 2011
abstract, full text

Malek, Kourosh, Franco, Alejandro A.
Microstructure-Based Modeling of Aging Mechanisms in Catalyst Layers of Polymer Electrolyte Fuel Cells
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8088-8101, JUN 30 2011 2011
abstract, full text

Liang, Xiao, Montoya, Alejandro, Haynes, Brian S.
Molecular Dynamics Study of Acid-Catalyzed Hydrolysis of Dimethyl Ether in Aqueous Solution
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8199-8206, JUN 30 2011 2011
abstract, full text

Schulz, Robert, Vargiu, Attilio V., Ruggerone, Paolo, Kleinekathoefer, Ulrich
Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8278-8287, JUN 30 2011 2011
abstract, full text

Wolfson, Mikhail Y., Nam, Kwangho, Chakraborty, Arup K.
The Effect of Mutations on the Alloreactive T Cell Receptor/Peptide-MHC Interface Structure: A Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8317-8327, JUN 30 2011 2011
abstract, full text

Veeraraghavan, Narayanan, Ganguly, Abir, Golden, Barbara L., Bevilacqua, Philip C., Hammes-Schiffer, Sharon
Mechanistic Strategies in the HDV Ribozyme: Chelated and Diffuse Metal Ion Interactions and Active Site Protonation
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8346-8357, JUN 30 2011 2011
abstract, full text

Mtei, Regina P., Lyashenko, Ganna, Stein, Benjamin, Rubie, Nick, Hille, Russ, Kirk, Martin L.
Spectroscopic and Electronic Structure Studies of a Dimethyl Sulfoxide Reductase Catalytic Intermediate: Implications for Electron- and Atom-Transfer Reactivity
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9762-9774, JUN 29 2011 2011
abstract, full text

White, Katherine H., Orzechowski, Marek, Fourmy, Dominique, Visscher, Koen
Mechanical Unfolding of the Beet Western Yellow Virus-1 Frameshift Signal
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9775-9782, JUN 29 2011 2011
abstract, full text

Heddi, Brahim, Anh Tuan Phan
Structure of Human Telomeric DNA in Crowded Solution
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9824-9833, JUN 29 2011 2011
abstract, full text

Leonov, Hadas, Astrahan, Peleg, Krugliak, Miriam, Arkin, Isaiah T.
How Do Aminoadamantanes Block the Influenza M2 Channel, and How Does Resistance Develop?
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9903-9911, JUN 29 2011 2011
abstract, full text

Borkar, Aditi Narendra, Rout, Manoj Kumar, Hosur, Ramakrishna V.
Visualization of Early Events in Acetic Acid Denaturation of HIV-1 Protease: A Molecular Dynamics Study
PLOS ONE, 6: Art. No. e19830, JUN 29 2011 2011
abstract, full text

Zimmermann, Michael T., Kloczkowski, Andrzej, Jernigan, Robert L.
MAVENs: Motion analysis and visualization of elastic networks and structural ensembles
BMC BIOINFORMATICS, 12: Art. No. 264, JUN 28 2011 2011
abstract, full text

Truong, Khue, Su, Yang, Song, Jing, Chen, Yuan
Entropy-Driven Mechanism of an E3 Ligase
BIOCHEMISTRY, 50:5757-5766, JUN 28 2011 2011
abstract, full text

Furini, Simone, Domene, Carmen
Selectivity and Permeation of Alkali Metal Ions in K(+)-channels
JOURNAL OF MOLECULAR BIOLOGY, 409:867-878, JUN 24 2011 2011
abstract, full text

Alberti, Margarita, Pirani, Fernando
Features of Ar Solvation Shells in Neutral and Ionic Clustering: The Competitive Role of Two-Body and Many-Body Interactions
JOURNAL OF PHYSICAL CHEMISTRY A, 115:6394-6404, JUN 23 2011 2011
abstract, full text

Lee, Hwankyu, Pastor, Richard W.
Coarse-Grained Model for PEGylated Lipids: Effect of PEGylation on the Size and Shape of Self-Assembled Structures
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7830-7837, JUN 23 2011 2011
abstract, full text

Kolar, Michal, Kubar, Tomas, Hobza, Pavel
On the Role of London Dispersion Forces in Biomolecular Structure Determination
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8038-8046, JUN 23 2011 2011
abstract, full text

Milani, Alberto, Casalegno, Mose, Castiglioni, Chiara, Raos, Guido
Coarse-Grained Simulations of Model Polymer Nanofibres
MACROMOLECULAR THEORY AND SIMULATIONS, 20:305-319, JUN 22 2011 2011
abstract, full text

Shagolsem, Lenin S., Sommer, Jens-Uwe
Order and Phase Behavior of a Cylinder Forming Diblock Copolymers and Nano-Particles Mixture in Confinement: A Molecular Dynamics Study
MACROMOLECULAR THEORY AND SIMULATIONS, 20:329-339, JUN 22 2011 2011
abstract, full text

Ahadi, Elias, Konermann, Lars
Ejection of Solvated Ions from Electrosprayed Methanol/Water Nanodroplets Studied by Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:9354-9363, JUN 22 2011 2011
abstract, full text

Liu, Yanxin, Hsin, Jen, Kim, HyeongJun, Selvin, Paul R., Schulten, Klaus
Extension of a Three-Helix Bundle Domain of Myosin VI and Key Role of Calmodulins
BIOPHYSICAL JOURNAL, 100:2964-2973, JUN 22 2011 2011
abstract, full text

Jones, Peter M., George, Anthony M.
Molecular-Dynamics Simulations of the ATP/apo State of a Multidrug ATP-Binding Cassette Transporter Provide a Structural and Mechanistic Basis for the Asymmetric Occluded State
BIOPHYSICAL JOURNAL, 100:3025-3034, JUN 22 2011 2011
abstract, full text

Parthasarathy, Sudharsan, Altuve, Adriana, Terzyan, Simon, Zhang, Xuejun, Kuczera, Krzysztof, Rivera, Mario, Benson, David R.
Accommodating a Nonconservative Internal Mutation by Water-Mediated Hydrogen Bonding between beta-Sheet Strands: A Comparison of Human and Rat Type B (Mitochondrial) Cytochrome b(5)
BIOCHEMISTRY, 50:5544-5554, JUN 21 2011 2011
abstract, full text

Wu, Sangwook, Liu, Shubin, Davis, Charles H., Stafford, Darrel W., Kulman, John D., Pedersen, Lee G.
A hetero-dimer model for concerted action of vitamin K carboxylase and vitamin K reductase in vitamin K cycle
JOURNAL OF THEORETICAL BIOLOGY, 279:143-149, JUN 21 2011 2011
abstract, full text

Wang, B., Pantelides, S. T.
Controllable healing of defects and nitrogen doping of graphene by CO and NO molecules
PHYSICAL REVIEW B, 83: Art. No. 245403, JUN 17 2011 2011
abstract, full text

Karayiannis, Nikos Ch., Malshe, Rohit, de Pablo, Juan J., Laso, Manuel
Fivefold symmetry as an inhibitor to hard-sphere crystallization
PHYSICAL REVIEW E, 83: Art. No. 061505, JUN 16 2011 2011
abstract, full text

Muchova, Eva, Gladich, Ivan, Picaud, Sylvain, Hoang, Paul N. M., Roeselova, Martina
The Ice-Vapor Interface and the Melting Point of Ice I(h) for the Polarizable POL3 Water Model
JOURNAL OF PHYSICAL CHEMISTRY A, 115:5973-5982, JUN 16 2011 2011
abstract, full text

Mason, Phillip E.
Molecular Dynamics Study on the Microscopic Details of the Evaporation of Water
JOURNAL OF PHYSICAL CHEMISTRY A, 115:6054-6058, JUN 16 2011 2011
abstract, full text

Henry, Rowan M., Caplan, David, Fadda, Elisa, Pomes, Regis
Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase
JOURNAL OF PHYSICS-CONDENSED MATTER, 23: Art. No. 234102, JUN 15 2011 2011
abstract, full text

Quevedo, Mario A., Nieto, Leandro E., Brinon, Margarita C.
P-glycoprotein limits the absorption of the anti-HIV drug zidovudine through rat intestinal segments
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES, 43:151-159, JUN 14 2011 2011
abstract, full text

Tian, Jianhui, Garcia, Angel E.
Simulations of the confinement of ubiquitin in self-assembled reverse micelles
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 225101, JUN 14 2011 2011
abstract, full text

Dougan, Lorna, Genchev, Georgi Z., Lu, Hui, Fernandez, Julio M.
Probing osmolyte participation in the unfolding transition state of a protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:9759-9764, JUN 14 2011 2011
abstract, full text

Xu, Lin, Sang, Peng, Zou, Jian-Wei, Xu, Ming-Biao, Li, Xue-Ming, Yu, Qing-Sen
Evaluation of nucleotide C-Br center dot center dot center dot O-P contacts from ONIOM calculations: Theoretical insight into halogen bonding in nucleic acids
CHEMICAL PHYSICS LETTERS, 509:175-180, JUN 14 2011 2011
abstract, full text

Mitra, Devrani, Pelmenschikov, Vladimir, Guo, Yisong, Case, David A., Wang, Hongxin, Dong, Weibing, Tan, Ming-Liang, Ichiye, Toshiko, Jenney, Francis E., Jr., Adams, Michael W. W., Yoda, Yoshitaka, Zhao, Jiyong, Cramer, Stephen P.
Dynamics of the [4Fe-4S] Cluster in Pyrococcus furiosus D14C Ferredoxin via Nuclear Resonance Vibrational and Resonance Raman Spectroscopies, Force Field Simulations, and Density Functional Theory Calculations
BIOCHEMISTRY, 50:5220-5235, JUN 14 2011 2011
abstract, full text

Arias, Hugo R., Gu, Ruo-Xu, Feuerbach, Dominik, Guo, Bao-Bao, Ye, Yong, Wei, Dong-Qing
Novel Positive Allosteric Modulators of the Human alpha 7 Nicotinic Acetylcholine Receptor
BIOCHEMISTRY, 50:5263-5278, JUN 14 2011 2011
abstract, full text

Guo, Taiyu, Ding, Tony Weixi, Pei, Qing-Xiang, Zhang, Yong-Wei
Effect of sp(3)-hybridized defects on the oscillatory behavior of carbon nanotube oscillators
PHYSICS LETTERS A, 375:2400-2404, JUN 13 2011 2011
abstract, full text

Warenius, Hilmar M., Kilburn, Jeremy D., Essex, Jon W., Maurer, Richard I., Blaydes, Jeremy P., Agarwala, Usha, Seabra, Laurence A.
Selective anticancer activity of a hexapeptide with sequence homology to a non-kinase domain of Cyclin Dependent Kinase 4
MOLECULAR CANCER, 10: Art. No. 75, JUN 13 2011 2011
abstract, full text

Wei, Dong-Qing, Gao, Lin, Zhang, Jiao, Yan, Li-Wei, Hu, Jin-He, Chen, Lang, Gong, Zi-Zheng, Guo, Yong-Xin, Han, Yu
Role of dipole elongation in orientationally ordered liquids
PHYSICAL REVIEW E, 83: Art. No. 061703, JUN 10 2011 2011
abstract, full text

Wieninger, Silke A., Serpersu, Engin H., Ullmann, G. Matthias
ATP Binding Enables Broad Antibiotic Selectivity of Aminoglycoside Phosphotransferase(3 ')-IIIa: An Elastic Network Analysis
JOURNAL OF MOLECULAR BIOLOGY, 409:450-465, JUN 10 2011 2011
abstract, full text

Jahnen-Dechent, Willi, Heiss, Alexander, Schaefer, Cora, Ketteler, Markus
Fetuin-A Regulation of Calcified Matrix Metabolism
CIRCULATION RESEARCH, 108:1494-1509, JUN 10 2011 2011
abstract, full text

Wickham, Stephanie E., Hotze, Eileen M., Farrand, Allison J., Polekhina, Galina, Nero, Tracy L., Tomlinson, Stephen, Parker, Michael W., Tweten, Rodney K.
Mapping the Intermedilysin-Human CD59 Receptor Interface Reveals a Deep Correspondence with the Binding Site on CD59 for Complement Binding Proteins C8 alpha and C9
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:20952-20962, JUN 10 2011 2011
abstract, full text

Riihimaki, Tiina A., Hiltunen, Soili, Rangl, Martina, Nordlund, Henri R., Maatta, Juha Ae, Ebner, Andreas, Hinterdorfer, Peter, Kulomaa, Markku S., Takkinen, Kristiina, Hytonen, Vesa P.
Modification of the loops in the ligand-binding site turns avidin into a steroid-binding protein
BMC BIOTECHNOLOGY, 11: Art. No. 64, JUN 9 2011 2011
abstract, full text

Dixit, Purushottam D., Asthagiri, D.
An Elastic-Network-Based Local Molecular Field Analysis of Zinc Finger Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7374-7382, JUN 9 2011 2011
abstract, full text

Radford, Isolde H., Fersht, Alan R., Settanni, Giovanni
Combination of Markov State Models and Kinetic Networks for the Analysis of Molecular Dynamics Simulations of Peptide Folding
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7459-7471, JUN 9 2011 2011
abstract, full text

Tanner, David E., Ma, Wen, Chen, Zhongzhou, Schulten, Klaus
Theoretical and Computational Investigation of Flagellin Translocation and Bacterial Flagellum Growth
BIOPHYSICAL JOURNAL, 100:2548-2556, JUN 8 2011 2011
abstract, full text

Sun, Chongbo, Tang, Tian, Uludag, Hasan, Cuervo, Javier E.
Molecular Dynamics Simulations of DNA/PEI Complexes: Effect of PEI Branching and Protonation State
BIOPHYSICAL JOURNAL, 100:2754-2763, JUN 8 2011 2011
abstract, full text

Bereau, Tristan, Deserno, Markus, Bachmann, Michael
Structural Basis of Folding Cooperativity in Model Proteins: Insights from a Microcanonical Perspective
BIOPHYSICAL JOURNAL, 100:2764-2772, JUN 8 2011 2011
abstract, full text

Yu, Xiang, Zheng, Jie
Polymorphic Structures of Alzheimer's beta-Amyloid Globulomers
PLOS ONE, 6: Art. No. e20575, JUN 7 2011 2011
abstract, full text

Bonner, Lisa A., Laban, Uros, Chemel, Benjamin R., Juncosa, Jose I., Lill, Markus A., Watts, Val J., Nichols, David E.
Mapping the Catechol Binding Site in Dopamine D(1) Receptors: Synthesis and Evaluation of Two Parallel Series of Bicyclic Dopamine Analogues
CHEMMEDCHEM, 6:1024-1040, JUN 6 2011 2011
abstract, full text

Orsi, Mario, Noro, Massimo G., Essex, Jonathan W.
Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 8:826-841, JUN 6 2011 2011
abstract, full text

Teufel, Daniel P., Johnson, Christopher M., Lum, Jenifer K., Neuweiler, Hannes
Backbone-Driven Collapse in Unfolded Protein Chains
JOURNAL OF MOLECULAR BIOLOGY, 409:250-262, JUN 3 2011 2011
abstract, full text

Walsh, Jason M., Bouamaied, Imenne, Brown, Tom, Wilhelmsson, L. Marcus, Beuning, Penny J.
Discrimination against the Cytosine Analog tC by Escherichia coli DNA Polymerase IV DinB
JOURNAL OF MOLECULAR BIOLOGY, 409:89-100, JUN 3 2011 2011
abstract, full text

Zomot, Elia, Bahar, Ivet
Protonation of Glutamate 208 Induces the Release of Agmatine in an Outward-facing Conformation of an Arginine/Agmatine Antiporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:19693-19701, JUN 3 2011 2011
abstract, full text

Dai, Zheng-Wei, Ling, Jun, Huang, Xiao-Jun, Wan, Ling-Shu, Xu, Zhi-Kang
Molecular Simulation on the Interactions of Water with Polypropylene Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 115:10702-10708, JUN 2 2011 2011
abstract, full text

Madsen, Jesper J., Linderoth, Lars, Subramanian, Arun K., Andresen, Thomas L., Peters, Gunther H.
Secretory Phospholipase A(2) Activity toward Diverse Substrates
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6853-6861, JUN 2 2011 2011
abstract, full text

Arcario, Mark J., Ohkubo, Y. Zenmei, Tajkhorshid, Emad
Capturing Spontaneous Partitioning of Peripheral Proteins Using a Biphasic Membrane-Mimetic Model
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7029-7037, JUN 2 2011 2011
abstract, full text

Sousa, Sergio Filipe, Tamames, Bruno, Fernandes, Pedro Alexandrino, Ramos, Maria Joao
Detailed Atomistic Analysis of the HIV-1 Protease Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7045-7057, JUN 2 2011 2011
abstract, full text

Verde, Ana Vila, Campen, R. Kramer
Disaccharide Topology Induces Slowdown in Local Water Dynamics
JOURNAL OF PHYSICAL CHEMISTRY B, 115:7069-7084, JUN 2 2011 2011
abstract, full text

Tan, Yaw Sing, Fuentes, Gloria, Verma, Chandra
A comparison of the dynamics of Pantothenate Synthetase from M. tuberculosis and E. coli: Computational studies
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1715-1727, JUN 2011 2011
abstract, full text

Li, Cui, Shen, Jie, Li, Weihua, Lu, Chunhua, Liu, Guixia, Tang, Yun
Possible ligand release pathway of dipeptidyl peptidase IV investigated by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1800-1809, JUN 2011 2011
abstract, full text

Samofalova, D. A., Karpov, P. A., Nuporko, A. Yu., Blume, Ya. B.
Reconstruction of the Spatial Structure of Plant Phosphatases Types 1 and 2A in Complexes with Okadaic Acid
CYTOLOGY AND GENETICS, 45:153-162, JUN 2011 2011
abstract, full text

Cristiani, Andrea, Brisotto, Nicola, Cedrati, Fabian Chatwin, Floris, Matteo, Scapozza, Leonardo, Moro, Stefano
ClickMD: an intuitive web-oriented molecular dynamics platform
FUTURE MEDICINAL CHEMISTRY, 3:923-931, JUN 2011 2011
abstract, full text

Solovyeva, Vita, Huth, Michael
Defect-induced shift of the Peierls transition in TTF-TCNQ thin films
SYNTHETIC METALS, 161:976-983, JUN 2011 2011
abstract, full text

Zhang, Dapeng, Iyer, Lakshminarayan M., Aravind, L.
A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems
NUCLEIC ACIDS RESEARCH, 39:4532-4552, JUN 2011 2011
abstract, full text

St-Pierre, Jean-Francois, Karttunen, Mikko, Mousseau, Normand, Rog, Tomasz, Bunker, Alex
Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1583-1594, JUN 2011 2011
abstract, full text

Giorgino, Toni, De Fabritiis, Gianni
A High-Throughput Steered Molecular Dynamics Study on the Free Energy Profile of Ion Permeation through Gramicidin A
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1943-1950, JUN 2011 2011
abstract, full text

Kenzaki, Hiroo, Koga, Nobuyasu, Hori, Naoto, Kanada, Ryo, Li, Wenfei, Okazaki, Kei-ichi, Yao, Xin-Qiu, Takada, Shoji
CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1979-1989, JUN 2011 2011
abstract, full text

Shin, Andrew J., Telesco, Shannon E., Choi, Sung-Hee, Lemmon, Mark A., Radhakrishnan, Ravi
Molecular dynamics analysis of conserved hydrophobic and hydrophilic bond-interaction networks in ErbB family kinases
BIOCHEMICAL JOURNAL, 436:241-251, JUN 1 2011 2011
abstract, full text

Shi, Wuxian, Punta, Marco, Bohon, Jen, Sauder, J. Michael, D'Mello, Rhijuta, Sullivan, Mike, Toomey, John, Abel, Don, Lippi, Marco, Passerini, Andrea, Frasconi, Paolo, Burley, Stephen K., Rost, Burkhard, Chance, Mark R.
Characterization of metalloproteins by high-throughput X-ray absorption spectroscopy
GENOME RESEARCH, 21:898-907, JUN 2011 2011
abstract, full text

Joly, L., Merabia, S., Barrat, J-L.
Effective temperatures of a heated Brownian particle
EPL, 94: Art. No. 50007, JUN 2011 2011
abstract, full text

Banu, Hussaina, Renuka, N., Vasanthakumar, Geetha
Reduced catalytic activity of human CYP2C9 natural alleles for gliclazide: Molecular dynamics simulation and docking studies
BIOCHIMIE, 93:1028-1036, JUN 2011 2011
abstract, full text

Dai, Weimin, You, Zhonglu, Zhou, He, Zhang, Jian, Hu, Yiqiao
Structure-function relationships of the human bitter taste receptor hTAS2R1: insights from molecular modeling studies
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:229-240, JUN 2011 2011
abstract, full text

Imbrici, Paola, D'Adamo, Maria Cristina, Grottesi, Alessandro, Biscarini, Andrea, Pessia, Mauro
Episodic ataxia type 1 mutations affect fast inactivation of K(+) channels by a reduction in either subunit surface expression or affinity for inactivation domain
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY, 300:C1314-C1322, JUN 2011 2011
abstract, full text

Bakan, Ahmet, Meireles, Lidio M., Bahar, Ivet
ProDy: Protein Dynamics Inferred from Theory and Experiments
BIOINFORMATICS, 27:1575-1577, JUN 1 2011 2011
abstract, full text

Eugenia Chiari, Maria, Vera, Domingo Mariano A., Maria Palacios, Sara, Cecilia Carpinella, Maria
Tyrosinase inhibitory activity of a 6-isoprenoid-substituted flavanone isolated from Dalea elegans
BIOORGANIC & MEDICINAL CHEMISTRY, 19:3474-3482, JUN 1 2011 2011
abstract, full text

Zhao, Peng, Liao, Qing-hua, Ren, Cheng-Feng, Wei, Jing
Identification of ligand binding site on RXR gamma using molecular docking and dynamics methods
JOURNAL OF MOLECULAR MODELING, 17:1259-1265, JUN 2011 2011
abstract, full text

Hasenpusch, Daniel, Bornscheuer, Uwe T., Langel, Walter
Simulation on the structure of pig liver esterase
JOURNAL OF MOLECULAR MODELING, 17:1493-1506, JUN 2011 2011
abstract, full text

Morando, Maria A., Nurisso, Alessandra, Grenouillat, Nathalie, Vauzeilles, Boris, Beau, Jean-Marie, Canada, F. Javier, Jimenez-Barbero, Jesus, Imberty, Anne
NMR and molecular modeling reveal key structural features of synthetic nodulation factors
GLYCOBIOLOGY, 21:824-833, JUN 2011 2011
abstract, full text

Winter, Nicolas D., Murphy, Ryan K. J., O'Halloran, Thomas V., Schatz, George C.
Development and modeling of arsenic-trioxide--loaded thermosensitive liposomes for anticancer drug delivery
JOURNAL OF LIPOSOME RESEARCH, 21:106-115, JUN 2011 2011
abstract, full text

Vorobyov, Igor, Allen, Toby W.
On the role of anionic lipids in charged protein interactions with membranes
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:1673-1683, JUN 2011 2011
abstract, full text

Oard, Svetlana V.
Deciphering a mechanism of membrane permeabilization by alpha-hordothionin peptide
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:1737-1745, JUN 2011 2011
abstract, full text

Kazantsev, Alexei V., Rambo, Robert P., Karimpour, Sina, Santalucia, John, Jr., Tainer, John A., Pace, Norman R.
Solution structure of RNase P RNA
RNA-A PUBLICATION OF THE RNA SOCIETY, 17:1159-1171, JUN 2011 2011
abstract, full text

Laine, Elodie, de Beauchene, Isaure Chauvot, Perahia, David, Auclair, Christian, Tchertanov, Luba
Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002068, JUN 2011 2011
abstract, full text

Katranidis, Alexandros, Melachroinos, Alexandros, Karagiannidis, Panagiotis G., Lousinian, Sylvie, Papadopoulos, Georgios, Logothetidis, Stergios, Choli-Papadopoulou, Theodora
BIOFUNCTIONALIZATION OF PET/SiO(2) SURFACES FOR SINGLE MOLECULE EXPERIMENTS AND MEDICAL APPLICATIONS
NANO, 6:271-277, JUN 2011 2011
abstract, full text

Floquet, Nicolas, Hernandez, Jean-Francois, Boucher, Jean-Luc, Martinez, Jean
L-Arginine Binding to Human Inducible Nitric Oxide Synthase: An Antisymmetric Funnel Route toward Isoform-Specific Inhibitors?
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1325-1335, JUN 2011 2011
abstract, full text

Zhang, Tao, Liu, Limin Angela, Lewis, David F. V., Wei, Dong-Qing
Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1336-1346, JUN 2011 2011
abstract, full text

Kelley, Anne Myers
Electron-Phonon Coupling in CdSe Nanocrystals from an Atomistic Phonon Model
ACS NANO, 5:5254-5262, JUN 2011 2011
abstract, full text

Veldhuis, N. A., Kuiper, M. J., Dobson, R. C. J., Pearson, R. B., Camakaris, J.
In silico modeling of the Menkes copper-translocating P-type ATPase 3rd metal binding domain predicts that phosphorylation regulates copper-binding
BIOMETALS, 24:477-487, JUN 2011 2011
abstract, full text

Yokota, Rio, Bardhan, Jaydeep P., Knepley, Matthew G., Barba, L. A., Hamada, Tsuyoshi
Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUS and a billion unknowns
COMPUTER PHYSICS COMMUNICATIONS, 182:1272-1283, JUN 2011 2011
abstract, full text

Kote-Jarai, Z., Al Olama, A. Amin, Leongamornlert, D., Tymrakiewicz, M., Saunders, E., Guy, M., Giles, G. G., Severi, G., Southey, M., Hopper, J. L., Sit, K. C., Harris, J. M., Batra, J., Spurdle, A. B., Clements, J. A., Hamdy, F., Neal, D., Donovan, J., Muir, K., Pharoah, P. D. P., Chanock, S. J., Brown, N., Benlloch, S., Castro, E., Mahmud, N., O'Brien, L., Hall, A., Sawyer, E., Wilkinson, R., Easton, D. F., Eeles, R. A.
Identification of a novel prostate cancer susceptibility variant in the KLK3 gene transcript
HUMAN GENETICS, 129:687-694, JUN 2011 2011
abstract, full text

Moin, Syed Tarique, Hofer, Thomas S., Sattar, Rabia, Ul-Haq, Zaheer
Molecular dynamics simulation of mammalian 15S-lipoxygenase with AMBER force field
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:715-726, JUN 2011 2011
abstract, full text

Muh, Frank, Zouni, Athina
Light-induced water oxidation in photosystem II
FRONTIERS IN BIOSCIENCE-LANDMARK, 16:3072-3132, JUN 1 2011 2011
abstract, full text

Jani, Vinod, Sonavane, Uddhavesh B., Joshi, Rajendra
Microsecond Scale Replica Exchange Molecular Dynamic Simulation of Villin Headpiece: An Insight into the Folding Landscape
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:845-860, JUN 2011 2011
abstract, full text

Wang, Yue, Bian, Fuyong, Deng, Shengrong, Shi, Qiang, Ge, Maofa, Wang, Shu, Zhang, Xingkang, Xu, Sichuan
The Key Residues of Active Sites on the Catalytic Fragment for Paclitaxel Interacting with Poly (ADP-Ribose) Polymerase
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:881-893, JUN 2011 2011
abstract, full text

Berski, Slawomir, Latajka, Zdzislaw, Gordon, Agnieszka J.
Electron Localization Function and Electron Localizability Indicator Applied to Study the Bonding in the Peroxynitrous Acid HOONO
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1528-1540, JUN 2011 2011
abstract, full text

Artemova, Svetlana, Grudinin, Sergei, Redon, Stephane
Fast Construction of Assembly Trees for Molecular Graphs
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1589-1598, JUN 2011 2011
abstract, full text

Hansson, Anders, Souza, Paulo C. T., Silveira, Rodrigo L., Martinez, Leandro, Skaf, Munir S.
CHARMM Force Field Parameterization of Rosiglitazone
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1346-1354, JUN-JUL 2011 2011
abstract, full text

Lee, Kyung-Hoon, Holl, Mark M. Banaszak
Free Energy Simulation to Investigate the Effect of Amino Acid Sequence Environment on the Severity of Osteogenesis Imperfecta by Glycine Mutations in Collagen
BIOPOLYMERS, 95:401-409, JUN 2011 2011
abstract, full text

Bober, Marta, Morgelin, Matthias, Olin, Anders I., von Pawel-Rammingen, Ulrich, Collin, Mattias
The Membrane Bound LRR Lipoprotein Slr, and the Cell Wall-Anchored M1 Protein from Streptococcus pyogenes Both Interact with Type I Collagen
PLOS ONE, 6: Art. No. e20345, MAY 31 2011 2011
abstract, full text

Riihimaki, Tiina A., Kukkurainen, Sampo, Varjonen, Suvi, Horha, Jarno, Nyholm, Thomas K. M., Kulomaa, Markku S., Hytonen, Vesa P.
Construction of Chimeric Dual-Chain Avidin by Tandem Fusion of the Related Avidins
PLOS ONE, 6: Art. No. e20535, MAY 31 2011 2011
abstract, full text

Sheng, Yuebiao, Wang, Wei, Chen, P.
Peptide adsorption on the hydrophobic surface: A free energy perspective
JOURNAL OF MOLECULAR STRUCTURE, 995:142-147, MAY 31 2011 2011
abstract, full text

Pereira Silva, Pedro S., Ghalib, Raza Murad, Mehdi, Sayed Hasan, Hashim, Rokiah, Sulaiman, Othman, Ramos Silva, Manuela
Crystal structure, ab initio calculations and fingerprint plots of a new polymorph of N ',N '',N '''-triphenylbiuret
JOURNAL OF MOLECULAR STRUCTURE, 995:66-71, MAY 31 2011 2011
abstract, full text

Han, Minwoo, Hong, Minhyung, Sim, Eunji
Influence of the block hydrophilicity of AB(2) miktoarm star copolymers on cluster formation in solutions
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 204901, MAY 28 2011 2011
abstract, full text

Lucero, Melissa J., Aguilera, Irene, Diaconu, Cristian V., Palacios, Pablo, Wahnon, Perla, Scuseria, Gustavo E.
Screened hybrid and self-consistent GW calculations of cadmium/magnesium indium sulfide materials
PHYSICAL REVIEW B, 83: Art. No. 205128, MAY 25 2011 2011
abstract, full text

Sknepnek, Rastko, Vernizzi, Graziano, de la Cruz, Monica Olvera
Shape Change of Nanocontainers via a Reversible Ionic Buckling
PHYSICAL REVIEW LETTERS, 106: Art. No. 215504, MAY 25 2011 2011
abstract, full text

Barman, Arghya, Schuerer, Stephan, Prabhakar, Rajeev
Computational Modeling of Substrate Specificity and Catalysis of the beta-Secretase (BACE1) Enzyme
BIOCHEMISTRY, 50:4337-4349, MAY 24 2011 2011
abstract, full text

Thaulow, Christian, Sen, Dipanjan, Buehler, Markus J.
Atomistic study of the effect of crack tip ledges on the nucleation of dislocations in silicon single crystals at elevated temperature
MATERIALS SCIENCE AND ENGINEERING A-STRUCTURAL MATERIALS PROPERTIES MICROSTRUCTURE AND PROCESSING, 528:4357-4364, MAY 24 2011 2011
abstract, full text

Thakur, Sidharth, Pasquinelli, Melissa A.
Adapting Visual-Analytical Tools for the Exploration of Structural and Dynamical Features of Polymer Conformations
MACROMOLECULAR THEORY AND SIMULATIONS, 20:286-298, MAY 23 2011 2011
abstract, full text

Schreiner, Eduard, Trabuco, Leonardo G., Freddolino, Peter L., Schulten, Klaus
Stereochemical errors and their implications for molecular dynamics simulations
BMC BIOINFORMATICS, 12: Art. No. 190, MAY 23 2011 2011
abstract, full text

Babu, Jeetu S., Sathian, Sarith P.
The role of activation energy and reduced viscosity on the enhancement of water flow through carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 194509, MAY 21 2011 2011
abstract, full text

Stewart, Mikaela D., Morgan, Brittany, Massi, Francesca, Igumenova, Tatyana I.
Probing the Determinants of Diacylglycerol Binding Affinity in the C1B Domain of Protein Kinase C alpha
JOURNAL OF MOLECULAR BIOLOGY, 408:949-970, MAY 20 2011 2011
abstract, full text

Carbone, A., Dib, L.
Co-evolution and information signals in biological sequences
THEORETICAL COMPUTER SCIENCE, 412:2486-2495, MAY 20 2011 2011
abstract, full text

Bai, Qifeng, Shen, Yulin, Yao, Xiaojun, Wang, Fang, Du, Yuping, Wang, Qin, Jin, Nengzhi, Hai, Jun, Hu, Tiejun, Yang, Jinbo
Modeling a New Water Channel That Allows SET9 to Dimethylate p53
PLOS ONE, 6: Art. No. e19856, MAY 19 2011 2011
abstract, full text

Braun, Sebastian, Humphreys, Christine, Fraser, Elizabeth, Brancale, Andrea, Bochtler, Matthias, Dale, Trevor C.
Amyloid-Associated Nucleic Acid Hybridisation
PLOS ONE, 6: Art. No. e19125, MAY 19 2011 2011
abstract, full text

Autieri, Emmanuel, Chiessi, Ester, Lonardi, Alice, Paradossi, Gaio, Sega, Marcello
Conformation and Dynamics of Poly(N-isopropyl acrylamide) Trimers in Water: A Molecular Dynamics and Metadynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY B, 115:5827-5839, MAY 19 2011 2011
abstract, full text

Stare, Jernej, Mavri, Janez, Grdadolnik, Joze, Zidar, Jernej, Maksic, Zvonimir B., Vianello, Robert
Hydrogen Bond Dynamics of Histamine Monocation in Aqueous Solution: Car-Parrinello Molecular Dynamics and Vibrational Spectroscopy Study
JOURNAL OF PHYSICAL CHEMISTRY B, 115:5999-6010, MAY 19 2011 2011
abstract, full text

Ramachandran, Abhijit, Guo, Qingjiang, Iqbal, Samir M., Liu, Yaling
Coarse-Grained Molecular Dynamics Simulation of DNA Trans location in Chemically Modified Nanopores
JOURNAL OF PHYSICAL CHEMISTRY B, 115:6138-6148, MAY 19 2011 2011
abstract, full text

Chan, Peter W. Y., Yakunin, Alexander F., Edwards, Elizabeth A., Pai, Emil F.
Mapping the Reaction Coordinates of Enzymatic Defluorination
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:7461-7468, MAY 18 2011 2011
abstract, full text

Gumbart, James, Chipot, Christophe, Schulten, Klaus
Free Energy of Nascent-Chain Folding in the Translocon
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:7602-7607, MAY 18 2011 2011
abstract, full text

Chen, Po-Chia, Kuyucak, Serdar
Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints
BIOPHYSICAL JOURNAL, 100:2466-2474, MAY 18 2011 2011
abstract, full text

Balasubramanian, Ganesh, Murad, Sohail, Kappiyoor, Ravi, Puri, Ishwar K.
Structure of aqueous MgSO(4) solution: Dilute to concentrated
CHEMICAL PHYSICS LETTERS, 508:38-42, MAY 18 2011 2011
abstract, full text

Johnson, Christopher N., Spring, Alexander M., Sergueev, Dimitri, Shaw, Barbara R., Germann, Markus W.
Structural Basis of the RNase H1 Activity on Stereo Regular Borano Phosphonate DNA/RNA Hybrids
BIOCHEMISTRY, 50:3903-3912, MAY 17 2011 2011
abstract, full text

Verde, Ana Vila, Beltramo, Peter J., Maranas, Janna K.
Adsorption of Homopolypeptides on Gold Investigated Using Atomistic Molecular Dynamics
LANGMUIR, 27:5918-5926, MAY 17 2011 2011
abstract, full text

Piatek, Rafal J., Bruzdziak, Piotr, Zalewska-Piatek, Beata M., Wojciechowski, Marek A., Namiesnik, Justyna M., Kur, Jozef W.
Analysis of the unique structural and physicochemical properties of the DraD/AfaD invasin in the context of its belonging to the family of chaperone/usher type fimbrial subunits
BMC STRUCTURAL BIOLOGY, 11: Art. No. 25, MAY 16 2011 2011
abstract, full text

Katsoulis, Ioannis A., Kythreoti, Georgia, Papakyriakou, Athanasios, Koltsida, Konstantina, Anastasopoulou, Panoula, Stathakis, Christos I., Mavridis, Ioannis, Cottin, Thomas, Saridakis, Emmanuel, Vourloumis, Dionisios
Synthesis of 5,6-Spiroethers and Evaluation of their Affinities for the Bacterial A Site
CHEMBIOCHEM, 12:1188-1192, MAY 16 2011 2011
full text

Gauto, Diego F., Di Lella, Santiago, Estrin, Dario A., Monaco, Hugo L., Marti, Marcelo A.
Structural basis for ligand recognition in a mushroom lectin: solvent structure as specificity predictor
CARBOHYDRATE RESEARCH, 346:939-948, MAY 15 2011 2011
abstract, full text

Wang, Tianfang, Andreazza, Hayley J., Pukala, Tara L., Sherman, Patrick J., Calabrese, Antonio N., Bowie, John H.
Histidine-containing host-defence skin peptides of anurans bind Cu(2+). An electrospray ionisation mass spectrometry and computational modelling study
RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 25:1209-1221, MAY 15 2011 2011
abstract, full text

Wei, Shuai, Knotts, Thomas A.
Effects of tethering a multistate folding protein to a surface
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 185101, MAY 14 2011 2011
abstract, full text

Gotz, Alexandra, Tyynismaa, Henna, Euro, Liliya, Ellonen, Pekka, Hyotylainen, Tuulia, Ojala, Tiina, Hamalainen, Riikka H., Tommiska, Johanna, Raivio, Taneli, Oresic, Matej, Karikoski, Riitta, Tammela, Outi, Simola, Kalle O. J., Paetau, Anders, Tyni, Tiina, Suomalainen, Anu
Exome Sequencing Identifies Mitochondrial Alanyl-tRNA Synthetase Mutations in Infantile Mitochondrial Cardiomyopathy
AMERICAN JOURNAL OF HUMAN GENETICS, 88:635-642, MAY 13 2011 2011
abstract, full text

Balamurugan, K., Singam, E. R. Azhagiya, Subramanian, V.
Effect of Curvature on the alpha-Helix Breaking Tendency of Carbon Based Nanomaterials
JOURNAL OF PHYSICAL CHEMISTRY C, 115:8886-8892, MAY 12 2011 2011
abstract, full text

Atta-Fynn, Raymond, Bylaska, Eric J., Schenter, Gregory K., de Jong, Wibe A.
Hydration Shell Structure and Dynamics of Curium(III) in Aqueous Solution: First Principles and Empirical Studies
JOURNAL OF PHYSICAL CHEMISTRY A, 115:4665-4677, MAY 12 2011 2011
abstract, full text

Chong, Song-Ho, Lee, Chewook, Kang, Guipeun, Park, Mirae, Ham, Sihyun
Structural and Thermodynamic Investigations on the Aggregation and Folding of Acylphosphatase by Molecular Dynamics Simulations and Solvation Free Energy Analysis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:7075-7083, MAY 11 2011 2011
abstract, full text

Desai, Tapan G.
Thermal transport in nanoclusters
APPLIED PHYSICS LETTERS, 98: Art. No. 193107, MAY 9 2011 2011
abstract, full text

Velez-Vega, Camillo, Escobedo, Fernando A.
Characterizing the Structural Behavior of Selected A beta-42 Monomers with Different Solubilities
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4900-4910, MAY 5 2011 2011
abstract, full text

Perlmutter, Jason D., Sachs, Jonathan N.
Interleaflet Interaction and Asymmetry in Phase Separated Lipid Bilayers: Molecular Dynamics Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6563-6577, MAY 4 2011 2011
abstract, full text

Holterhues, Julia, Bordignon, Enrica, Klose, Daniel, Rickert, Christian, Klare, Johann P., Martell, Swetlana, Li, Lin, Engelhard, Martin, Steinhofft, Heinz-Juergen
The Signal Transfer from the Receptor NpSRII to the Transducer NpHtrIl Is Not Hampered by the D75N Mutation
BIOPHYSICAL JOURNAL, 100:2275-2282, MAY 4 2011 2011
abstract, full text

Matthes, Dirk, Gapsys, Vytautas, Daebel, Venita, de Groot, Bert L.
Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization
PLOS ONE, 6: Art. No. e19129, MAY 3 2011 2011
abstract, full text

Czub, Jacek, Grubmueller, Helmut
Torsional elasticity and energetics of F(1)-ATPase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:7408-7413, MAY 3 2011 2011
abstract, full text

Grabosch, Carsten, Hartmann, Mirja, Schmidt-Lassen, Joern, Lindhorst, Thisbe K.
Squaric Acid Monoamide Mannosides as Ligands for the Bacterial Lectin FimH: Covalent Inhibition or Not?
CHEMBIOCHEM, 12:1066-1074, MAY 2 2011 2011
abstract, full text

Dechassa, Mekonnen Lemma, Wyns, Katharina, Li, Ming, Hall, Michael A., Wang, Michelle D., Luger, Karolin
Structure and Scm3-mediated assembly of budding yeast centromeric nucleosomes
NATURE COMMUNICATIONS, 2: Art. No. 313, MAY 2011 2011
abstract, full text

Sonntag, Yonathan, Musgaard, Maria, Olesen, Claus, Schiott, Birgit, Moller, Jesper Vuust, Nissen, Poul, Thogersen, Lea
Mutual adaptation of a membrane protein and its lipid bilayer during conformational changes
NATURE COMMUNICATIONS, 2: Art. No. 304, MAY 2011 2011
abstract, full text

Zeebe, Richard E.
On the molecular diffusion coefficients of dissolved CO(2), HCO(3)(-), and CO(3)(2-) and their dependence on isotopic mass
GEOCHIMICA ET COSMOCHIMICA ACTA, 75:2483-2498, MAY 1 2011 2011
abstract, full text

Aprikian, Pavel, Interlandi, Gianluca, Kidd, Brian A., Le Trong, Isolde, Tchesnokova, Veronika, Yakovenko, Olga, Whitfield, Matt J., Bullitt, Esther, Stenkamp, Ronald E., Thomas, Wendy E., Sokurenko, Evgeni V.
The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor
PLOS BIOLOGY, 9: Art. No. e1000617, MAY 2011 2011
abstract, full text

Jofre, Claudio, Guzman, Fanny, Cardenas, Constanza, Albericio, Fernando, Marshall, Sergio H.
A natural peptide and its variants derived from the processing of infectious pancreatic necrosis virus (IPNV) displaying enhanced antimicrobial activity: A novel alternative for the control of bacterial diseases
PEPTIDES, 32:852-858, MAY 2011 2011
abstract, full text

Vemparala, Satyavani, Mehrotra, Sonali, Balaram, Hemalatha
Role of loop dynamics in thermal stability of mesophilic and thermophilic adenylosuccinate synthetase: A molecular dynamics and normal mode analysis study
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:630-637, MAY 2011 2011
abstract, full text

Yang, Chenghua, van der Woerd, Mark J., Muthurajan, Uma M., Hansen, Jeffrey C., Luger, Karolin
Biophysical analysis and small-angle X-ray scattering-derived structures of MeCP2-nucleosome complexes
NUCLEIC ACIDS RESEARCH, 39:4122-4135, MAY 2011 2011
abstract, full text

Wolff, K., Vendruscolo, M., Porto, M.
Asymmetric folding pathways and transient misfolding in a coarse-grained model of proteins
EPL, 94: Art. No. 48005, MAY 2011 2011
abstract, full text

Oehme, Daniel P., Wilson, David J. D., Brownlee, Robert T. C.
Effect of Structural Stress on the Flexibility and Adaptability of HIV-1 Protease
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1064-1073, MAY 2011 2011
abstract, full text

Sommer, Bjoern, Dingersen, Tim, Gamroth, Christian, Schneider, Sebastian E., Robert, Sebastian, Krueger, Jens, Dietz, Karl-Josef
CELLmicrocosmos 2.2 Membrane Editor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:1165-1182, MAY 2011 2011
abstract, full text

Mitchell, J. S., Laughton, C. A., Harris, Sarah A.
Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA
NUCLEIC ACIDS RESEARCH, 39:3928-3938, MAY 2011 2011
abstract, full text

Datta, K. K. R., Vinu, Ajayan, Mandal, Saikat, Al-Deyab, Salem, Hill, Jonathan P., Ariga, Katsuhiko
Base-Selective Adsorption of Nucleosides to Pore-Engineered Nanocarbon, Carbon Nanocage
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 11:3959-3964, MAY 2011 2011
abstract, full text

Astrakas, Loukas, Gousias, Christos, Tzaphlidou, Margaret
Electric field effects on chignolin conformation
JOURNAL OF APPLIED PHYSICS, 109: Art. No. 094702, MAY 1 2011 2011
abstract, full text

Pietra, Francesco
On the Putative Binding Site of RFamide-Family Neuropeptides from the Western Atlantic Clam Sunray Venus and Cephalopods on Acid-Sensing Ion Channels. An Automated Docking and Molecular-Dynamics Study with hASIC1a Homology Model
CHEMISTRY & BIODIVERSITY, 8:816-826, MAY 2011 2011
abstract, full text

Malkhed, Vasavi, Gudlur, Bargavi, Kondagari, Bhargavi, Dulapalli, Ramasree, Vuruputuri, Uma
Study of interactions between Mycobacterium tuberculosis proteins: SigK and anti-SigK
JOURNAL OF MOLECULAR MODELING, 17:1109-1119, MAY 2011 2011
abstract, full text

Lin, Ying-Wu, Ying, Tian-Lei, Liao, Li-Fu
Molecular modeling and dynamics simulation of a histidine-tagged cytochrome b (5)
JOURNAL OF MOLECULAR MODELING, 17:971-978, MAY 2011 2011
abstract, full text

Richard, Ryan M., Herbert, John M.
Time-Dependent Density-Functional Description of the (1)L(a) State in Polycyclic Aromatic Hydrocarbons: Charge-Transfer Character in Disguise?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1296-1306, MAY 2011 2011
abstract, full text

Kutzner, Carsten, Czub, Jacek, Grubmueller, Helmut
Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1381-1393, MAY 2011 2011
abstract, full text

Spill, Yannick G., Pasquali, Samuela, Derreumaux, Philippe
Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1502-1510, MAY 2011 2011
abstract, full text

Sukhwal, Anshul, Bhattacharyya, Moitrayee, Vishveshwara, Saraswathi
Network approach for capturing ligand-induced subtle global changes in protein structures
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 67:429-439, MAY 2011 2011
abstract, full text

Dech, Stephan, Cramer, Tobias, Ladisch, Reinhild, Bruns, Nico, Tiller, Joerg C.
Solid-Solid Interface Adsorption of Proteins and Enzymes in Nanophase-Separated Amphiphilic Conetworks
BIOMACROMOLECULES, 12:1594-1601, MAY 2011 2011
abstract, full text

Zhao, Jun, Yu, Xiang, Liang, Guizhao, Zheng, Jie
Heterogeneous Triangular Structures of Human Islet Amyloid Polypeptide (Amylin) with Internal Hydrophobic Cavity and External Wrapping Morphology Reveal the Polymorphic Nature of Amyloid Fibrils
BIOMACROMOLECULES, 12:1781-1794, MAY 2011 2011
abstract, full text

McCole, Ruth B., Loughran, Noeleen B., Chahal, Mandeep, Fernandes, Luis P., Roberts, Roland G., Fraternali, Franca, O'Connell, Mary J., Oakey, Rebecca J.
A CASE-BY-CASE EVOLUTIONARY ANALYSIS OF FOUR IMPRINTED RETROGENES
EVOLUTION, 65:1413-1427, MAY 2011 2011
abstract, full text

Androutsopoulos, Vasilis P., Papakyriakou, Athanasios, Vourloumis, Dionisios, Spandidos, Demetrios A.
Comparative CYP1A1 and CYP1B1 substrate and inhibitor profile of dietary flavonoids
BIOORGANIC & MEDICINAL CHEMISTRY, 19:2842-2849, MAY 1 2011 2011
abstract, full text

Khrenova, Maria G., Domratcheva, Tatiana, Schlichting, Ilme, Grigorenko, Bella L., Nemukhin, Alexander V.
Computational Characterization of Reaction Intermediates in the Photocycle of the Sensory Domain of the AppA Blue Light Photoreceptor
PHOTOCHEMISTRY AND PHOTOBIOLOGY, 87:564-573, MAY-JUN 2011 2011
abstract, full text

Teulon, Jean-Marie, Delcuze, Yannick, Odorico, Michael, Chen, Shu-wen W., Parot, Pierre, Pellequer, Jean-Luc
Single and multiple bonds in (strept)avidin-biotin interactions
JOURNAL OF MOLECULAR RECOGNITION, 24:490-502, MAY-JUN 2011 2011
abstract, full text

Minh-Hieu Trinh, Odorico, Michael, Bellanger, Laurent, Jacquemond, Mireille, Parot, Pierre, Pellequer, Jean-Luc
Tobacco mosaic virus as an AFM tip calibrator
JOURNAL OF MOLECULAR RECOGNITION, 24:503-510, MAY-JUN 2011 2011
abstract, full text

Ponomarev, Sergei Y., Audie, Joseph
Computational prediction and analysis of the DR6-NAPP interaction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1376-1395, MAY 2011 2011
abstract, full text

Simpson, Lisa M., Wall, Ian D., Blaney, Frank E., Reynolds, Christopher A.
Modeling GPCR active state conformations: The beta(2)-adrenergic receptor
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1441-1457, MAY 2011 2011
abstract, full text

Sander, Tommy, Frolund, Bente, Bruun, Anne Techau, Ivanov, Ivaylo, McCammon, James Andrew, Balle, Thomas
New insights into the GABA(A) receptor structure and orthosteric ligand binding: Receptor modeling guided by experimental data
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1458-1477, MAY 2011 2011
abstract, full text

Gao, Mu, Skolnick, Jeffrey
New benchmark metrics for protein-protein docking methods
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1623-1634, MAY 2011 2011
abstract, full text

Martinez, Leandro, Malliavin, Therese E., Blondel, Arnaud
Mechanism of reactant and product dissociation from the anthrax edema factor: A locally enhanced sampling and steered molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1649-1661, MAY 2011 2011
abstract, full text

Sampathkumar, Parthasarathy, Gheyi, Tarun, Miller, Stacy A., Bain, Kevin T., Dickey, Mark, Bonanno, Jeffrey B., Kim, Seung Joong, Phillips, Jeremy, Pieper, Ursula, Fernandez-Martinez, Javier, Franke, Josef D., Martel, Anne, Tsuruta, Hiro, Atwell, Shane, Thompson, Devon A., Emtage, J. Spencer, Wasserman, Stephen R., Rout, Michael P., Sali, Andrej, Sauder, J. Michael, Burley, Stephen K.
Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1672-1677, MAY 2011 2011
full text

Tan, Yeqiang, Song, Yihu, Cao, Qing, Zheng, Qiang
Characterization of carbon black-filled immiscible polypropylene/polystyrene blends
POLYMER INTERNATIONAL, 60:823-832, MAY 2011 2011
abstract, full text

Chou, H., Tam, M. F., Chiang, C. -H., Chou, C. -T., Tai, H. -Y., Shen, H. -D.
Transaldolases are novel and immunoglobulin E cross-reacting fungal allergens
CLINICAL AND EXPERIMENTAL ALLERGY, 41:739-749, MAY 2011 2011
abstract, full text

Fezoua-Boubegtiten, Zahia, Desbat, Bernard, Brisson, Alain, Gounou, Celine, Laguerre, Michel, Lecomte, Sophie
Effect of Mg(2+) versus Ca(2+) on the behavior of Annexin A5 in a membrane-bound state
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:641-649, MAY 2011 2011
abstract, full text

Levine, Benjamin G., Stone, John E., Kohlmeyer, Axel
Fast analysis of molecular dynamics trajectories with graphics processing units-Radial distribution function histogramming
JOURNAL OF COMPUTATIONAL PHYSICS, 230:3556-3569, MAY 1 2011 2011
abstract, full text

Bellesia, Giovanni, Jewett, Andrew I., Shea, Joan-Emma
Relative stability of de novo four-helix bundle proteins: Insights from coarse grained molecular simulations
PROTEIN SCIENCE, 20:818-826, MAY 2011 2011
abstract, full text

Paparcone, Raffaella, Buehler, Markus J.
Failure of A beta(1-40) amyloid fibrils under tensile loading
BIOMATERIALS, 32:3367-3374, MAY 2011 2011
abstract, full text

Sapay, Nicolas, Tieleman, D. Peter
Combination of the CHARMM27 Force Field with United-Atom Lipid Force Fields
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1400-1410, MAY 2011 2011
abstract, full text

Unni, Samir, Huang, Yong, Hanson, Robert M., Tobias, Malcolm, Krishnan, Sriram, Li, Wilfred W., Nielsen, Jens E., Baker, Nathan A.
Web Servers and Services for Electrostatics Calculations with APBS and PDB2PQR
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1488-1491, MAY 2011 2011
abstract, full text

Mavromoustakos, Thomas, Chatzigeorgiou, Petros, Koukoulitsa, Catherine, Durdagi, Serdar
Partial Interdigitation of Lipid Bilayers
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1172-1183, MAY 2011 2011
abstract, full text

Rodrigues, Tiago, Dos Santos, Daniel J. V. A., Moreira, Rui, Lopes, Francisca, Guedes, Rita C.
A Quantum Mechanical Study of Novel Potential Inhibitors of Cytochrome bc(1) as Antimalarial Compounds
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1196-1207, MAY 2011 2011
abstract, full text

Cerqueira, N. M. F. S. A., Ribeiro, J., Fernandes, P. A., Ramos, M. J.
vsLab-An Implementation for Virtual High-Throughput Screening Using AutoDock and VMD
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:1208-1212, MAY 2011 2011
abstract, full text

Maya-Nunez, Guadalupe, Janovick, Jo Ann, Aguilar-Rojas, Arturo, Jardon-Valadez, Eduardo, Leanos-Miranda, Alfredo, Zarinan, Teresa, Ulloa-Aguirre, Alfredo, Michael Conn, P.
Biochemical mechanism of pathogenesis of human gonadotropin-releasing hormone receptor mutants Thr104Ile and Tyr108Cys associated with familial hypogonadotropic hypogonadism
MOLECULAR AND CELLULAR ENDOCRINOLOGY, 337:16-23, APR 30 2011 2011
abstract, full text

Vorontsov, Ivan I., Miyashita, Osamu
Crystal Molecular Dynamics Simulations to Speed Up MM/PB(GB)SA Evaluation of Binding Free Energies of Di-Mannose Deoxy Analogs with P51G-m4-Cyanovirin-N
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1043-1053, APR 30 2011 2011
abstract, full text

Li, Xianfeng, Latour, Robert A.
The Temperature Intervals With Global Exchange of Replicas Empirical Accelerated Sampling Method: Parameter Sensitivity and Extension to a Complex Molecular System
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1091-1100, APR 30 2011 2011
abstract, full text

Seeber, Michele, Felline, Angelo, Raimondi, Francesco, Muff, Stefanie, Friedman, Ran, Rao, Francesco, Caflisch, Amedeo, Fanelli, Francesca
Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:1183-1194, APR 30 2011 2011
abstract, full text

Morlighem, Jean-Etienne, Aoki, Shintaro, Kishima, Mami, Hanami, Mitsue, Ogawa, Chihiro, Jalloh, Amadu, Takahashi, Yukari, Kawai, Yuki, Saga, Satomi, Hayashi, Eiji, Ban, Toshiaki, Izumi, Shinyu, Wada, Akira, Mano, Masayuki, Fukunaga, Megumu, Kijima, Yoshiyuki, Shiomi, Shoji, Inoue, Kaoru, Hata, Takeshi, Koretsune, Yukihiro, Kudo, Koichiro, Himeno, Yuji, Hirai, Aizan, Takahashi, Kazuo, Sakai-Tagawa, Yuko, Iwatsuki-Horimoto, Kiyoko, Kawaoka, Yoshihiro, Hayashizaki, Yoshihide, Ishikawa, Toshihisa
Mutation Analysis of 2009 Pandemic Influenza A(H1N1) Viruses Collected in Japan during the Peak Phase of the Pandemic
PLOS ONE, 6: Art. No. e18956, APR 29 2011 2011
abstract, full text

Dopieralski, Przemyslaw D., Burakowski, Andrzej, Latajka, Zdzislaw, Olovsson, Ivar
Hydration of NaHCO(3), KHCO(3), (HCO(3)(-))(2), HCO(3)(-) and CO(3)(2-) from molecular dynamics simulation and speed of sound measurements
CHEMICAL PHYSICS LETTERS, 507:89-95, APR 29 2011 2011
abstract, full text

Tu Guogang, Li Shaohua
Homology Modeling and Docking Studies of Cannabinoid Receptor CB1
ACTA CHIMICA SINICA, 69:1007-1010, APR 28 2011 2011
abstract, full text

Gomaa, Mohamed S., Bridgens, Caroline E., Aboraia, Ahmed S., Veal, Gareth J., Redfern, Christopher P. F., Brancale, Andrea, Armstrong, Jane L., Simons, Claire
Small Molecule Inhibitors of Retinoic Acid 4-Hydroxylase (CYP26): Synthesis and Biological Evaluation of Imidazole Methyl 3-(4-(aryl-2-ylamino)phenyl)propanoates
JOURNAL OF MEDICINAL CHEMISTRY, 54:2778-2791, APR 28 2011 2011
abstract, full text

Aubin-Tam, Marie-Eve, Appleyard, David C., Ferrari, Enrico, Garbin, Valeria, Fadiran, Oluwatimilehin O., Kunkel, Jacquelyn, Lang, Matthew J.
Adhesion through Single Peptide Aptamers
JOURNAL OF PHYSICAL CHEMISTRY A, 115:3657-3664, APR 28 2011 2011
abstract, full text

Speelman, Amy L., Munoz-Losa, Aurora, Hinkle, Katie L., VanBeek, Darren B., Mennucci, Benedetta, Krueger, Brent P.
Using Molecular Dynamics and Quantum Mechanics Calculations To Model Fluorescence Observables
JOURNAL OF PHYSICAL CHEMISTRY A, 115:3997-4008, APR 28 2011 2011
abstract, full text

Damjanovic, Ana, Brooks, Bernard R., Garcia-Moreno, Bertrand E.
Conformational Relaxation and Water Penetration Coupled to Ionization of Internal Groups in Proteins
JOURNAL OF PHYSICAL CHEMISTRY A, 115:4042-4053, APR 28 2011 2011
abstract, full text

Crane, Andrew J., Mueller, Erich A.
Self-Assembly of T-Shaped Polyphilic Molecules in Solvent Mixtures
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4592-4605, APR 28 2011 2011
abstract, full text

Cilpa, G., Koivuniemi, A., Hyvonen, M. T., Riekkola, M. -L.
A Molecular Dynamics Approach for the Association of ApolipoproteinB-100 and Chondroitin-6-sulfate
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4818-4825, APR 28 2011 2011
abstract, full text

Patra, Niladri, Kral, Petr
Controlled Self-Assem