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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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

Plazinski, Wojciech, Knys-Dzieciuch, Agnieszka
Interactions between CD44 protein and hyaluronan: insights from the computational study
MOLECULAR BIOSYSTEMS, 8:543-547, 2012 2012
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

Battisti, Anna, Tenenbaum, Alexander
Molecular dynamics simulation of intrinsically disordered proteins
MOLECULAR SIMULATION, 38:139-143, 2012 2012
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

Espinoza-Fonseca, L. Michel
Dynamic optimization of signal transduction via intrinsic disorder
MOLECULAR BIOSYSTEMS, 8:194-197, 2012 2012
abstract, full text

Espinoza-Fonseca, L. Michel
Aromatic residues link binding and function of intrinsically disordered proteins
MOLECULAR BIOSYSTEMS, 8:237-246, 2012 2012
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

Nandi, Nilashis
CHIRALITY IN BIOLOGICAL NANOSPACES Reactions in Active Sites Introduction
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 1-46, 2012 2012
full text

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
full text

Nandi, Nilashis
Chiral discrimination in the active site of ligases
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 123-163, 2012 2012
full text

Nandi, Nilashis
Chiral discrimination in the active site of oxidoreductases
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 47-64, 2012 2012
full text

Nandi, Nilashis
Transferases and chiral discrimination
CHIRALITY IN BIOLOGICAL NANOSPACES: REACTIONS IN ACTIVE SITES, 65-105, 2012 2012
full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

Gannon, G., O'Dwyer, C., Larsson, J. A., Thompson, D.
Interdigitating Organic Bilayers Direct the Short Inter layer Spacing in Hybrid Organic-Inorganic Layered Vanadium Oxide Nanostructures
JOURNAL OF PHYSICAL CHEMISTRY B, 115:14518-14525, DEC 15 2011 2011
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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
abstract, full text

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-Assembly of Filled Micelles on Nanotubes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:6146-6149, APR 27 2011 2011
abstract, full text

Swedberg, Joakim E., de Veer, Simon J., Sit, Kei C., Reboul, Cyril F., Buckle, Ashley M., Harris, Jonathan M.
Mastering the Canonical Loop of Serine Protease Inhibitors: Enhancing Potency by Optimising the Internal Hydrogen Bond Network
PLOS ONE, 6: Art. No. e19302, APR 27 2011 2011
abstract, full text

Gerken, Thomas A., Jamison, Oliver, Perrine, Cynthia L., Collette, Jeremy C., Moinova, Helen, Ravi, Lakshmeswari, Markowitz, Sanford D., Shen, Wei, Patel, Himatkumar, Tabak, Lawrence A.
Emerging Paradigms for the Initiation of Mucin-type Protein O-Glycosylation by the Polypeptide GalNAc Transferase Family of Glycosyltransferases
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:14493-14507, APR 22 2011 2011
abstract, full text

Kishi, Ryohei, Nakano, Masayoshi
Quantum Master Equation Method Based on the Broken-Symmetry Time-Dependent Density Functional Theory: Application to Dynamic Polarizability of Open-Shell Molecular Systems
JOURNAL OF PHYSICAL CHEMISTRY A, 115:3565-3575, APR 21 2011 2011
abstract, full text

Beckham, Gregg T., Crowley, Michael F.
Examination of the alpha-Chitin Structure and Decrystallization Thermodynamics at the Nanoscale
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4516-4522, APR 21 2011 2011
abstract, full text

Agirrezabala, Xabier, Schreiner, Eduard, Trabuco, Leonardo G., Lei, Jianlin, Ortiz-Meoz, Rodrigo F., Schulten, Klaus, Green, Rachel, Frank, Joachim
Structural insights into cognate versus near-cognate discrimination during decoding
EMBO JOURNAL, 30:1497-1507, APR 20 2011 2011
abstract, full text

Hall, Benjamin A., Chetwynd, Alan P., Sansom, Mark S. P.
Exploring Peptide-Membrane Interactions with Coarse-Grained MD Simulations
BIOPHYSICAL JOURNAL, 100:1940-1948, APR 20 2011 2011
abstract, full text

Wu, Jian, Walker, Victoria E. J., Boyd, Russell J.
A theoretical study of the structure and conductivity of polycytosineacetylene
CHEMICAL PHYSICS LETTERS, 506:243-247, APR 20 2011 2011
abstract, full text

Azenha, Manuel, Szefczyk, Borys, Loureiro, Dianne, Kathirvel, Porkodi, Cordeiro, M. Natalia D. S., Fernando-Silva, Antonio
Molecular Dynamics Simulations of Pregelification Mixtures for the Production of Imprinted Xerogels
LANGMUIR, 27:5062-5070, APR 19 2011 2011
abstract, full text

Markovic, Marijana, Judas, Nenad, Sabolovic, Jasmina
Combined Experimental and Computational Study of cis-trans Isomerism in Bis(L-valinato)copper(II)
INORGANIC CHEMISTRY, 50:3632-3644, APR 18 2011 2011
abstract, full text

Sharifi, Monir, Koehler, Christof, Toelle, Pia, Frauenheim, Thomas, Wark, Michael
Proton Conductivity of SO(3)H-Functionalized Benzene-Periodic Mesoporous Organosilica
SMALL, 7:1086-1097, APR 18 2011 2011
abstract, full text

Eken, A. E., Tozzi, E. J., Klingenberg, D. J., Bauhofer, W.
A simulation study on the combined effects of nanotube shape and shear flow on the electrical percolation thresholds of carbon nanotube/polymer composites
JOURNAL OF APPLIED PHYSICS, 109: Art. No. 084342, APR 15 2011 2011
abstract, full text

Zervoudi, Efthalia, Papakyriakou, Athanasios, Georgiadou, Dimitra, Evnouchidou, Irini, Gajda, Anna, Poreba, Marcin, Salvesen, Guy S., Drag, Marcin, Hattor, Akira, Swevers, Luc, Vourloumis, Dionisios, Stratikos, Efstratios
Probing the S1 specificity pocket of the aminopeptidases that generate antigenic peptides
BIOCHEMICAL JOURNAL, 435:411-420, APR 15 2011 2011
abstract, full text

Zhang, Yuehua, Thomas, Thommey P., Lee, Kyung-Hoon, Li, Minghsin, Zong, Hong, Desai, Ankur M., Kotlyar, Alina, Huang, Baohua, Holl, Mark M. Banaszak, Baker, James R., Jr.
Polyvalent saccharide-functionalized generation 3 poly(amidoamine) dendrimer-methotrexate conjugate as a potential anticancer agent
BIOORGANIC & MEDICINAL CHEMISTRY, 19:2557-2564, APR 15 2011 2011
abstract, full text

Alfonso, Maria, Espinosa, Arturo, Tarraga, Alberto, Molina, Pedro
A Simple but Effective Dual Redox and Fluorescent Ion Pair Receptor Based on a Ferrocene-Imidazopyrene Dyad
ORGANIC LETTERS, 13:2078-2081, APR 15 2011 2011
abstract, full text

Mitra, Pralay, Pal, Debnath
Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:787-796, APR 15 2011 2011
abstract, full text

Hamacher, Kay
Efficient Quantification of the Importance of Contacts for the Dynamical Stability of Proteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:810-815, APR 15 2011 2011
abstract, full text

Pieridou, G., Avgousti-Menelaou, C., Tamamis, P., Archontis, G., Hayes, S. C.
UV Resonance Raman Study of TTR(105-115) Structural Evolution as a Function of Temperature
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4088-4098, APR 14 2011 2011
abstract, full text

Beckham, Gregg T., Matthews, James F., Peters, Baron, Bomble, Yannick J., Himmel, Michael E., Crowley, Michael F.
Molecular-Level Origins of Biomass Recalcitrance: Decrystallization Free Energies for Four Common Cellulose Polymorphs
JOURNAL OF PHYSICAL CHEMISTRY B, 115:4118-4127, APR 14 2011 2011
abstract, full text

Rupp, Bernd, Guenther, Sebastian, Makhmoor, Talat, Schlundt, Andreas, Dickhaut, Katharina, Gupta, Shashank, Choudhary, Iqbal, Wiesmueller, Karl-Heinz, Jung, Guenther, Freund, Christian, Falk, Kirsten, Roetzschke, Olaf, Kuehne, Ronald
Characterization of Structural Features Controlling the Receptiveness of Empty Class II MHC Molecules
PLOS ONE, 6: Art. No. e18662, APR 14 2011 2011
abstract, full text

Ma, Liang, Xie, Caifeng, Ma, Yinghua, Liu, Juan, Xiang, Mingli, Ye, Xia, Zheng, Hao, Chen, Zhizhi, Xu, Qinyuan, Chen, Tao, Chen, Jinying, Yang, Jincheng, Qiu, Neng, Wang, Guangcheng, Liang, Xiaolin, Peng, Aihua, Yang, Shengyong, Wei, Yuquan, Chen, Lijuan
Synthesis and Biological Evaluation of Novel 5-Benzylidenethiazolidine-2,4-dione Derivatives for the Treatment of Inflammatory Diseases
JOURNAL OF MEDICINAL CHEMISTRY, 54:2060-2068, APR 14 2011 2011
abstract, full text

Guo, Peijun, Sknepnek, Rastko, de la Cruz, Monica Olvera
Electrostatic-Driven Ridge Formation on Nanoparticles Coated with Charged End-Group Ligands
JOURNAL OF PHYSICAL CHEMISTRY C, 115:6484-6490, APR 14 2011 2011
abstract, full text

Martin, Erik, Samoilova, Rimma I., Narasimhulu, Kupala V., Lin, Tzu-Jen, O'Malley, Patrick J., Wraight, Colin A., Dikanov, Sergei A.
Hydrogen Bonding and Spin Density Distribution in the Q(B) Semiquinone of Bacterial Reaction Centers and Comparison with the Q(A) Site
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:5525-5537, APR 13 2011 2011
abstract, full text

Tang, Grace W., Altman, Russ B.
Remote Thioredoxin Recognition Using Evolutionary Conservation and Structural Dynamics
STRUCTURE, 19:461-470, APR 13 2011 2011
abstract, full text

Lee, Hwankyu, Larson, Ronald G.
Effects of PEGylation on the Size and Internal Structure of Dendrimers: Self-Penetration of Long PEG Chains into the Dendrimer Core
MACROMOLECULES, 44:2291-2298, APR 12 2011 2011
abstract, full text

Berski, Slawomir, Latajka, Zdzislaw, Gordon, Agnieszka J.
Oxygen bound iodine (O-I): The Electron Localization Function (ELF) study on bonding in cis- and trans-IONO
CHEMICAL PHYSICS LETTERS, 506:15-21, APR 11 2011 2011
abstract, full text

Oloo, Eliud O., Yethon, Jeremy A., Ochs, Martina M., Carpick, Bruce, Oomen, Raymond
Structure-guided Antigen Engineering Yields Pneumolysin Mutants Suitable for Vaccination against Pneumococcal Disease
JOURNAL OF BIOLOGICAL CHEMISTRY, Issue 14, , APR 8 2011 2011
abstract, full text

Jin, Lin, Auerbach, Scott M., Monson, Peter A.
Modeling three-dimensional network formation with an atomic lattice model: Application to silicic acid polymerization
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 134703, APR 7 2011 2011
abstract, full text

Mueller, Robyn M., North, Michael A., Hati, Chee Yang Sanchita, Bhattacharyya, Sudeep
Interplay of Flavin's Redox States and Protein Dynamics: An Insight from QM/MM Simulations of Dihydronicotinamide Riboside Quinone Oxidoreductase 2
JOURNAL OF PHYSICAL CHEMISTRY B, 115:3632-3641, APR 7 2011 2011
abstract, full text

Lee, Hwankyu, Larson, Ronald G.
Membrane Pore Formation Induced by Acetylated and Polyethylene Glycol-Conjugated Polyamidoamine Dendrimers
JOURNAL OF PHYSICAL CHEMISTRY C, 115:5316-5322, APR 7 2011 2011
abstract, full text

Suyetin, Mikhail V., Vakhrushev, Alexander V.
Guided Carbon Nanocapsules for Hydrogen Storage
JOURNAL OF PHYSICAL CHEMISTRY C, 115:5485-5491, APR 7 2011 2011
abstract, full text

Murail, Samuel, Wallner, Bjorn, Trudell, James R., Bertaccini, Edward, Lindahl, Erik
Microsecond Simulations Indicate that Ethanol Binds between Subunits and Could Stabilize an Open-State Model of a Glycine Receptor
BIOPHYSICAL JOURNAL, 100:1642-1650, APR 6 2011 2011
abstract, full text

Ikeshoji, Tamio, Tsuchida, Eiji, Morishita, Tetsuya, Ikeda, Kazutaka, Matsuo, Motoaki, Kawazoe, Yoshiyuki, Orimo, Shin-ichi
Fast-ionic conductivity of Li(+) in LiBH(4)
PHYSICAL REVIEW B, 83: Art. No. 144301, APR 6 2011 2011
abstract, full text

Freed, Alexander S., Cramer, Steven M.
Protein-Surface Interaction Maps for Ion-Exchange Chromatography
LANGMUIR, 27:3561-3568, APR 5 2011 2011
abstract, full text

Manna, Moutusi, Mukhopadhyay, Chaitali
Molecular Dynamics Simulations of the Interactions of Kinin Peptides with an Anionic POPG Bilayer
LANGMUIR, 27:3713-3722, APR 5 2011 2011
abstract, full text

Yang, Cheng, Lu, Diannan, Liu, Zheng
How PEGylation Enhances the Stability and Potency of Insulin: A Molecular Dynamics Simulation
BIOCHEMISTRY, 50:2585-2593, APR 5 2011 2011
abstract, full text

Torrent-Sucarrat, Miquel, Ruiz-Lopez, Manuel F., Martins-Costa, Marilia, Francisco, Joseph S., Anglada, Josep M.
Protonation of Water Clusters Induced by Hydroperoxyl Radical Surface Adsorption
CHEMISTRY-A EUROPEAN JOURNAL, 17:5076-5085, APR 2011 2011
abstract, full text

Bruno, Agostino, Beato, Claudia, Costantino, Gabriele
Molecular dynamics simulations and docking studies on 3D models of the heterodimeric and homodimeric 5-HT(2A) receptor subtype
FUTURE MEDICINAL CHEMISTRY, 3:665-681, APR 2011 2011
abstract, full text

Nakagawa, Tomoki, Satake, Ryoko, Sato, Masaru, Kino, Kuniki
Structure-Based Modification of D-Alanine-D-Alanine Ligase from Thermotoga maritima ATCC 43589 for Depsipeptide Synthesis
BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 75:700-704, APR 2011 2011
abstract, full text

Robinson, Mark W., Corvo, Ileana, Jones, Peter M., George, Anthony M., Padula, Matthew P., To, Joyce, Cancela, Martin, Rinaldi, Gabriel, Tort, Jose F., Roche, Leda, Dalton, John P.
Collagenolytic Activities of the Major Secreted Cathepsin L Peptidases Involved in the Virulence of the Helminth Pathogen, Fasciola hepatica
PLOS NEGLECTED TROPICAL DISEASES, 5: Art. No. e1012, APR 2011 2011
abstract, full text

Bruno, Agostino, Amori, Laura, Costantino, Gabriele
Addressing the Conformational Flexibility of Serine Racemase by Combining Targeted Molecular Dynamics, Conformational Sampling and Docking Studies
MOLECULAR INFORMATICS, 30:317-328, APR 2011 2011
abstract, full text

Perez-Castillo, Yunierkis, Froeyen, Matheus, Angel Cabrera-Perez, Miguel, Nowe, Ann
Molecular dynamics and docking simulations as a proof of high flexibility in E. coli FabH and its relevance for accurate inhibitor modeling
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:371-393, APR 2011 2011
abstract, full text

Quiroga, Sandra L., Almaraz, Alejandra E., Amorebieta, Valentin T., Perissinotti, Laura L., Olabe, Jose A.
Addition and Redox Reactivity of Hydrogen Sulfides (H(2)S/HS(-)) with Nitroprusside: New Chemistry of Nitrososulfide Ligands
CHEMISTRY-A EUROPEAN JOURNAL, 17:4145-4156, APR 2011 2011
abstract, full text

Vilar, Santiago, Karpiak, Joel, Berk, Barkin, Costanzi, Stefano
In silico analysis of the binding of agonists and blockers to the beta(2)-adrenergic receptor
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:809-817, APR 2011 2011
abstract, full text

Durrant, Jacob D., McCammon, J. Andrew
BINANA: A novel algorithm for ligand-binding characterization
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:888-893, APR 2011 2011
abstract, full text

Bahrami, M., Kalantarinejad, R., Aghaei, M. J., Azadi, N.
Simulation of the Interaction of Carbon Nanotubes and External Flow
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 8:563-567, APR 2011 2011
abstract, full text

Liang Hao, Liu Tao, Chen FangJin, Liu ZhaoQing, Liu ShaoJun
A full-length 3D structure for MAPK/ERK kinase 2 (MEK2)
SCIENCE CHINA-LIFE SCIENCES, 54:336-341, APR 2011 2011
abstract, full text

Buch, Idit, Tsai, Chung-Jung, Wolfson, Haim J., Nussinov, Ruth
Symmetry-Based Self-assembled Nanotubes Constructed Using Native Protein Structures: The Key Role of Flexible Linkers
PROTEIN AND PEPTIDE LETTERS, 18:362-372, APR 2011 2011
abstract, full text

Zwier, Matthew C., Kaus, Joseph W., Chong, Lillian T.
Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na(+)/Cl(-), Methane/Benzene, and K(+)/18-Crown-6 Ether
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1189-1197, APR 2011 2011
abstract, full text

Mak, C. H., Chung, Wen-Yeuan, Markovskiy, Nikolay D.
RNA Conformational Sampling: II. Arbitrary Length Multinucleotide Loop Closure
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:1198-1207, APR 2011 2011
abstract, full text

Lee, Jun Hyuck, Park, HaJeung, Park, Soo Jeong, Kim, Hak Jun, Eom, Soo Hyun
The structural flexibility of the shank1 PDZ domain is important for its binding to different ligands
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 407:207-212, APR 1 2011 2011
abstract, full text

Ohkubo, Takahiro, Kidena, Koh, Takimoto, Naohiko, Ohira, Akihiro
Molecular dynamics simulations of Nafion and sulfonated polyether sulfone membranes. I. Effect of hydration on aqueous phase structure
JOURNAL OF MOLECULAR MODELING, 17:739-755, APR 2011 2011
abstract, full text

Purohit, Rituraj, Rajendran, Vidya, Sethumadhavan, Rao
Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: An in silico analysis
JOURNAL OF MOLECULAR MODELING, 17:869-877, APR 2011 2011
abstract, full text

Turcheniuk, Kostiantyn V., Rozhenko, Alexander B., Shevchenko, Igor V.
Synthesis and Some Chemical Properties of a 1,2 lambda(3)sigma(3)-Thiaphosphirane
EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 11, 1762-1767, APR 2011 2011
abstract, full text

Basan, Markus, Prost, Jacques, Joanny, Jean-Francois, Elgeti, Jens
Dissipative particle dynamics simulations for biological tissues: rheology and competition
PHYSICAL BIOLOGY, 8: Art. No. 026014, APR 2011 2011
abstract, full text

Chen, Rong, Mark, Alan E.
The effect of membrane curvature on the conformation of antimicrobial peptides: implications for binding and the mechanism of action
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:545-553, APR 2011 2011
abstract, full text

Polverini, Eugenia, Lardi, Paolo, Mazzini, Alberto, Sorbi, Robert T., Virna, Conti, Ramoni, Roberto, Favilla, Roberto
Characterization of a Deswapped Triple Mutant Bovine Odorant Binding Protein
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 12:2294-2314, APR 2011 2011
abstract, full text

Avila, Carolina M., Lopes, Alexandra B., Goncalves, Arlan S., da Silva, Leandro L., Romeiro, Nelilma C., Miranda, Ana Luisa P., Sant'Anna, Carlos M. R., Barreiro, Eliezer J., Fraga, Carlos A. M.
Structure-based design and biological profile of (E)-N-(4-Nitrobenzylidene)-2-naphthohydrazide, a novel small molecule inhibitor of I kappa B kinase-beta
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 46:1245-1253, APR 2011 2011
abstract, full text

Tak-Tak, Lotfi, Barbault, Florent, Maurel, Francois, Busca, Patricia, Le Merrer, Yves
Synthesis of purin-2-yl and purin-6-yl-aminoglucitols as C-nucleosidic ATP mimics and biological evaluation as FGFR3 inhibitors
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 46:1254-1262, APR 2011 2011
abstract, full text

Kumar, G. Senthil, Upadhyay, Sanjeev, Mathew, M. K., Sarma, Siddhartha P.
Solution structure of BTK-2, a novel hK(v)1.1 inhibiting scorpion toxin, from the eastern Indian scorpion Mesobuthus tamulus
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:459-469, APR 2011 2011
abstract, full text

Sosnowski, Tomasz R., Kolinski, Michal, Gradon, Leon
Interactions of Benzo[a]pyrene and Diesel Exhaust Particulate Matter with the Lung Surfactant System
ANNALS OF OCCUPATIONAL HYGIENE, 55:329-338, APR 2011 2011
abstract, full text

Kleinlogel, Sonja, Feldbauer, Katrin, Dempski, Robert E., Fotis, Heike, Wood, Phillip G., Bamann, Christian, Bamberg, Ernst
Ultra light-sensitive and fast neuronal activation with the Ca(2+)-permeable channelrhodopsin CatCh
NATURE NEUROSCIENCE, 14:513-U152, APR 2011 2011
abstract, full text

Li, Zhenhai, Yang, Wei
Force fluctuation on pulling a ssDNA from a carbon nanotube
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY, 10:221-227, APR 2011 2011
abstract, full text

McNicholas, S., Potterton, E., Wilson, K. S., Noble, M. E. M.
Presenting your structures: the CCP4mg molecular-graphics software
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 67:386-394, APR 2011 2011
abstract, full text

Haider, Shozeb, Joseph, Caleb G., Neidle, Stephen, Fierke, Carol A., Fuchter, Matthew J.
On the function of the internal cavity of histone deacetylase protein 8: R37 is a crucial residue for catalysis
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 21:2129-2132, APR 1 2011 2011
abstract, full text

Tomczak, Aurelie, Pisabarro, M. Teresa
Identification of CCR2-binding features in Cytl1 by a CCL2-like chemokine model
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1277-1292, APR 2011 2011
abstract, full text

Nuttall, Stewart D., Wilkins, Michelle L., Streltsov, Victor A., Pontes-Braz, Luisa, Dolezal, Olan, Tran, Hung, Liu, Chun-Qiang
Isolation, kinetic analysis, and structural characterization of an antibody targeting the Bacillus anthracis major spore surface protein BclA
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:1306-1317, APR 2011 2011
abstract, full text

Shakerzadeh, M., Teo, E. H. T., Sorkin, A., Bosman, M., Tay, B. K., Su, H.
Plasma density induced formation of nanocrystals in physical vapor deposited carbon films
CARBON, 49:1733-1744, APR 2011 2011
abstract, full text

Gomez, Fernando A., Cardenas, Constanza, Henriquez, Vitalia, Marshall, Sergio H.
Characterization of a functional toxin-antitoxin module in the genome of the fish pathogen Piscirickettsia salmonis
FEMS MICROBIOLOGY LETTERS, 317:83-92, APR 2011 2011
abstract, full text

Olmez, Elif Ozkirimli, Alakent, Burak
Alpha7 Helix Plays an Important Role in the Conformational Stability of PTP1B
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:675-693, APR 2011 2011
abstract, full text

Xu, Xianjin, Su, Jiguo, Chen, Weizu, Wang, Cunxin
Thermal Stability and Unfolding Pathways of Sso7d and its Mutant F31A: Insight from Molecular Dynamics Simulation
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:717-727, APR 2011 2011
abstract, full text

Zhao, Yunjie, Gong, Zhou, Xiao, Yi
Improvements of the Hierarchical Approach for Predicting RNA Tertiary Structure
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:815-826, APR 2011 2011
abstract, full text

Strzelecki, Janusz W., Strzelecka, Joanna, Mikulska, Karolina, Tszydel, Mariusz, Balter, Aleksander, Nowak, Wieslaw
Nanomechanics of new materials - AFM and computer modelling studies of trichoptera silk
CENTRAL EUROPEAN JOURNAL OF PHYSICS, 9:482-491, APR 2011 2011
abstract, full text

Wang, Hai-Jing, Kleinhammes, Alfred, Tang, Pei, Xu, Yan, Wu, Yue
Temperature dependence of lysozyme hydration and the role of elastic energy
PHYSICAL REVIEW E, 83: Art. No. 031924, MAR 31 2011 2011
abstract, full text

Xiu, Peng, Yang, Zaixing, Zhou, Bo, Das, Payel, Fang, Haiping, Zhou, Ruhong
Urea-Induced Drying of Hydrophobic Nanotubes: Comparison of Different Urea Models
JOURNAL OF PHYSICAL CHEMISTRY B, 115:2988-2994, MAR 31 2011 2011
abstract, full text

Wu, Jian, Walker, Victoria E. J., Boyd, Russell J.
Theoretical Study of Polaron Formation in Poly(G)-Poly(C) Cations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:3136-3145, MAR 31 2011 2011
abstract, full text

Neugebauer, Johannes, Veldstra, Jan, Buda, Francesco
Theoretical Spectroscopy of Astaxanthin in Crustacyanin Proteins: Absorption, Circular Dichroism, and Nuclear Magnetic Resonance
JOURNAL OF PHYSICAL CHEMISTRY B, 115:3216-3225, MAR 31 2011 2011
abstract, full text

Alfonso-Prieto, M., Oberhofer, H., Klein, M. L., Rovira, C., Blumberger, J.
Proton Transfer Drives Protein Radical Formation in Helicobacter pylori Catalase but Not in Penicillium vitale Catalase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:4285-4298, MAR 30 2011 2011
abstract, full text

Fan, Helen Y., Shek, Yuen Lai, Amiri, Amir, Dubins, David N., Heerklotz, Heiko, Macgregor, Robert B., Jr., Chalikian, Tigran V.
Volumetric Characterization of Sodium-Induced G-Quadruplex Formation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:4518-4526, MAR 30 2011 2011
abstract, full text

Zhang, Zhiyong, Wriggers, Willy
Polymorphism of the Epidermal Growth Factor Receptor Extracellular Ligand Binding Domain: The Dimer Interface Depends on Domain Stabilization
BIOCHEMISTRY, 50:2144-2156, MAR 29 2011 2011
abstract, full text

De, Sandip, Ghasemi, S. Alireza, Willand, Alexander, Genovese, Luigi, Kanhere, Dilip, Goedecker, Stefan
The effect of ionization on the global minima of small and medium sized silicon and magnesium clusters
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 124302, MAR 28 2011 2011
abstract, full text

Kumar, Hemant, Mukherjee, Biswaroop, Lin, Shiang-Tai, Dasgupta, Chandan, Sood, A. K., Maiti, Prabal K.
Thermodynamics of water entry in hydrophobic channels of carbon nanotubes
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 124105, MAR 28 2011 2011
abstract, full text

Latorre, Mauricio, Olivares, Felipe, Reyes-Jara, Angelica, Lopez, Guadalupe, Gonzalez, Mauricio
CutC is induced late during copper exposure and can modify intracellular copper content in Enterococcus faecalis
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 406:633-637, MAR 25 2011 2011
abstract, full text

Hall, Lisa M., Stevens, Mark J., Frischknecht, Amalie L.
Effect of Polymer Architecture and Ionic Aggregation on the Scattering Peak in Model Ionomers
PHYSICAL REVIEW LETTERS, 106: Art. No. 127801, MAR 23 2011 2011
abstract, full text

Qiao, Baofu, Cerda, Juan J., Holm, Christian
Atomistic Study of Surface Effects on Polyelectrolyte Adsorption: Case Study of a Poly(styrenesulfonate) Monolayer
MACROMOLECULES, 44:1707-1718, MAR 22 2011 2011
abstract, full text

Moore, Stan G., Wheeler, Dean R.
Chemical potential perturbation: A method to predict chemical potentials in periodic molecular simulations
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 114514, MAR 21 2011 2011
abstract, full text

Ruiz, Jose, Vicente, Consuelo, de Haro, Concepcion, Espinosa, Arturo
Synthesis and Antiproliferative Activity of a C,N-Cycloplatinated(II) Complex with a Potentially Intercalative Anthraquinone Pendant
INORGANIC CHEMISTRY, 50:2151-2158, MAR 21 2011 2011
abstract, full text

Oroz, Javier, Valbuena, Alejandro, Manuel Vera, Andres, Mendieta, Jesus, Gomez-Puertas, Paulino, Carrion-Vazquez, Mariano
Nanomechanics of the Cadherin Ectodomain "CANALIZATION" BYCa2 BINDING RESULTS IN A NEW MECHANICAL ELEMENT
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:9405-9418, MAR 18 2011 2011
abstract, full text

Matthews, James F., Bergenstrahle, Malin, Beckham, Gregg T., Himmel, Michael E., Nimlos, Mark R., Brady, John W., Crowley, Michael F.
High-Temperature Behavior of Cellulose I
JOURNAL OF PHYSICAL CHEMISTRY B, 115:2155-2166, MAR 17 2011 2011
abstract, full text

Zhang, Jianguo, Su, Jiaye, Guo, Hongxia
An Atomistic Simulation for 4-Cyano-4 '-pentylbiphenyl and Its Homologue with a Reoptimized Force Field
JOURNAL OF PHYSICAL CHEMISTRY B, 115:2214-2227, MAR 17 2011 2011
abstract, full text

Aliaga, Alvaro E., Ahumada, Hernan, Sepulveda, Karen, Gomez-Jeria, Juan S., Garrido, Carlos, Weiss-Lopez, Boris E., Campos-Vallette, Marcelo M.
SERS, Molecular Dynamics and Molecular Orbital Studies of the MRKDV Peptide on Silver and Membrane Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 115:3982-3989, MAR 17 2011 2011
abstract, full text

Callejas-Tovar, Rafael, Liao, Wenta, de la Hoz, Julibeth M. Martinez, Balbuena, Perla B.
Molecular Dynamics Simulations of Surface Oxidation on Pt(111) and Pt/PtCo/Pt(3)Co(111)
JOURNAL OF PHYSICAL CHEMISTRY C, 115:4104-4113, MAR 17 2011 2011
abstract, full text

Schwaiger, Christine S., Bjelkmar, Par, Hess, Berk, Lindahl, Erik
3(10)-Helix Conformation Facilitates the Transition of a Voltage Sensor S4 Segment toward the Down State
BIOPHYSICAL JOURNAL, 100:1446-1454, MAR 16 2011 2011
abstract, full text

Mihailescu, Mihaela, Vaswani, Rishi G., Jardon-Valadez, Eduardo, Castro-Roman, Francisco, Freites, J. Alfredo, Worcester, David L., Chamberlin, A. Richard, Tobias, Douglas J., White, Stephen H.
Acyl-Chain Methyl Distributions of Liquid-Ordered and -Disordered Membranes
BIOPHYSICAL JOURNAL, 100:1455-1462, MAR 16 2011 2011
abstract, full text

de Joannis, Jason, Coppock, Patrick S., Yin, Fuchang, Mori, Makoto, Zamorano, Absalom, Kindt, James T.
Atomistic Simulation of Cholesterol Effects on Miscibility of Saturated and Unsaturated Phospholipids: Implications for Liquid-Ordered/Liquid-Disordered Phase Coexistence
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3625-3634, MAR 16 2011 2011
abstract, full text

Lee, One-Sun, Stupp, Samuel I., Schatz, George C.
Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3677-3683, MAR 16 2011 2011
abstract, full text

Yong Nam Ahn, Gupta, Ashish, Chauhan, Anuj, Kopelevich, Dmitry I.
Molecular Transport through Surfactant-Covered Oil-Water Interfaces: Role of Physical Properties of Solutes and Surfactants in Creating Energy Barriers for Transport
LANGMUIR, 27:2420-2436, MAR 15 2011 2011
abstract, full text

Haspel, Nurit, Zanuy, David, Nussinov, Ruth, Teesalu, Tambet, Ruoslahti, Erkki, Aleman, Carlos
Binding of a C-End Rule Peptide to the Neuropilin-1 Receptor: A Molecular Modeling Approach
BIOCHEMISTRY, 50:1755-1762, MAR 15 2011 2011
abstract, full text

Hartono, Yossa Dwi, Lee, Angelina Noviani, Lee-Huang, Sylvia, Zhang, Dawei
Computational study of bindings of HL9, a nonapeptide fragment of human lysozyme, to HIV-1 fusion protein gp41
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 21:1607-1611, MAR 15 2011 2011
abstract, full text

Taubert, Stefan, Kaila, Ville R. I., Sundholm, Dage
Aromatic Pathways in Conjugated Rings Connected by Single Bonds
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111:848-857, MAR 15 2011 2011
abstract, full text

Zhang, Qi Charles, Yeh, Tzu-lan, Leyva, Alfonso, Frank, Leslie G., Miller, Jason, Kim, Yujin E., Langen, Ralf, Finkbeiner, Steven, Amzel, Mario L., Ross, Christopher A., Poirier, Michelle A.
A Compact beta Model of huntingtin Toxicity
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:8188-8196, MAR 11 2011 2011
abstract, full text

Sharma, Alok K., Ye, Liwen, Baer, Christina E., Shanmugasundaram, Kumaran, Alber, Tom, Alper, Seth L., Rigby, Alan C.
Solution Structure of the Guanine Nucleotide-binding STAS Domain of SLC26-related SulP Protein Rv1739c from Mycobacterium tuberculosis
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:8534-8544, MAR 11 2011 2011
abstract, full text

Zidar, Jernej, Merzel, Franci
Probing Amyloid-Beta Fibril Stability by Increasing Ionic Strengths
JOURNAL OF PHYSICAL CHEMISTRY B, 115:2075-2081, MAR 10 2011 2011
abstract, full text

Curutchet, Carles, Kongsted, Jacob, Munoz-Losa, Aurora, Hossein-Nejad, Hoda, Scholes, Gregory D., Mennucci, Benedetta
Photosynthetic Light-Harvesting Is Tuned by the Heterogeneous Polarizable Environment of the Protein
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133:3078-3084, MAR 9 2011 2011
abstract, full text

Grafmueller, Andrea, Voth, Gregory A.
Intrinsic Bending of Microtubule Protofilaments
STRUCTURE, 19:409-417, MAR 9 2011 2011
abstract, full text

Hung, Andrew, Yarovsky, Irene
Gap Junction Hemichannel Interactions with Zwitterionic Lipid, Anionic Lipid, and Cholesterol: Molecular Simulation Studies
BIOCHEMISTRY, 50:1492-1504, MAR 8 2011 2011
abstract, full text

Ito, Mika, Johansson, Jan, Stromberg, Roger, Nilsson, Lennart
Unfolding of the Amyloid beta-Peptide Central Helix: Mechanistic Insights from Molecular Dynamics Simulations
PLOS ONE, 6: Art. No. e17587, MAR 7 2011 2011
abstract, full text

Ng, Ming-Yaw, Chang, Yia-Chung
Laser-induced breathing modes in metallic nanoparticles: A symmetric molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 094116, MAR 7 2011 2011
abstract, full text

Uhart, Marina, Iglesias, Alberto A., Bustos, Diego M.
Structurally Constrained Residues Outside the Binding Motif Are Essential in the Interaction of 14-3-3 and Phosphorylated Partner
JOURNAL OF MOLECULAR BIOLOGY, 406:552-557, MAR 4 2011 2011
abstract, full text

Jamison, Francis W., I.I., Foster, Theresa J., Barker, Jacob A., Hills, Ronald D., Jr., Guvench, Olgun
Mechanism of Binding Site Conformational Switching in the CD44-Hyaluronan Protein-Carbohydrate Binding Interaction
JOURNAL OF MOLECULAR BIOLOGY, 406:631-647, MAR 4 2011 2011
abstract, full text

Bobadilla, Alfredo D., Seminario, Jorge M.
DNA-CNT Interactions and Gating Mechanism Using MD and DFT
JOURNAL OF PHYSICAL CHEMISTRY C, 115:3466-3474, MAR 3 2011 2011
abstract, full text

Cui, Haosheng, Lyman, Edward, Voth, Gregory A.
Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins
BIOPHYSICAL JOURNAL, 100:1271-1279, MAR 2 2011 2011
abstract, full text

Wang, Ting, Duan, Yong
Retinal release from opsin in molecular dynamics simulations
JOURNAL OF MOLECULAR RECOGNITION, 24:350-358, MAR-APR 2011 2011
abstract, full text

Lu, Pinyi, Bevan, David R., Lewis, Stephanie N., Hontecillas, Raquel, Bassaganya-Riera, Josep
Molecular modeling of lanthionine synthetase component C-like protein 2: a potential target for the discovery of novel type 2 diabetes prophylactics and therapeutics
JOURNAL OF MOLECULAR MODELING, 17:543-553, MAR 2011 2011
abstract, full text

Li, Li, Yu, Long, Huang, Qiang
Molecular trigger for pre-transfer editing pathway in Valyl-tRNA synthetase: A molecular dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 17:555-564, MAR 2011 2011
abstract, full text

Silvestre-Ryan, Jordi, Lin, Yuchun, Chu, Jhih-Wei
"Fluctuograms'' Reveal the Intermittent Intra-Protein Communication in Subtilisin Carlsberg and Correlate Mechanical Coupling with Co-Evolution
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1002023, MAR 2011 2011
abstract, full text

Kirchmair, Johannes, Rollinger, Judith M., Liedl, Klaus R., Seidel, Nora, Krumbholz, Andi, Schmidtke, Michaela
Novel neuraminidase inhibitors: identification, biological evaluation and investigations of the binding mode
FUTURE MEDICINAL CHEMISTRY, 3:437-450, MAR 2011 2011
abstract, full text

Obiol-Pardo, C., Rubio-Martinez, J., Imperial, S.
The Methylerythritol Phosphate (MEP) Pathway for Isoprenoid Biosynthesis as a Target for the Development of New Drugs Against Tuberculosis
CURRENT MEDICINAL CHEMISTRY, 18:1325-1338, MAR 2011 2011
abstract, full text

Yesylevskyy, S. O., Savytskyi, O. V., Odynets, K. A., Kornelyuk, A. I.
Interdomain compactization in human tyrosyl-tRNA synthetase studied by the hierarchical rotations technique
BIOPHYSICAL CHEMISTRY, 154:90-98, MAR 2011 2011
abstract, full text

Boechi, Leonardo, Marti, Marcelo A., Vergara, Alessandro, Sica, Filomena, Mazzarella, Lelio, Estrin, Dario A., Merlino, Antonello
Protonation of Histidine 55 Affects the Oxygen Access to Heme in the Alpha Chain of the Hemoglobin from the Antarctic Fish Trematomus bernacchii
IUBMB LIFE, 63:175-182, MAR 2011 2011
abstract, full text

Heroux, Maxime S., Mohan, Anne D., Olsen, Kenneth W.
Ligand Migration in the Truncated Hemoglobin of Mycobacterium tuberculosis
IUBMB LIFE, 63:214-220, MAR 2011 2011
abstract, full text

Helal, Mohamed A., Chittiboyina, Amar G., Avery, Mitchell A.
New Insights into the Binding Mode of Melanin Concentrating Hormone Receptor-1 Antagonists: Homology Modeling and Explicit Membrane Molecular Dynamics Simulation Study
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:635-646, MAR 2011 2011
abstract, full text

Krongsuk, Sriprajak, Kerdcharoen, Teerakiat
Effects of surface concentration on the porphine monolayers: Molecular simulations at the nanoscale water-gas interface
APPLIED SURFACE SCIENCE, 257:6270-6275, MAR 1 2011 2011
abstract, full text

Patra, Niladri, Song, Yuanbo, Kral, Petr
Self-Assembly of Graphene Nanostructures on Nanotubes
ACS NANO, 5:1798-1804, MAR 2011 2011
abstract, full text

Joshi, Amit, Kate, Sandesh, Poon, Vincent, Mondal, Dhananjoy, Boggara, Mohan B., Saraph, Arundhati, Martin, Jacob T., McAlpine, Ryan, Day, Ryan, Garcia, Angel E., Mogridge, Jeremy, Kane, Ravi S.
Structure-Based Design of a Heptavalent Anthrax Toxin Inhibitor
BIOMACROMOLECULES, 12:791-796, MAR 2011 2011
abstract, full text

Yasuda, Masaaki, Mimura, Ryosuke, Kawata, Hiroaki, Hirai, Yoshihiko
Computational study on structural modification of single-walled carbon nanotubes by electron irradiation
JOURNAL OF APPLIED PHYSICS, 109: Art. No. 054304, MAR 1 2011 2011
abstract, full text

Lim, M. C. G., Zhong, Z. W.
Effects of electromigration on copper atoms in carbon nanotube channels
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 390:963-971, MAR 1 2011 2011
abstract, full text

Polverini, Eugenia, Coll, Eoin P., Tieleman, D. Peter, Harauz, George
Conformational choreography of a molecular switch region in myelin basic protein-Molecular dynamics shows induced folding and secondary structure type conversion upon threonyl phosphorylation in both aqueous and membrane-associated environments
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:674-683, MAR 2011 2011
abstract, full text

Shahlaei, Mohsen, Madadkar-Sobhani, Armin, Mahnam, Karim, Fassihi, Afshin, Saghaie, Lotfollah, Mansourian, Mahboubeh
Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:802-817, MAR 2011 2011
abstract, full text

Anandakrishnan, Ramu, Daga, Mayank, Onufriev, Alexey V.
An n log n Generalized Born Approximation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:544-559, MAR 2011 2011
abstract, full text

Rommel, Judith B., Goumans, T. P. M., Kaestner, Johannes
Locating Instantons in Many Degrees of Freedom
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:690-698, MAR 2011 2011
abstract, full text

Wohlert, Jakob, Berglund, Lars A.
A Coarse-Grained Model for Molecular Dynamics Simulations of Native Cellulose
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:753-760, MAR 2011 2011
abstract, full text

Pascual, Isel, Gomez, Hansel, Pons, Tirso, Chappe, Mae, Angel Vargas, Miguel, Valdes, Gilberto, Lopez, Ali, Saroyan, Angelika, Charli, Jean-Louis, de los Angeles Chavez, Maria
Effect of divalent cations on the porcine kidney cortex membrane-bound form of dipeptidyl peptidase IV
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 43:363-371, MAR 2011 2011
abstract, full text

Kulczycka, Katarzyna, Dlugosz, Maciej, Trylska, Joanna
Molecular dynamics of ribosomal elongation factors G and Tu
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:289-303, MAR 2011 2011
abstract, full text

Qiu, Hu, Shen, Rong, Guo, Wanlin
Vibrating carbon nanotubes as water pumps
NANO RESEARCH, 4:284-289, MAR 2011 2011
abstract, full text

Awasthi, Shanjana, Brown, Kevin, King, Catherine, Awasthi, Vibhudutta, Bondugula, Rajkumar
A Toll-Like Receptor-4-Interacting Surfactant Protein-A-Derived Peptide Suppresses Tumor Necrosis Factor-alpha Release from Mouse JAWS II Dendritic Cells
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS, 336:672-681, MAR 2011 2011
abstract, full text

Janovec, Ladislav, Kozurkova, Maria, Sabolova, Danica, Ungvarsky, Jan, Paulikova, Helena, Plsikova, Jana, Vantova, Zuzana, Imrich, Jan
Cytotoxic 3,6-bis((imidazolidinone)imino)acridines: Synthesis, DNA binding and molecular modeling
BIOORGANIC & MEDICINAL CHEMISTRY, 19:1790-1801, MAR 1 2011 2011
abstract, full text

Huarte-Larranaga, F., Aguilar, A., Lucas, J. M., Alberti, M.
A 3D-analysis of the Cl(-)-benzene dimer solvation by Ar atoms
THEORETICAL CHEMISTRY ACCOUNTS, 128:757-767, MAR 2011 2011
abstract, full text

Gumbart, James, Chipot, Christophe, Schulten, Klaus
Free-energy cost for translocon-assisted insertion of membrane proteins
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:3596-3601, MAR 1 2011 2011
abstract, full text

Lin, Ying-Wu
Structural insights into a low-spin myoglobin variant with bis-histidine coordination from molecular modeling
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:679-684, MAR 2011 2011
abstract, full text

Hayes, Joseph M., Skamnaki, Vicky T., Archontis, Georgios, Lamprakis, Christos, Sarrou, Josephine, Bischler, Nicolas, Skaltsounis, Alexios-Leandros, Zographos, Spyros E., Oikonomakos, Nikos G.
Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules examined
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:703-719, MAR 2011 2011
abstract, full text

Wong, Sergio E., Sellers, Ben D., Jacobson, Matthew P.
Effects of somatic mutations on CDR loop flexibility during affinity maturation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:821-829, MAR 2011 2011
abstract, full text

Cho, Kyung-Bin, Lai, Wenzhen, Hamberg, Mats, Raman, C. S., Shaik, Sason
The reaction mechanism of allene oxide synthase: Interplay of theoretical QM/MM calculations and experimental investigations
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 507:14-25, MAR 1 2011 2011
abstract, full text

Rao, Geeta Vittal, Brooks, Charles L.
Functional Epitopes for Site 1 of Human Prolactin
BIOCHEMISTRY, 50:1347-1358, MAR 1 2011 2011
abstract, full text

Rodriguez Limardo, Ramiro G., Ferreiro, Dardo N., Roitberg, Adrian E., Marti, Marcelo A., Turjanski, Adrian G.
p38 gamma Activation Triggers Dynamical Changes in Allosteric Docking Sites
BIOCHEMISTRY, 50:1384-1395, MAR 1 2011 2011
abstract, full text

Trabuco, Leonardo G., Schreiner, Eduard, Gumbart, James, Hsin, Jen, Villa, Elizabeth, Schulten, Klaus
Applications of the molecular dynamics flexible fitting method
JOURNAL OF STRUCTURAL BIOLOGY, 173:420-427, MAR 2011 2011
abstract, full text

Birmanns, Stefan, Rusu, Mirabela, Wriggers, Willy
Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes
JOURNAL OF STRUCTURAL BIOLOGY, 173:428-435, MAR 2011 2011
abstract, full text

Wriggers, Willy, Alamo, Lorenzo, Padron, Raul
Matching structural densities from different biophysical origins with gain and bias
JOURNAL OF STRUCTURAL BIOLOGY, 173:445-450, MAR 2011 2011
abstract, full text

Lim, M. C. G., Zhong, Z. W.
Dynamical behavior of copper atoms in a carbon nanotube channel
CARBON, 49:996-1005, MAR 2011 2011
abstract, full text

Philip, Benjamin N., Kiss, Andor J., Lee, Richard E., Jr.
The protective role of aquaporins in the freeze-tolerant insect Eurosta solidaginis: functional characterization and tissue abundance of EsAQP1
JOURNAL OF EXPERIMENTAL BIOLOGY, 214:848-857, MAR 2011 2011
abstract, full text

Singh, Abhishek K., Penev, Evgeni S., Yakobson, Boris I.
Armchair or Zigzag? A tool for characterizing graphene edge
COMPUTER PHYSICS COMMUNICATIONS, 182:804-807, MAR 2011 2011
abstract, full text

Hu, Yan, Bojikova-Fournier, Svetla, King, Allison M., MacRae, Thomas H.
The structural stability and chaperone activity of artemin, a ferritin homologue from diapause-destined Artemia embryos, depend on different cysteine residues
CELL STRESS & CHAPERONES, 16:133-141, MAR 2011 2011
abstract, full text

Secundo, Francesco, Fiala, Stefano, Fraaije, Marco W., de Gonzalo, Gonzalo, Meli, Massimiliano, Zambianchi, Francesca, Ottolina, Gianluca
Effects of Water Miscible Organic Solvents on the Activity and Conformation of the Baeyer-Villiger Monooxygenases From Thermobifida fusca and Acinetobacter calcoaceticus: A Comparative Study
BIOTECHNOLOGY AND BIOENGINEERING, 108:491-499, MAR 2011 2011
abstract, full text

Gan, Y., Chen, Z., Montgomery-Smith, S.
Improved Material Point Method for Simulating the Zona Failure Response in Piezo-Assisted Intracytoplasmic Sperm Injection
CMES-COMPUTER MODELING IN ENGINEERING & SCIENCES, 73:45-75, MAR 2011 2011
abstract, full text

Yao Xuexia, Xu Suming
Activation Mechanism Study of Glucokinase by M197V Mutation
ACTA CHIMICA SINICA, 69:405-410, FEB 28 2011 2011
abstract, full text

Peplowski, Lukasz, Sikora, Mateusz, Nowak, Wieslaw, Cieplak, Marek
Molecular jamming-The cystine slipknot mechanical clamp in all-atom simulations
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 085102, FEB 28 2011 2011
abstract, full text

Zhang, Yiyang, Li, Shuiqing, Yan, Wen, Yao, Qiang, Tse, Stephen D.
Role of dipole-dipole interaction on enhancing Brownian coagulation of charge-neutral nanoparticles in the free molecular regime
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 084501, FEB 28 2011 2011
abstract, full text

NategholEslam, Mostafa, Holland, Bryan W., Gray, C. G., Tomberli, Bruno
Drift-oscillatory steering with the forward-reverse method for calculating the potential of mean force
PHYSICAL REVIEW E, 83: Art. No. 021114, FEB 28 2011 2011
abstract, full text

Foote, Andrew D., Morin, Phillip A., Durban, John W., Pitman, Robert L., Wade, Paul, Willerslev, Eske, Gilbert, M. Thomas P., da Fonseca, Rute R.
Positive selection on the killer whale mitogenome
BIOLOGY LETTERS, 7:116-118, FEB 23 2011 2011
abstract, full text

Project, Elad, Nachliel, Esther, Gutman, Menachem
The Dynamics of Ca(2+) Ions within the Solvation Shell of Calbindin D9k
PLOS ONE, 6: Art. No. e14718, FEB 22 2011 2011
abstract, full text

Varilly, Patrick, Patel, Amish J., Chandler, David
An improved coarse-grained model of solvation and the hydrophobic effect
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 074109, FEB 21 2011 2011
abstract, full text

Saha, Leton C., Mian, Shabeer A., Kim, Hyojeong, Saha, Joyanta K., Matin, Mohammad A., Jang, Joonkyung
Molecular Dynamics of Carbon Nanotubes Deposited on a Silicon Surface via Collision: Temperature Dependence
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 32:515-518, FEB 20 2011 2011
abstract, full text

Hancock, Stephen P., Hiller, David A., Perona, John J., Jen-Jacobson, Linda
The Energetic Contribution of Induced Electrostatic Asymmetry to DNA Bending by a Site-Specific Protein
JOURNAL OF MOLECULAR BIOLOGY, 406:285-312, FEB 18 2011 2011
abstract, full text

Rodrigues, Juliana F., Mathias-Santos, Camila, Sbrogio-Almeida, Maria Elisabete, Amorim, Jaime H., Cabrera-Crespo, Joaquim, Balan, Andrea, Ferreira, Luis C. S.
Functional Diversity of Heat-labile Toxins (LT) Produced by Enterotoxigenic Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:5222-5233, FEB 18 2011 2011
abstract, full text

Knaup, Jan M., Li, Han, Vlassak, Joost J., Kaxiras, Efthimios
Influence of CH(2) content and network defects on the elastic properties of organosilicate glasses
PHYSICAL REVIEW B, 83: Art. No. 054204, FEB 17 2011 2011
abstract, full text

Sammalkorpi, M., Sanders, S., Panagiotopoulos, A. Z., Karttunen, M., Haataja, M.
Simulations of Micellization of Sodium Hexyl Sulfate
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1403-1410, FEB 17 2011 2011
abstract, full text

Yan, Chunli, Kaoud, Tamer, Lee, Sunbae, Dalby, Kevin N., Ren, Pengyu
Understanding the Specificity of a Docking Interaction between JNK1 and the Scaffolding Protein JIP1
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1491-1502, FEB 17 2011 2011
abstract, full text

Hsin, Jen, Schulten, Klaus
Improved Resolution of Tertiary Structure Elasticity in Muscle Protein
BIOPHYSICAL JOURNAL, 100:L22-L24, FEB 16 2011 2011
abstract, full text

Calero, Carles, Faraudo, Jordi, Aguilella-Arzo, Marcel
First-passage-time analysis of atomic-resolution simulations of the ionic transport in a bacterial porin
PHYSICAL REVIEW E, 83: Art. No. 021908, FEB 16 2011 2011
abstract, full text

Plasencia, Ines, Survery, Sabeen, Ibragimova, Sania, Hansen, Jesper S., Kjellbom, Per, Helix-Nielsen, Claus, Johanson, Urban, Mouritsen, Ole G.
Structure and Stability of the Spinach Aquaporin SoPIP2;1 in Detergent Micelles and Lipid Membranes
PLOS ONE, 6: Art. No. e14674, FEB 14 2011 2011
abstract, full text

Gimenez, M. C., Schmicker, Wolfgang
Monte Carlo simulation of nanowires of different metals and two-metal alloys
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 064707, FEB 14 2011 2011
abstract, full text

Santiso, Erik E., Trout, Bernhardt L.
A general set of order parameters for molecular crystals
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 064109, FEB 14 2011 2011
abstract, full text

Haiko, Johanna, Laakkonen, Liisa, Westerlund-Wikstrom, Benita, Korhonen, Timo K.
Molecular adaptation of a plant-bacterium outer membrane protease towards plague virulence factor Pla
BMC EVOLUTIONARY BIOLOGY, 11: Art. No. 43, FEB 11 2011 2011
abstract, full text

Michel, Lea Vacca, Kalmeta, Breanna, McCreary, Mark, Snyder, Joy, Craig, Paul, Pichichero, Michael E.
Vaccine candidate P6 of nontypable Haemophilus influenzae is not a transmembrane protein based on protein structural analysis
VACCINE, 29:1624-1627, FEB 11 2011 2011
abstract, full text

Henry, David J., Szarek, Pawel, Hirai, Kosuke, Ichikawa, Kazuhide, Tachibana, Akitomo, Yarovsky, Irene
Reactivity and Regioselectivity of Aluminum Nanoclusters: Insights from Regional Density Functional Theory
JOURNAL OF PHYSICAL CHEMISTRY C, 115:1714-1723, FEB 10 2011 2011
abstract, full text

Liu, Yingzhe, Chipot, Christophe, Shao, Xueguang, Cai, Wensheng
Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide
JOURNAL OF PHYSICAL CHEMISTRY C, 115:1851-1856, FEB 10 2011 2011
abstract, full text

Joutsuka, Tatsuya, Ando, Koji
Hydration Structure in Dilute Hydrofluoric Acid
JOURNAL OF PHYSICAL CHEMISTRY A, 115:671-677, FEB 10 2011 2011
abstract, full text

Joutsuka, Tatsuya, Ando, Koji
Dynamics of Proton Transfer and Vibrational Relaxation in Dilute Hydrofluoric Acid
JOURNAL OF PHYSICAL CHEMISTRY A, 115:678-684, FEB 10 2011 2011
abstract, full text

Oliveira, Augusto F., Gemming, Sibylle, Seifert, Gotthard
Conformational Analysis of Aqueous BMP-2 Using Atomistic Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1122-1130, FEB 10 2011 2011
abstract, full text

Chang, Zhongwen, Luo, Yin, Zhang, Yun, Wei, Guanghong
Interactions of A beta 25-35 beta-Barrel-like Oligomers with Anionic Lipid Bilayer and Resulting Membrane Leakage: An All-Atom Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1165-1174, FEB 10 2011 2011
abstract, full text

Mroginski, Maria Andrea, Kaminski, Steve, von Stetten, David, Ringsdorf, Simone, Gaertner, Wolfgang, Essen, Lars-Oliver, Hildebrandt, Peter
Structure of the Chromophore Binding Pocket in the Pr State of Plant Phytochrome phyA
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1220-1231, FEB 10 2011 2011
abstract, full text

Lu, Yan, Wei, Guanghong, Derreumaux, Philippe
Effects of G33A and G33I Mutations on the Structures of Monomer and Dimer of the Amyloid-beta Fragment 29-42 by Replica Exchange Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:1282-1288, FEB 10 2011 2011
abstract, full text

Su, Zhi-Yuan, Wang, Yeng-Tseng
Coarse-Grained Molecular Dynamics Simulations of Cobra Cytotoxin A3 Interactions with a Lipid Bilayer: Penetration of Loops into Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:796-802, FEB 10 2011 2011
abstract, full text

Nechushtai, Rachel, Lammert, Heiko, Michaeli, Dorit, Eisenberg-Domovich, Yael, Zuris, John A., Luca, Maria A., Capraro, Dominique T., Fish, Alex, Shimshon, Odelia, Roy, Melinda, Schug, Alexander, Whitford, Paul C., Livnah, Oded, Onuchic, Jose N., Jennings, Patricia A.
Allostery in the ferredoxin protein motif does not involve a conformational switch
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108:2240-2245, FEB 8 2011 2011
abstract, full text

Harada, Ryuhei, Kitao, Akio
Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models
CHEMICAL PHYSICS LETTERS, 503:145-152, FEB 8 2011 2011
abstract, full text

Garate, J. -A., English, Niall J., MacElroy, J. M. D.
Human aquaporin 4 gating dynamics in dc and ac electric fields: A molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 055110, FEB 7 2011 2011
abstract, full text

Li, Xiang, Ko, Yeon-Jae, Wang, Haopeng, Bowen, Kit H., Guevara-Garcia, Alfredo, Martinez, Ana
Photoelectron and computational studies of the copper-nucleoside anionic complexes, Cu(-)(cytidine) and Cu(-)(uridine)
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 054318, FEB 7 2011 2011
abstract, full text

Woods, Christopher J., Malaisree, Maturos, Hannongbua, Supot, Mulholland, Adrian J.
A water-swap reaction coordinate for the calculation of absolute protein-ligand binding free energies
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 054114, FEB 7 2011 2011
abstract, full text

Stavrakoudis, Athanassios
Cis-trans isomerization of the Epstein-Barr virus determinant peptide EENLLDFVRF after the DM1 TCR recognition of the HLA-B*4405/peptide complex
FEBS LETTERS, 585:485-491, FEB 4 2011 2011
abstract, full text

Brandt, Tobias, Holzmann, Nicole, Muley, Laveena, Khayat, Maan, Wegscheid-Gerlach, Christof, Baum, Bernhard, Heine, Andreas, Hangauer, David, Klebe, Gerhard
Congeneric but Still Distinct: How Closely Related Trypsin Ligands Exhibit Different Thermodynamic and Structural Properties
JOURNAL OF MOLECULAR BIOLOGY, 405:1170-1187, FEB 4 2011 2011
abstract, full text

Teoh, Chai Lean, Pham, Chi L. L., Todorova, Nevena, Hung, Andrew, Lincoln, Craig N., Lees, Emma, Lam, Yuen Han, Binger, Katrina J., Thomson, Neil H., Radford, Sheena E., Smith, Trevor A., Mueller, Shirley A., Engel, Andreas, Griffin, Michael D. W., Yarovsky, Irene, Gooley, Paul R., Howlett, Geoffrey J.
A Structural Model for Apolipoprotein C-II Amyloid Fibrils: Experimental Characterization and Molecular Dynamics Simulations
JOURNAL OF MOLECULAR BIOLOGY, 405:1246-1266, FEB 4 2011 2011
abstract, full text

Bessadok, Anis, Garcia, Elisabeth, Jacquet, Helene, Martin, Solenne, Garrigues, Alexia, Loiseau, Nicolas, Andre, Francois, Orlowski, Stephane, Vivaudou, Michel
Recognition of Sulfonylurea Receptor (ABCC8/9) Ligands by the Multidrug Resistance Transporter P-glycoprotein (ABCB1) FUNCTIONAL SIMILARITIES BASED ON COMMON STRUCTURAL FEATURES BETWEEN TWO MULTISPECIFIC ABC PROTEINS
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:3552-3569, FEB 4 2011 2011
abstract, full text

Sapir, Liel, Harries, Daniel
Linking Trehalose Self-Association with Binary Aqueous Solution Equation of State
JOURNAL OF PHYSICAL CHEMISTRY B, 115:624-634, FEB 3 2011 2011
abstract, full text

White, Andrew, Jiang, Shaoyi
Local and Bulk Hydration of Zwitterionic Glycine and its Analogues through Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 115:660-667, FEB 3 2011 2011
abstract, full text

Kohagen, Miriam, Brehm, Martin, Thar, Jens, Zhao, Wei, Mueller-Plathe, Florian, Kirchner, Barbara
Performance of Quantum Chemically Derived Charges and Persistence of Ion Cages in Ionic Liquids. A Molecular Dynamics Simulations Study of 1-n-Butyl-3-methylimidazolium Bromide
JOURNAL OF PHYSICAL CHEMISTRY B, 115:693-702, FEB 3 2011 2011
abstract, full text

Olbrich, Carsten, Struempfer, Johan, Schulten, Klaus, Kleinekathoefer, Ulrich
Quest for Spatially Correlated Fluctuations in the FMO Light-Harvesting Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 115:758-764, FEB 3 2011 2011
abstract, full text

Bastug, Turgut, Kuyucak, Serdar
Comparative Study of the Energetics of Ion Permeation in Kv1.2 and KcsA Potassium Channels
BIOPHYSICAL JOURNAL, 100:629-636, FEB 2 2011 2011
abstract, full text

Kokhan, Oleksandr, Shinkarev, Vladimir P.
All-Atom Molecular Dynamics Simulations Reveal Significant Differences in Interaction between Antimycin and Conserved Amino Acid Residues in Bovine and Bacterial bc(1) Complexes
BIOPHYSICAL JOURNAL, 100:720-728, FEB 2 2011 2011
abstract, full text

Srivastava, Mugdha, Abhilash, P. C., Singh, Nandita
Remediation of Lindane Using Engineered Nanoparticles
JOURNAL OF BIOMEDICAL NANOTECHNOLOGY, 7:172-174, FEB 2011 2011
abstract, full text

Skjevik, Age Aleksander, Haug, Bengt Erik, Lygre, Henning, Teigen, Knut
Intramolecular hydrogen bonding in articaine can be related to superior bone tissue penetration: A molecular dynamics study
BIOPHYSICAL CHEMISTRY, 154:18-25, FEB 2011 2011
abstract, full text

Lin, Chen, Chinnappan, Raja, Acharya, Khem, Pellequer, Jean-Luc, Jankowiak, Ryszard
On stabilization of a neutral aromatic ligand by pi-cation interactions in monoclonal antibodies
BIOPHYSICAL CHEMISTRY, 154:35-40, FEB 2011 2011
abstract, full text

de Weers, Michel, Tai, Yu-Tzu, van der Veer, Michael S., Bakker, Joost M., Vink, Tom, Jacobs, Danielle C. H., Oomen, Lukas A., Peipp, Matthias, Valerius, Thomas, Slootstra, Jerry W., Mutis, Tuna, Bleeker, Wim K., Anderson, Kenneth C., Lokhorst, Henk M., van de Winkel, Jan G. J., Parren, Paul W. H. I.
Daratumumab, a Novel Therapeutic Human CD38 Monoclonal Antibody, Induces Killing of Multiple Myeloma and Other Hematological Tumors
JOURNAL OF IMMUNOLOGY, 186:1840-1848, FEB 1 2011 2011
abstract, full text

Zhuang, Shulin, Liu, Weiping
Investigation of the binding specificity of Erbin-PDZ affinity clamp by molecular dynamics simulations
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 963:448-452, FEB 2011 2011
abstract, full text

Fadeeva, M. S., Bertsova, Y. V., Euro, L., Bogachev, A. V.
Cys377 Residue in NqrF Subunit Confers Ag(+) Sensitivity of Na(+)-Translocating NADH:quinone Oxidoreductase from Vibrio harveyi
BIOCHEMISTRY-MOSCOW, 76:186-195, FEB 2011 2011
abstract, full text

Zhang, Ji-Long, Zheng, Qing-Chuan, Zhang, Hong-Xing
Theoretical improvement of the specific inhibitor of human carbonic anhydrase VII
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 35:50-56, FEB 2011 2011
abstract, full text

Panek, Jaroslaw J., Mazzarello, Riccardo, Novic, Marjana, Jezierska-Mazzarello, Aneta
Impact of Mercury(II) on proteinase K catalytic center: investigations via classical and Born-Oppenheimer molecular dynamics
MOLECULAR DIVERSITY, 15:215-226, FEB 2011 2011
abstract, full text

de Serrano, V. S., Davis, M. F., Gaff, J. F., Zhang, Qi, Chen, Z., D'Antonio, E. L., Bowden, E. F., Rose, R., Franzen, S.
X-ray structure of the metcyano form of dehaloperoxidase from Amphitrite ornata: evidence for photoreductive dissociation of the iron-cyanide bond
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 66:770-782, JUL 2010 2010
abstract, full text

Shityakov, Sergey, Dandekar, Thomas
MOLECULAR DYNAMICS SIMULATION OF POPC AND POPE LIPID MEMBRANE BILAYERS ENFORCED BY AN INTERCALATED SINGLE-WALL CARBON NANOTUBE
NANO, 6:19-29, FEB 2011 2011
abstract, full text

Nowosieski, Marcin, Hoffmann, Marcin, Wyrwicz, Lucjan S., Stepniak, Piotr, Plewczynski, Dariusz M., Lazniewski, Michal, Ginalski, Krzysztof, Rychlewski, Leszek
Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:455-462, FEB 2011 2011
abstract, full text

Hung, Andrew, Yarovsky, Irene
Inhibition of peptide aggregation by lipids: Insights from coarse-grained molecular simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:597-607, FEB 2011 2011
abstract, full text

Yun, Sijung, Yun, Sajung, Guy, H. Robert
Analysis of the stabilities of hexameric amyloid-beta(1-42) models using discrete molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:657-662, FEB 2011 2011
abstract, full text

Yun, Sijung, Guy, H. Robert
Stability tests on known and misfolded structures with discrete and all atom molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:663-675, FEB 2011 2011
abstract, full text

Shang, Yi, Nguyen, Hai, Wickstrom, Lauren, Okur, Asim, Simmerling, Carlos
Improving the description of salt bridge strength and geometry in a Generalized Born model
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:676-684, FEB 2011 2011
abstract, full text

Sakhteman, Amirhossein, Lahtela-Kakkonen, Maija, Poso, Antti
Studying the catechol binding cavity in comparative models of human dopamine D(2) receptor
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:685-692, FEB 2011 2011
abstract, full text

Durrant, Jacob D., de Oliveira, Cesar Augusto F., McCammon, J. Andrew
POVME: An algorithm for measuring binding-pocket volumes
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:773-776, FEB 2011 2011
abstract, full text

Gossett, J. Jared, Harvey, Stephen C.
Computational Screening and Design of DNA-Linked Molecular Nanowires
NANO LETTERS, 11:604-608, FEB 2011 2011
abstract, full text

Addington, Trevor, Calisto, Barbara, Alfonso-Prieto, Mercedes, Rovira, Carme, Fita, Ignasi, Planas, Antoni
Re-engineering specificity in 1,3-1,4-beta-glucanase to accept branched xyloglucan substrates
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:365-375, FEB 2011 2011
abstract, full text

Novak, Brian R., Moldovan, Dorel, Waldrop, Grover L., de Queiroz, Marcio S.
Behavior of the ATP grasp domain of biotin carboxylase monomers and dimers studied using molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:622-632, FEB 2011 2011
abstract, full text

Falconi, Mattia, Oteri, Francesco, Di Palma, Francesco, Pandey, Saurabh, Battistoni, Andrea, Desideri, Alessandro
Structural-dynamical investigation of the ZnuA histidine-rich loop: involvement in zinc management and transport
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 25:181-194, FEB 2011 2011
abstract, full text

Kotsikorou, Eyangelia, Lynch, Diane L., Abood, Mary E., Reggio, Patricia H.
Lipid bilayer molecular dynamics study of lipid-derived agonists of the putative cannabinoid receptor, GPR55
CHEMISTRY AND PHYSICS OF LIPIDS, 164:131-143, FEB 2011 2011
abstract, full text

Chen, Wei, Lou, Jizhong, Hsin, Jen, Schulten, Klaus, Harvey, Stephen C., Zhu, Cheng
Molecular Dynamics Simulations of Forced Unbending of Integrin alpha(V)beta(3)
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1001086, FEB 2011 2011
abstract, full text

Tang, Yizhe, Bringa, Eduardo M., Remington, Bruce A., Meyers, Marc A.
Growth and collapse of nanovoids in tantalum monocrystals
ACTA MATERIALIA, 59:1354-1372, FEB 2011 2011
abstract, full text

Uzel, Sebastien G. M., Buehler, Markus J.
Molecular structure, mechanical behavior and failure mechanism of the C-terminal cross-link domain in type I collagen
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS, 4:153-161, FEB 2011 2011
abstract, full text

Niazi, Umar H. K., Bibby, Jaclyn, Sutcliffe, Michael J.
In-silico characterization of the effects of phosphorylated tyrosines 86 and 106 on structure and binding of MAL: insight into hyperinflammatory response to infection by the human malaria parasites
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 31:53-65, FEB 2011 2011
abstract, full text

Guimaraes, Ana P., Oliveira, Aline A., da Cunha, Elaine F. F., Ramalho, Teodorico C., Franca, Tanos C. C.
Design of New Chemotherapeutics Against the Deadly Anthrax Disease. Docking and Molecular Dynamics Studies of Inhibitors Containing Pyrrolidine and Riboamidrazone Rings on Nucleoside Hydrolase from Bacillus anthracis
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:455-469, FEB 2011 2011
abstract, full text

Chakrabarti, Bornali, Bairagya, Hridoy R., Mallik, Payel, Mukhopadhyay, Bishnu P., Bera, Asim K.
An Insight to Conserved Water Molecular Dynamics of Catalytic and Structural Zn(+2) ions in Matrix Metalloproteinase 13 of Human
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:503-516, FEB 2011 2011
abstract, full text

Olbrich, Carsten, Liebers, Joerg, Kleinekathoefer, Ulrich
Modeling of light-harvesting in purple bacteria using a time-dependent Hamiltonian approach
PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS, 248:393-398, FEB 2011 2011
abstract, full text

Huang, Yongqi, Liu, Zhirong
Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 12:1410-1430, FEB 2011 2011
abstract, full text

Calderon, Christopher P.
Estimation and Inference of Diffusion Coefficients in Complex Biomolecular Environments
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:280-290, FEB 2011 2011
abstract, full text

Kawatsu, Tsutomu, Lundberg, Marcus, Morokuma, Keiji
Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:390-401, FEB 2011 2011
abstract, full text

Stavrakoudis, Athanassios, Tsoulos, Ioannis G.
Configurational Entropy Reallocation and Complex Loop Dynamics of the Mosquito-Stage Pvs25 Protein Complexed with the Fab Fragment of the Malaria Transmission Blocking Antibody 2A8
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7:515-524, FEB 2011 2011
abstract, full text

Rosini, Elena, Molla, Gianluca, Ghisla, Sandro, Pollegioni, Loredano
On the reaction of d-amino acid oxidase with dioxygen: O(2) diffusion pathways and enhancement of reactivity
FEBS JOURNAL, 278:482-492, FEB 2011 2011
abstract, full text

Albecka, Anna, Montserret, Roland, Krey, Thomas, Tarr, Alexander W., Diesis, Eric, Ball, Jonathan K., Descamps, Veronique, Duverlie, Gilles, Rey, Felix, Penin, Francois, Dubuisson, Jean
Identification of New Functional Regions in Hepatitis C Virus Envelope Glycoprotein E2
JOURNAL OF VIROLOGY, 85:1777-1792, FEB 2011 2011
abstract, full text

Gushchin, Ivan Yu, Gordeliy, Valentin I., Grudinin, Sergei
Role of the HAMP Domain Region of Sensory Rhodopsin Transducers in Signal Transduction
BIOCHEMISTRY, 50:574-580, FEB 1 2011 2011
abstract, full text

Kalikka, Janne, Akola, Jaakko
Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 40:181-194, FEB 2011 2011
abstract, full text

Shyu, Conrad, Cavileer, Timothy D., Nagler, James J., Ytreberg, F. Marty
Computational estimation of rainbow trout estrogen receptor binding affinities for environmental estrogens
TOXICOLOGY AND APPLIED PHARMACOLOGY, 250:322-326, FEB 1 2011 2011
abstract, full text

Khurana, Ekta, DeVane, Russell H., Dal Peraro, Matteo, Klein, Michael L.
Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1808:530-537, FEB 2011 2011
abstract, full text

Kim, Jun Soo, Pradhan, Prabhakar, Backman, Vadim, Szleifer, Igal
The influence of chromosome density variations on the increase in nuclear disorder strength in carcinogenesis
PHYSICAL BIOLOGY, 8: Art. No. 015004, FEB 2011 2011
abstract, full text

Lim, M. C. G., Zhong, Z. W.
The junction size effect on the electromigration flow of copper atoms through carbon-nanotube junctions
PHYSICA E-LOW-DIMENSIONAL SYSTEMS & NANOSTRUCTURES, 43:862-868, FEB 2011 2011
abstract, full text

Bauer, Brad A., Davis, Joseph E., Taufer, Michela, Patel, Sandeep
Molecular Dynamics Simulations of Aqueous Ions at the Liquid-Vapor Interface Accelerated Using Graphics Processors
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:375-385, FEB 2011 2011
abstract, full text

Jaramillo-Botero, Andres, Su, Julius, Qi, An, Goddard, William A., I.I.I.
Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments
JOURNAL OF COMPUTATIONAL CHEMISTRY, 32:497-512, FEB 2011 2011
abstract, full text

Naghavi, S. Shahab, Gruhn, Thomas, Alijani, Vajiheh, Fecher, Gerhard H., Felser, Claudia, Medjanik, Katerina, Kutnyakhov, Dmytro, Nepijko, Sergej A., Schoenhense, Gerd, Rieger, Ralph, Baumgarten, Martin, Muellen, Klaus
Theoretical study of new acceptor and donor molecules based on polycyclic aromatic hydrocarbons
JOURNAL OF MOLECULAR SPECTROSCOPY, 265:95-101, FEB 2011 2011
abstract, full text

Kyrychenko, Alexander, Sevriukov, Igor Yu, Syzova, Zoya A., Ladokhin, Alexey S., Doroshenko, Andrey O.
Partitioning of 2,6-Bis(1H-Benzimidazol-2-yl)pyridine fluorophore into a phospholipid bilayer: Complementary use of fluorescence quenching studies and molecular dynamics simulations
BIOPHYSICAL CHEMISTRY, 154:8-17, FEB 2011 2011
abstract, full text

Barnaby, Omar S., Cerny, Ronald L., Clarke, William, Hage, David S.
Comparison of modification sites formed on human serum albumin at various stages of glycation
CLINICA CHIMICA ACTA, 412:277-285, JAN 30 2011 2011
abstract, full text

Hilder, Tamsyn A., Gordon, Dan, Chung, Shin-Ho
Synthetic cation-selective nanotube: Permeant cations chaperoned by anions
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 045103, JAN 28 2011 2011
abstract, full text

Karino, Yasuhito, Matubayasi, Nobuyuki
Free-energy analysis of hydration effect on protein with explicit solvent: Equilibrium fluctuation of cytochrome c
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 041105, JAN 28 2011 2011
abstract, full text

Kieseritzky, Gernot, Knapp, Ernst-Walter
Charge Transport in the ClC-type Chloride-Proton Anti-porter from Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:2976-2986, JAN 28 2011 2011
abstract, full text

Bodnar, Mandy, Wang, Haihong, Riedel, Thomas, Hintze, Stefan, Kato, Erzsebet, Fallah, Ghada, Groeger-Arndt, Helke, Giniatullin, Rashid, Grohmann, Marcus, Hausmann, Ralf, Schmalzing, Guenther, Illes, Peter, Rubini, Patrizia
Amino Acid Residues Constituting the Agonist Binding Site of the Human P2X3 Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:2739-2749, JAN 28 2011 2011
abstract, full text

Panecka, Joanna, Mura, Cameron, Trylska, Joanna
Molecular Dynamics of Potential rRNA Binders: Single-Stranded Nucleic Acids and Some Analogues
JOURNAL OF PHYSICAL CHEMISTRY B, 115:532-546, JAN 27 2011 2011
abstract, full text

Shan, Jufang, Javitch, Jonathan A., Shi, Lei, Weinstein, Harel
The Substrate-Driven Transition to an Inward-Facing Conformation in the Functional Mechanism of the Dopamine Transporter
PLOS ONE, 6: Art. No. e16350, JAN 27 2011 2011
abstract, full text

Lazarus, Michael B., Nam, Yunsun, Jiang, Jiaoyang, Sliz, Piotr, Walker, Suzanne
Structure of human O-GlcNAc transferase and its complex with a peptide substrate
NATURE, 469:564-U168, JAN 27 2011 2011
abstract, full text

Streltsov, Victor A., Varghese, Joseph N., Masters, Colin L., Nuttall, Stewart D.
Crystal Structure of the Amyloid-beta p3 Fragment Provides a Model for Oligomer Formation in Alzheimer's Disease
JOURNAL OF NEUROSCIENCE, 31:1419-1426, JAN 26 2011 2011
abstract, full text

Rostkowski, Michal, Olsson, Mats H. M., Sondergaard, Chresten R., Jensen, Jan H.
Graphical analysis of pH-dependent properties of proteins predicted using PROPKA
BMC STRUCTURAL BIOLOGY, 11: Art. No. 6, JAN 26 2011 2011
abstract, full text

Zuniga, Leandro, Marquez, Valeria, Gonzalez-Nilo, Fernando D., Chipot, Christophe, Pablo Cid, L., Sepulveda, Francisco V., Isabel Niemeyer, Maria
Gating of a pH-Sensitive K(2P) Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter
PLOS ONE, 6: Art. No. e16141, JAN 25 2011 2011
abstract, full text

Costelle, Leila, Jaervi, Tommi T., Raeisaenen, Minna T., Tuboltsev, Vladimir, Raisanen, Jyrki
Binding of deposited gold clusters to thiol self-assembled monolayers on Au(111) surfaces
APPLIED PHYSICS LETTERS, 98: Art. No. 043107, JAN 24 2011 2011
abstract, full text

Liu, Li, Fang, Ying, Huang, Qingsheng, Wu, Jianhua
A Rigidity-Enhanced Antimicrobial Activity: A Case for Linear Cationic alpha-Helical Peptide HP(2-20) and Its Four Analogues
PLOS ONE, 6: Art. No. e16441, JAN 24 2011 2011
abstract, full text

Brown, C. J., Lim, J. J., Leonard, T., Lim, H. C. A., Chia, C. S. B., Verma, C. S., Lane, D. P.
Stabilizing the eIF4G1 alpha-Helix Increases Its Binding Affinity with eIF4E: Implications for Peptidomimetic Design Strategies
JOURNAL OF MOLECULAR BIOLOGY, 405:736-753, JAN 21 2011 2011
abstract, full text

Jezierska-Mazzarello, Aneta, Panek, Jaroslaw J., Vuilleumier, Rodolphe, Koll, Aleksander, Ciccotti, Giovanni
Direct observation of the substitution effects on the hydrogen bridge dynamics in selected Schiff bases-A comparative molecular dynamics study
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 034308, JAN 21 2011 2011
abstract, full text

Yamazaki, Takeshi, Kovalenko, Andriy
Spatial Decomposition of Solvation Free Energy Based on the 3D Integral Equation Theory of Molecular Liquid: Application to Miniproteins
JOURNAL OF PHYSICAL CHEMISTRY B, 115:310-318, JAN 20 2011 2011
abstract, full text

Nury, Hugues, Van Renterghem, Catherine, Weng, Yun, Tran, Alphonso, Baaden, Marc, Dufresne, Virginie, Changeux, Jean-Pierre, Sonner, James M., Delarue, Marc, Corringer, Pierre-Jean
X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel
NATURE, 469:428-+, JAN 20 2011 2011
abstract, full text

Newstead, Simon, Drew, David, Cameron, Alexander D., Postis, Vincent L. G., Xia, Xiaobing, Fowler, Philip W., Ingram, Jean C., Carpenter, Elisabeth P., Sansom, Mark S. P., McPherson, Michael J., Baldwin, Stephen A., Iwata, So
Crystal structure of a prokaryotic homologue of the mammalian oligopeptide-proton symporters, PepT1 and PepT2
EMBO JOURNAL, 30:417-426, JAN 19 2011 2011
abstract, full text

Fritsch, Sebastian, Ivanov, Ivaylo, Wang, Hailong, Cheng, Xiaolin
Ion Selectivity Mechanism in a Bacterial Pentameric Ligand-Gated Ion Channel
BIOPHYSICAL JOURNAL, 100:390-398, JAN 19 2011 2011
abstract, full text

Brubaker, William D., Freites, J. Alfredo, Golchert, Kory J., Shapiro, Rebecca A., Morikis, Vasilios, Tobias, Douglas J., Martin, Rachel W.
Separating Instability from Aggregation Propensity in gamma S-Crystallin Variants
BIOPHYSICAL JOURNAL, 100:498-506, JAN 19 2011 2011
abstract, full text

Ma, L., Sundlass, N. K., Raines, R. T., Cui, Q.
Disruption and Formation of Surface Salt Bridges Are Coupled to DNA Binding by the Integration Host Factor: A Computational Analysis
BIOCHEMISTRY, 50:266-275, JAN 18 2011 2011
abstract, full text

Kieslich, Chris A., Gorham, Ronald D., Jr., Morikis, Dimitrios
Is the rigid-body assumption reasonable? Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar
JOURNAL OF NON-CRYSTALLINE SOLIDS, 357:707-716, JAN 15 2011 2011
abstract, full text

Cross, Sally H., McKie, Lisa, West, Katrine, Coghill, Emma L., Favor, Jack, Bhattacharya, Shoumo, Brown, Steve D. M., Jackson, Ian J.
The Opdc missense mutation of Pax2 has a milder than loss-of-function phenotype
HUMAN MOLECULAR GENETICS, 20:223-234, JAN 15 2011 2011
abstract, full text

Frick, Inga-Maria, Shannon, Oonagh, Akesson, Per, Morgelin, Matthias, Collin, Mattias, Schmidtchen, Artur, Bjorck, Lars
Antibacterial Activity of the Contact and Complement Systems Is Blocked by SIC, a Protein Secreted by Streptococcus pyogenes
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:1331-1340, JAN 14 2011 2011
abstract, full text

Sun, Sheng, Yin, Guangyao, Lee, Yi-Kuen, Wong, Joseph T. Y., Zhang, Tong-Yi
Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:684-688, JAN 14 2011 2011
abstract, full text

Toroz, Dimitrios, Rontani, Massimo, Corni, Stefano
Visualizing electron correlation by means of ab initio scanning tunneling spectroscopy images of single molecules
JOURNAL OF CHEMICAL PHYSICS, 134: Art. No. 024104, JAN 14 2011 2011
abstract, full text

Rosenbaum, Daniel M., Zhang, Cheng, Lyons, Joseph A., Holl, Ralph, Aragao, David, Arlow, Daniel H., Rasmussen, Soren G. F., Choi, Hee-Jung, DeVree, Brian T., Sunahara, Roger K., Chae, Pil Seok, Gellman, Samuel H., Dror, Ron O., Shaw, David E., Weis, William I., Caffrey, Martin, Gmeiner, Peter, Kobilka, Brian K.
Structure and function of an irreversible agonist-beta(2) adrenoceptor complex
NATURE, 469:236-240, JAN 13 2011 2011
abstract, full text

DeMille, Robert C., Cheatham, Thomas E., I.I.I., Molinero, Valeria
A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions
JOURNAL OF PHYSICAL CHEMISTRY B, 115:132-142, JAN 13 2011 2011
abstract, full text

Wang, Chunhua, Ye, Fengbin, Velardez, Gustavo F., Peters, Gunther H., Westh, Peter
Affinity of Four Polar Neurotransmitters for Lipid Bilayer Membranes
JOURNAL OF PHYSICAL CHEMISTRY B, 115:196-203, JAN 13 2011 2011
abstract, full text

Nguyen, Ha H., McAliley, James H., Bruce, David A.
Controlling the m-Poly(phenylene ethynylene) Helical Cavity Environment: Hydrogen Bond Stabilized Helical Structures
MACROMOLECULES, 44:60-67, JAN 11 2011 2011
abstract, full text

McArthur, Jeff R., Ostroumov, Vitaly, Al-Sabi, Ahmed, McMaster, Denis, French, Robert J.
Multiple, Distributed Interactions of mu-Conotoxin PIIIA Associated with Broad Targeting among Voltage-Gated Sodium Channels
BIOCHEMISTRY, 50:116-124, JAN 11 2011 2011
abstract, full text

Kepczynski, Mariusz, Jamroz, Dorota, Wytrwal, Magdalena, Bednar, Jan, Rzad, Ewa, Nowakowska, Maria
Interactions of a Hydrophobically Modified Polycation with Zwitterionic Lipid Membranes
LANGMUIR, 28:676-688, JAN 10 2011 2011
abstract, full text

Hilder, Tamsyn A., Chung, Shin-Ho
Carbon nanotube as a gramicidin analogue
CHEMICAL PHYSICS LETTERS, 501:423-426, JAN 7 2011 2011
abstract, full text

Bossis, Fabrizio, Palese, Luigi L.
Molecular dynamics in cytochrome c oxidase Mossbauer spectra deconvolution
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 404:438-442, JAN 7 2011 2011
abstract, full text

Kwiendacz, Jacek, Boczar, Marek, Wojcik, Marek J.
Car-Parrinello molecular dynamics simulations of infrared spectra of crystalline imidazole
CHEMICAL PHYSICS LETTERS, 501:623-627, JAN 7 2011 2011
abstract, full text

Labro, Alain J., Boulet, Inge R., Choveau, Frank S., Mayeur, Evy, Bruyns, Tine, Loussouarn, Gildas, Raes, Adam L., Snyders, Dirk J.
The S4-S5 Linker of KCNQ1 Channels Forms a Structural Scaffold with the S6 Segment Controlling Gate Closure
JOURNAL OF BIOLOGICAL CHEMISTRY, 286:717-725, JAN 7 2011 2011
abstract, full text

Xue, Ying, O'Mara, Megan L., Surawski, Peter P. T., Trau, Matt, Mark, Alan E.
Effect of Poly(ethylene glycol) (PEG) Spacers on the Conformational Properties of Small Peptides: A Molecular Dynamics Study
LANGMUIR, 27:296-303, JAN 4 2011 2011
abstract, full text

Wang, Teng, Chipot, Christophe, Shao, Xueguang, Cai, Wensheng
Structural Characterization of Micelles Formed of Cholesteryl-Functionalized Cyclodextrins
LANGMUIR, 27:91-97, JAN 4 2011 2011
abstract, full text

Marino, Nadia, Rabideau, Amy E., Doyle, Robert P.
Trifluoracetic Acid-Assisted Crystallization of Vitamin B(12) Results in Protonation of the Phosphate Group of the Nucleotide Loop: Insight into the Influence of Crystal Packing Forces on Vitamin B(12) Structures
INORGANIC CHEMISTRY, 50:220-230, JAN 3 2011 2011
abstract, full text

Krezel, Artur, Wojcik, Jacek, Maciejczyk, Maciej, Bal, Wojciech
Zn(II) Complexes of Glutathione Disulfide: Structural Basis of Elevated Stabilities
INORGANIC CHEMISTRY, 50:72-85, JAN 3 2011 2011
abstract, full text

Li, Binsen, Shahid, Ramza, Peshkepija, Paola, Zimmer, Marc
Water diffusion in and out of the beta-barrel of GFP and the fast maturing fluorescent protein, TurboGFP
CHEMICAL PHYSICS, 392:143-148, JAN 2 2011 2011
abstract, full text

Kozlovskaya, Veronika, Ankner, John F., O'Neill, Hugh, Zhang, Qiu, Kharlampieva, Eugenia
Localized entrapment of green fluorescent protein within nanostructured polymer films
SOFT MATTER, 7:11453-11463, 2011 2011
abstract, full text

Kirkensgaard, Jacob Judas Kain
Systematic progressions of core-shell polygon containing tiling patterns in melts of 2nd generation dendritic miktoarm star copolymers
SOFT MATTER, 7:10756-10762, 2011 2011
abstract, full text

Hughes, Meghan, Xu, Haixia, Frederix, Pim W. J. M., Smith, Andrew M., Hunt, Neil T., Tuttle, Tell, Kinloch, Ian A., Ulijn, Rein V.
Biocatalytic self-assembly of 2D peptide-based nanostructures
SOFT MATTER, 7:10032-10038, 2011 2011
abstract, full text

Yan, Fangyong, Earl, David J.
An all atom computer simulation study of the liquid crystalline phase behaviour of alkenic fluoroterphenyls
SOFT MATTER, 7:10266-10273, 2011 2011
abstract, full text

Engelbrecht, Tanja, Hauss, Thomas, Suess, Kevin, Vogel, Alexander, Roark, Matthew, Feller, Scott E., Neubert, Reinhard H. H., Dobner, Bodo
Characterisation of a new ceramide EOS species: synthesis and investigation of the thermotropic phase behaviour and influence on the bilayer architecture of stratum corneum lipid model membranes
SOFT MATTER, 7:8998-9011, 2011 2011
abstract, full text

Sun, Sheng, Wong, Joseph T. Y., Zhang, Tong-Yi
Effects of external electric fields on the self-assembly of phospholipids/water mixtures-coarse-grained molecular dynamics simulations
SOFT MATTER, 7:9307-9310, 2011 2011
abstract, full text

Zhao, Ya-Pu, Wang, Feng-Chao, Chi, Mei
Molecular Dynamics Simulation and Molecular Orbital Method
HANDBOOK OF ADHESION TECHNOLOGY, VOL 1 AND 2, 1351-1384, 2011 2011
abstract, full text

Pantano, Diego A., Moore, Preston B., Klein, Michael L., Discher, Dennis E.
Raft registration across bilayers in a molecularly detailed model
SOFT MATTER, 7:8182-8191, 2011 2011
abstract, full text

Hoelz, Lucas V. B., Bernardi, Rafael C., Horta, Bruno A. C., Araujo, Jocley Q., Albuquerque, Magaly G., da Silva, Joaquim F. M., Pascutti, Pedro G., de Alencastro, Ricardo B.
Dynamical behaviour of the human beta(1)-adrenoceptor under agonist binding
MOLECULAR SIMULATION, 37:907-913, 2011 2011
abstract, full text

Stavrakoudis, Athanassios
Molecular dynamics study of the human insulin B peptide SHLVEALYLVCGERGG complexed with HLA-DQ8 reveals important hydrogen bond interactions
MOLECULAR SIMULATION, 37:837-845, 2011 2011
abstract, full text

Hede, T., Li, X., Leck, C., Tu, Y., Agren, H.
Model HULIS compounds in nanoaerosol clusters - investigations of surface tension and aggregate formation using molecular dynamics simulations
ATMOSPHERIC CHEMISTRY AND PHYSICS, 11:6549-6557, 2011 2011
abstract, full text

Mitropoulos, V., Windhab, E. J., Fischer, P.
The interfacial behavior of designed ankyrin repeat proteins
SOFT MATTER, 7:7612-7615, 2011 2011
abstract, full text

Rao, K. Venkata, Mohapatra, Sudip, Kulkarni, Chidambar, Maji, Tapas Kumar, George, Subi J.
Extended phenylene based microporous organic polymers with selective carbon dioxide adsorption
JOURNAL OF MATERIALS CHEMISTRY, 21:12958-12963, 2011 2011
abstract, full text

Li, Y. W., Wuest, T., Landau, D. P.
Biologically Inspired Surface Physics: The HP Protein Model
NANOPHENOMENA AT SURFACES: FUNDAMENTALS OF EXOTIC CONDENSED MATTER PROPERTIES, 47:169-183, 2011 2011
abstract, full text

Legnani, Laura, Compostella, Federica, Grazioso, Giovanni, Albini, Franca Marinone, Toma, Lucio
Molecular dynamics simulations of the Salmonella typhi Vi antigenic polysaccharide and effects of the introduction of a zwitterionic motif
ORGANIC & BIOMOLECULAR CHEMISTRY, 9:5554-5559, 2011 2011
abstract, full text

Lu, You, Lan, Zhenggang, Thiel, Walter
Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50:6864-6867, 2011 2011
full text

Stepanova, Maria
Identification of dynamic structural domains in proteins, analysis of local bond flexibility and application for interpretation of NMR experiments
MOLECULAR SIMULATION, 37:729-732, 2011 2011
abstract, full text

Ollivierre, Jaylene N., Silva, Michelle C., Sefcikova, Jana, Beuning, Penny J.
Polymerase Switching in Response to DNA Damage
BIOPHYSICS OF DNA- PROTEIN INTERACTIONS: FROM SINGLE MOLECULES TO BIOLOGICAL SYSTEMS, 241-292, 2011 2011
full text

Johnson, Carey K., Liyanage, Mangala R., Osborn, Kenneth D., Zaidi, Asma
Single-Protein Dynamics and the Regulation of the Plasma-Membrane Ca(2+) Pump
CELL SIGNALING REACTIONS: SINGLE-MOLECULAR KINETIC ANALYSIS, 121-151, 2011 2011
abstract, full text

Hamdi, Mustapha, Ferreira, Antoine
Current State-of-the-Art on Nanorobotic Components and Design
DESIGN, MODELING AND CHARACTERIZATION OF BIO-NANOROBOTIC SYSTEMS, 1-40, 2011 2011
full text

Hamdi, Mustapha, Ferreira, Antoine
Methodology of Design and Characterization of Bionano- and Nanorobotic Devices
DESIGN, MODELING AND CHARACTERIZATION OF BIO-NANOROBOTIC SYSTEMS, 41-73, 2011 2011
full text

To, Albert C., Fu, Yao, Liu, Wing Kam
Denoising methods for thermomechanical decomposition for quasi-equilibrium molecular dynamics simulations
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING, 200:1979-1992, 2011 2011
abstract, full text

Wang, Shaoqing
A comparative first-principles study of orbital hybridization in two-dimensional C, Si, and Ge
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:11929-11938, 2011 2011
abstract, full text

Janocha, Simon, Bichet, Andreas, Zoellner, Andy, Bernhardt, Rita
Substitution of lysine with glutamic acid at position 193 in bovine CYP11A1 significantly affects protein oligomerization and solubility but not enzymatic activity
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1814:126-131, JAN 2011 2011
abstract, full text

Mak, C. H.
Loops MC: an all-atom Monte Carlo simulation program for RNAs based on inverse kinematic loop closure
MOLECULAR SIMULATION, 37:537-556, 2011 2011
abstract, full text

Trefalt, Gregor, Tadic, Bosiljka, Kosec, Marija
Formation of colloidal assemblies in suspensions for Pb(Mg(1/3)Nb(2/3))O(3) synthesis: Monte Carlo simulation study
SOFT MATTER, 7:5566-5577, 2011 2011
abstract, full text

Schor, Marieke, Bolhuis, Peter G.
The self-assembly mechanism of fibril-forming silk-based block copolymers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:10457-10467, 2011 2011
abstract, full text

Brini, Emiliano, Marcon, Valentina, van der Vegt, Nico F. A.
Conditional reversible work method for molecular coarse graining applications
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:10468-10474, 2011 2011
abstract, full text

Herbers, Claudia R., Johnston, Karen, van der Vegt, Nico F. A.
Modelling molecule-surface interactions-an automated quantum-classical approach using a genetic algorithm
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:10577-10583, 2011 2011
abstract, full text

dos Santos, Daniel J. V. A., Saenz-Mendez, Patricia, Eriksson, Leif A., Guedes, Rita C.
Properties and behaviour of tetracyclic allopsoralen derivatives inside a DPPC lipid bilayer model
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:10174-10182, 2011 2011
abstract, full text

Telesco, Shannon E., Shih, Andrew J., Jia, Fei, Radhakrishnan, Ravi
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network
MOLECULAR BIOSYSTEMS, 7:2066-2080, 2011 2011
abstract, full text

Constable, Edwin C., Devereux, Michael, Dunphy, Emma L., Housecroft, Catherine E., Rudd, Jennifer A., Zampese, Jennifer A.
Water-soluble alkylated bis{4 '-(4-pyridyl)-2,2 ':6 ',2 ''-terpyridine}-ruthenium(II) complexes for use as photosensitizers in water oxidation: a complementary experimental and TD-DFT investigation
DALTON TRANSACTIONS, 40:5505-5515, 2011 2011
abstract, full text

Stoeger, Berthold, Weil, Matthias, Baran, Enrique J., Gonzalez-Baro, Ana C., Malo, Sylvie, Rueff, Jean Michel, Petit, Sebastien, Lepetit, Marie Bernadette, Raveau, Bernard, Barrier, Nicolas
The dehydration of SrTeO(3)(H(2)O) - a topotactic reaction for preparation of the new metastable strontium oxotellurate(IV) phase epsilon-SrTeO(3)
DALTON TRANSACTIONS, 40:5538-5548, 2011 2011
abstract, full text

Suyetin, Mikhail V., Vakhrushev, Alexander V.
Nanocapsule with pump for methane storage
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9863-9870, 2011 2011
abstract, full text

Alberti, Margarita, Huarte-Larranaga, Fermin, Aguilar, Antonio, Lucas, Jose M., Pirani, Fernando
A 3D-analysis of cluster formation and dynamics of the X(-)-benzene (X = F, Cl, Br, I) ionic dimer solvated by Ar atoms
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:8251-8258, 2011 2011
abstract, full text

Li, Zhenlong, Dormidontova, Elena E.
Equilibrium chain exchange kinetics in block copolymer micelle solutions by dissipative particle dynamics simulations
SOFT MATTER, 7:4179-4188, 2011 2011
abstract, full text

Sayle, Thi X. T., Inkson, Beverley J., Karakoti, Ajay, Kumar, Amit, Molinari, Marco, Moebus, Guenter, Parker, Stephen C., Seal, Sudipta, Sayle, Dean C.
Mechanical properties of ceria nanorods and nanochains; the effect of dislocations, grain-boundaries and oriented attachment
NANOSCALE, 3:1823-1837, 2011 2011
abstract, full text

Chan, Henry, Kral, Petr
Self-standing nanoparticle membranes and capsules
NANOSCALE, 3:1881-1886, 2011 2011
abstract, full text

Farhadian, Nafiseh, Shariaty-niassar, Mojtaba, Malek, Kourosh, Maghari, Ali
Molecular Dynamics Simulation of Water and Ions in Nanopores of Lysozyme Protein Crystal
INTERNATIONAL JOURNAL OF CHEMICAL REACTOR ENGINEERING, 9: Art. No. A23, 2011 2011
abstract, full text

Lin, Xubo, Li, Yang, Gu, Ning
Molecular dynamics simulations of the interactions of charge-neutral PAMAM dendrimers with pulmonary surfactant
SOFT MATTER, 7:3882-3888, 2011 2011
abstract, full text

Ranjbartoreh, Ali Reza, Wang, Guoxiu
Effect of Topological Defects on Buckling Behavior of Single-walled Carbon Nanotube
NANOSCALE RESEARCH LETTERS, 6: Art. No. 28, 2011 2011
abstract, full text

Ruhayel, Rasha A., Zgani, Ibrahim, Berners-Price, Susan J., Farrell, Nicholas P.
Solution studies of dinuclear polyamine-linked platinum-based antitumour complexes
DALTON TRANSACTIONS, 40:4147-4154, 2011 2011
abstract, full text

Wu, Wei-Bin, Chen, Shu-Han, Hou, Jin-Qiang, Tan, Jia-Heng, Ou, Tian-Miao, Huang, Shi-Liang, Li, Ding, Gu, Lian-Quan, Huang, Zhi-Shu
Disubstituted 2-phenyl-benzopyranopyrimidine derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA
ORGANIC & BIOMOLECULAR CHEMISTRY, 9:2975-2986, 2011 2011
abstract, full text

Tikhomirov, V. A., Odinokov, A. V., Bagatur'yants, A. A., Alfimov, M. V.
MODELING THE SURFACE OF POLYSTYRENE AND THE ADSORPTION OF DYE MOLECULES ON THIS SURFACE
THEORETICAL AND EXPERIMENTAL CHEMISTRY, 46:342-349, JAN 2011 2011
abstract, full text

Ezaz, Tawhid, Sangid, Michael D., Sehitoglu, Huseyin
Energy barriers associated with slip-twin interactions
PHILOSOPHICAL MAGAZINE, 91:1464-1488, 2011 2011
abstract, full text

Li Xinying, Cao Xue
Interaction and Electron Density Properties of MKr(4)(2+) (M = Cu, Ag and Au): ab initio Calculation
AUSTRALIAN JOURNAL OF CHEMISTRY, 64:339-344, 2011 2011
abstract, full text

Aguilella, Vicente M., Queralt-Martin, Maria, Aguilella-Arzo, Marcel, Alcaraz, Antonio
Insights on the permeability of wide protein channels: measurement and interpretation of ion selectivity
INTEGRATIVE BIOLOGY, 3:159-172, 2011 2011
abstract, full text

Abroshan, Hadi, Akbarzadeh, Hamed, Taherkhani, Farid, Parsafar, Gholamabbas
Effect of water-methanol content on the structure of Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamics study
MOLECULAR PHYSICS, 109:709-724, 2011 2011
abstract, full text

Leclercq, Guy, de Cremoux, Patricia, This, Pascale, Jacquot, Yves
Lack of sufficient information on the specificity and selectivity of commercial phytoestrogens preparations for therapeutic purposes
MATURITAS, 68:56-64, JAN 2011 2011
abstract, full text

Parfitt, David, Chroneos, Alexander, Tarancon, Albert, Kilner, John A.
Oxygen ion diffusion in cation ordered/disordered GdBaCo(2)O(5+delta)
JOURNAL OF MATERIALS CHEMISTRY, 21:2183-2186, 2011 2011
abstract, full text

Lee, Michael V., Scipioni, Roberto, Boero, Mauro, Silvestrelli, Pier Luigi, Ariga, Katsuhiko
The initiation mechanisms for surface hydrosilylation with 1-alkenes
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:4862-4867, 2011 2011
abstract, full text

Carr, Rogan, Comer, Jeffrey, Ginsberg, Mark D., Aksimentiev, Aleksei
Modeling Pressure-Driven Transport of Proteins Through a Nanochannel
IEEE TRANSACTIONS ON NANOTECHNOLOGY, 10:75-82, JAN 2011 2011
abstract, full text

Vanni, Stefano, Neri, Marilisa, Tavernelli, Ivano, Rothlisberger, Ursula
Predicting Novel Binding Modes of Agonists to beta Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations
PLOS COMPUTATIONAL BIOLOGY, 7: Art. No. e1001053, JAN 2011 2011
abstract, full text

Feng, Jie, Pandey, Ras B., Berry, Rajiv J., Farmer, Barry L., Naik, Rajesh R., Heinz, Hendrik
Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules
SOFT MATTER, 7:2113-2120, 2011 2011
abstract, full text

Habibi, Mahnaz, Eslahchi, Changiz, Pezeshk, Hamid, Sadeghi, Mehdi
An Information Theoretic Approach to Secondary Structure Assignment
MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY, 65:5-20, 2011 2011
abstract, full text

Roomp, Kirsten, Domingues, Francisco S.
Predicting interactions between T cell receptors and MHC-peptide complexes
MOLECULAR IMMUNOLOGY, 48:553-562, JAN 2011 2011
abstract, full text

Calero, Carles, Faraudo, Jordi, Aguilella-Arzo, Marcel
Molecular dynamics simulations of concentrated aqueous electrolyte solutions
MOLECULAR SIMULATION, 37:123-134, 2011 2011
abstract, full text

Yang, Fan, Dearden, David V.
Guanidinium-capped cucurbit[7]uril molecular cages in the gas phase
SUPRAMOLECULAR CHEMISTRY, 23:53-58, 2011 2011
abstract, full text

Ibrahim, Hanadi, Kasselouri, Athena, You, Changjiang, Maillard, Philippe, Rosilio, Veronique, Pansu, Robert, Prognon, Patrice
Meso-tetraphenyl porphyrin derivatives: The effect of structural modifications on binding to DMPC liposomes and albumin
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY A-CHEMISTRY, 217:10-21, JAN 1 2011 2011
abstract, full text

Yang, Darren, Arya, Gaurav
Structure and binding of the H4 histone tail and the effects of lysine 16 acetylation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:2911-2921, 2011 2011
abstract, full text

Christov, Christo, Karabencheva, Tatyana
Computational insight into protein circular dichroism: detailed analysis of contributions of individual chromophores in TEM-1 beta-lactamase
THEORETICAL CHEMISTRY ACCOUNTS, 128:25-37, JAN 2011 2011
abstract, full text

Vinogradov, Serge N., Fernandez, Ivan, Hoogewijs, David, Arredondo-Peter, Raul
Phylogenetic Relationships of 3/3 and 2/2 Hemoglobins in Archaeplastida Genomes to Bacterial and Other Eukaryote Hemoglobins
MOLECULAR PLANT, 4:42-58, JAN 2011 2011
abstract, full text

Tian, Wen-de, Ma, Yu-qiang
Coarse-grained molecular simulation of interacting dendrimers
SOFT MATTER, 7:500-505, 2011 2011
abstract, full text

Ribone, Sergio R., Quevedo, Mario A., Madrid, Marcela, Brinon, Margarita C.
Rational Approaches for the Design of Effective Human Immunodeficiency Virus Type 1 Nonnucleoside Reverse Transcriptase Inhibitors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 51:130-138, JAN 2011 2011
abstract, full text

Andres Rivas-Pardo, Jaime, Caniuguir, Andres, Wilson, Christian A. M., Babul, Jorge, Guixe, Victoria
Divalent metal cation requirements of phosphofructokinase-2 from E. coli. Evidence for a high affinity binding site for Mn(2+)
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 505:60-66, JAN 1 2011 2011
abstract, full text

Frontiera, Renee R., Mathies, Richard A.
Femtosecond stimulated Raman spectroscopy
LASER & PHOTONICS REVIEWS, 5:102-113, JAN 2011 2011
abstract, full text

Berski, Slawomir, Latajka, Zdzislaw, Gordon, Agnieszka J.
On the multiple B-N bonding in boron compounds using the topological analysis of electron localization function (ELF)
NEW JOURNAL OF CHEMISTRY, 35:89-96, 2011 2011
abstract, full text

Ambaye, Nigus D., Gunzburg, Menachem J., Lim, Reece C. C., Price, John T., Wilce, Matthew C. J., Wilce, Jacqueline A.
Benzopyrazine derivatives: A novel class of growth factor receptor bound protein 7 antagonists
BIOORGANIC & MEDICINAL CHEMISTRY, 19:693-701, JAN 1 2011 2011
abstract, full text

Bialonska, Agata, Ciunik, Zbigniew
When a host becomes a guest-competition between decreasing hydrophobic spaces and supramolecular synthon propagation
CRYSTENGCOMM, 13:967-972, 2011 2011
abstract, full text

Rosen, Sarah A. J., Gaffney, Piers R. J., Gould, Ian R.
A theoretical investigation of inositol 1,3,4,5-tetrakisphosphate
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:1070-1081, 2011 2011
abstract, full text

Wang, Teng, Shao, Xueguang, Cai, Wensheng, Xue, Yonglai, Wang, Shuai, Feng, Xizeng
Predicting the coordination geometry for Mg(2+) in the p53 DNA-binding domain: insights from computational studies
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:1140-1151, 2011 2011
abstract, full text

Jiang, Jun, Mukamel, Shaul
Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:2394-2400, 2011 2011
abstract, full text

Zhao, Jun, Yu, Xiang, Liang, Guizhao, Zheng, Jie
Structural Polymorphism of Human Islet Amyloid Polypeptide (hIAPP) Oligomers Highlights the Importance of Interfacial Residue Interactions
BIOMACROMOLECULES, 12:210-220, JAN 2011 2011
abstract, full text

Dimitropoulos, Nikolaos, Papakyriakou, Athanasios, Dalkas, Georgios A., Chasapis, Christos T., Poulas, Konstantinos, Spyroulias, Georgios A.
A computational investigation on the role of glycosylation in the binding of alpha1 nicotinic acetylcholine receptor with two alpha-neurotoxins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:142-152, JAN 2011 2011
abstract, full text

Zhu, Wenpeng, Yang, Wei
Molecular dynamics study of configuration and stability of vacancy clusters in fcc Ag
PHILOSOPHICAL MAGAZINE, 91:3793-3809, 2011 2011
abstract, full text

Komaromi, I., Bagoly, Z., Muszbek, L.
Factor XIII: novel structural and functional aspects
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 9:9-20, JAN 2011 2011
abstract, full text

Bhushan, Shashi, Hoffmann, Thomas, Seidelt, Birgit, Frauenfeld, Jens, Mielke, Thorsten, Berninghausen, Otto, Wilson, Daniel N., Beckmann, Roland
SecM-Stalled Ribosomes Adopt an Altered Geometry at the Peptidyl Transferase Center
PLOS BIOLOGY, 9: Art. No. e1000581, JAN 2011 2011
abstract, full text

Prieto, Lidia, Lazaridis, Themis
Computational studies of colicin insertion into membranes: The closed state
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:126-141, JAN 2011 2011
abstract, full text

Gong, Qingguo, Menon, Lakshmi, Ilina, Tatiana, Miller, Lena G., Ahn, Jinwoo, Parniak, Michael A., Ishima, Rieko
Interaction of HIV-1 Reverse Transcriptase Ribonuclease H with an Acylhydrazone Inhibitor
CHEMICAL BIOLOGY & DRUG DESIGN, 77:39-47, JAN 2011 2011
abstract, full text

Antosiewicz, Jan M., Shugar, David
Poisson-Boltzmann continuum-solvation models: applications to pH-dependent properties of biomolecules
MOLECULAR BIOSYSTEMS, 7:2923-2949, 2011 2011
abstract, full text

Sun, Sheng, Wong, Joseph T. Y., Zhang, Tong-Yi
Molecular dynamics simulations of phase transition of lamellar lipid membrane in water under an electric field
SOFT MATTER, 7:147-152, 2011 2011
abstract, full text

Hoefert, Moritz Julian, Sambriski, Edward John, de Pablo, Juan Jose
Molecular pathways in DNA-DNA hybridization of surface-bound oligonucleotides
SOFT MATTER, 7:560-566, 2011 2011
abstract, full text

Vernizzi, Graziano, Zhang, Dongsheng, de la Cruz, Monica Olvera
Structural phase transitions and mechanical properties of binary ionic colloidal crystals at interfaces
SOFT MATTER, 7:6285-6293, 2011 2011
abstract, full text

Suyetin, M. V., Vakhrushev, A. V.
Temperature-sensitive nanocapsule for drug delivery
MICRO & NANO LETTERS, 6:39-42, JAN 2011 2011
abstract, full text

Sangid, Michael D., Ezaz, Tawhid, Sehitoglu, Huseyin, Robertson, Ian M.
Energy of slip transmission and nucleation at grain boundaries
ACTA MATERIALIA, 59:283-296, JAN 2011 2011
abstract, full text

Ciszewska, Malgorzata, Ruszczynska, Katarzyna, Oleszczuk, Marta, Chung, Nga N., Witkowska, Ewa, Schiller, Peter W., Wojcik, Jacek, Izdebski, Jan
Cyclic enkephalin-deltorphin hybrids containing a carbonyl bridge: structure and opioid activity
ACTA BIOCHIMICA POLONICA, 58:225-230, 2011 2011
abstract, full text

Qureshi, Nadia N., Morikis, Dimitrios, Schiller, Neal L.
Contribution of Specific Amino Acid Changes in Penicillin Binding Protein 1 to Amoxicillin Resistance in Clinical Helicobacter pylori isolates
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 55:101-109, JAN 2011 2011
abstract, full text

Ardevol, Albert, Rovira, Carme
The Molecular Mechanism of Enzymatic Glycosyl Transfer with Retention of Configuration: Evidence for a Short-Lived Oxocarbenium-Like Species
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50:10897-10901, 2011 2011
full text

di Dio, Philipp J., Bruessel, Marc, Muniz, Kilian, Ray, Rupashree Shyama, Zahn, Stefan, Kirchner, Barbara
Pd-N to Pd-O Rearrangement for a Carbamate Synthesis from Carbon Dioxide and Methane: A Density Functional and Ab Initio Molecular Dynamics Metadynamics Study
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 50:A40-A45, 2011 2011
full text

Liu, Di, Snee, Preston T.
Water-Soluble Semiconductor Nanocrystals Cap Exchanged with Metalated Ligands
ACS NANO, 5:546-550, JAN 2011 2011
abstract, full text

Milac, Adina L., Anishkin, Andriy, Fatakia, Sarosh N., Chow, Carson C., Sukharev, Sergei, Guy, H. Robert
Structural models of TREK channels and their gating mechanism
CHANNELS, 5:23-33, JAN-FEB 2011 2011
abstract, full text

Maksaev, Grigory, Milac, Adina, Anishkin, Andriy, Guy, H. Robert, Sukharev, Sergei
Analyses of gating thermodynamics and effects of deletions in the mechanosensitive channel TREK-1 Comparisons with structural models
CHANNELS, 5:34-42, JAN-FEB 2011 2011
abstract, full text

de Souza, Bibiana Monson, dos Santos Cabrera, Marcia Perez, Ruggiero Neto, Joao, Palma, Mario Sergio
Investigating the effect of different positioning of lysine residues along the peptide chain of mastoparans for their secondary structures and biological activities
AMINO ACIDS, 40:77-90, JAN 2011 2011
abstract, full text

Hsin, Jen, Struempfer, Johan, Lee, Eric H., Schulten, Klaus
Molecular Origin of the Hierarchical Elasticity of Titin: Simulation, Experiment, and Theory
ANNUAL REVIEW OF BIOPHYSICS, VOL 40, 40:187-203, 2011 2011
abstract, full text

Kubas, Adam, Hartung, Jens, Fink, Karin
How molecular oxygen binds to bis[trifluoroacetylacetonato(-1)]cobalt(II) - ab initio and density functional theory studies
DALTON TRANSACTIONS, 40:11289-11295, 2011 2011
abstract, full text

Sola, Antonia, Oton, Francisco, Espinosa, Arturo, Tarraga, Alberto, Molina, Pedro
Aldimines generated from aza-Wittig reaction between bis(iminophosphoranes) derived from 1,1 '- diazidoferrocene and aromatic or heteroaromatic aldehydes: electrochemical and optical behaviour towards metal cations
DALTON TRANSACTIONS, 40:12548-12559, 2011 2011
abstract, full text

Dubey, Kshatresh D., Ojha, Rajendra P.
Conformational flexibility and binding energy profile of c-Abl tyrosine kinase complexed with Imatinib: an insight from MD study
MOLECULAR SIMULATION, 37:1151-1163, 2011 2011
abstract, full text

Blinov, Nikolay, Dorosh, Lyudmyla, Wishart, David, Kovalenko, Andriy
3D-RISM-KH approach for biomolecular modelling at nanoscale: thermodynamics of fibril formation and beyond
MOLECULAR SIMULATION, 37:718-728, 2011 2011
abstract, full text

Casella, Girolamo, Saielli, Giacomo
DFT study of the interaction free energy of pi-pi complexes of fullerenes with buckybowls and viologen dimers
NEW JOURNAL OF CHEMISTRY, 35:1453-1459, 2011 2011
abstract, full text

Herbert, John M., Jacobson, Leif D.
Nature's most squishy ion: The important role of solvent polarization in the description of the hydrated electron
INTERNATIONAL REVIEWS IN PHYSICAL CHEMISTRY, 30:1-48, 2011 2011
abstract, full text

Plashkevych, Oleksandr, Chattopadhyaya, Jyoti
MOLECULAR STRUCTURE OF THE CORE-MODIFIED siRNA DUPLEXES CONTAINING DIASTEREOMERIC PAIR OF [C6 '(R)-OH]-VERSUS [C6 '(S)-OH]-CARBA-LNAs SUGGESTS A MODEL FOR RNAi ACTION
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 30:815-825, 2011 2011
abstract, full text

Jancso, Attila, Szunyogh, Daniel, Larsen, Flemming H., Thulstrup, Peter W., Christensen, Niels Johan, Gyurcsik, Bela, Hemmingsen, Lars
Towards the role of metal ions in the structural variability of proteins: Cd(II) speciation of a metal ion binding loop motif
METALLOMICS, 3:1331-1339, 2011 2011
abstract, full text

De Vico, Luca, Sorensen, Martin H., Iversen, Lars, Rogers, David M., Sorensen, Brian S., Brandbyge, Mads, Nygard, Jesper, Martinez, Karen L., Jensen, Jan H.
Quantifying signal changes in nano-wire based biosensors
NANOSCALE, 3:706-717, 2011 2011
abstract, full text

Herdes, Carmelo, Russo, Patricia A., Ribeiro Carrott, M. Manuela L., Carrott, Peter J. M.
Nitrogen Adsorption Studies on Non-porous Silica: the Annealing Effect over Surface Non-bridging Oxygen Atoms
ADSORPTION SCIENCE & TECHNOLOGY, 29:357-364, 2011 2011
abstract, full text

Sharma, Alok K., Rigby, Alan C., Alper, Seth L.
STAS Domain Structure and Function
CELLULAR PHYSIOLOGY AND BIOCHEMISTRY, 28:407-422, 2011 2011
abstract, full text

Boal, Frederic, Laguerre, Michel, Milochau, Alexandra, Lang, Jochen, Scotti, Pier A.
A charged prominence in the linker domain of the cysteine-string protein Csp alpha mediates its regulated interaction with the calcium sensor synaptotagmin 9 during exocytosis
FASEB JOURNAL, 25:132-143, JAN 2011 2011
abstract, full text

Bairagya, Hridoy R., Mukhopadhyay, Bishnu P., Bera, Asim K.
Conserved water mediated recognition and the dynamics of active site Cys 331 and Tyr 411 in hydrated structure of human IMPDH-II
JOURNAL OF MOLECULAR RECOGNITION, 24:35-44, JAN-FEB 2011 2011
abstract, full text

Gimenez-Oya, Victor, Villacanas, Oscar, Obiol-Pardo, Cristian, Antolin-Llovera, Meritxell, Rubio-Martinez, Jaime, Imperial, Santiago
Design of novel ligands of CDP-methylerythritol kinase by mimicking direct protein-protein and solvent-mediated interactions
JOURNAL OF MOLECULAR RECOGNITION, 24:71-80, JAN-FEB 2011 2011
abstract, full text

Schow, Eric V., Freites, J. Alfredo, Cheng, Philip, Bernsel, Andreas, von Heijne, Gunnar, White, Stephen H., Tobias, Douglas J.
Arginine in Membranes: The Connection Between Molecular Dynamics Simulations and Translocon-Mediated Insertion Experiments
JOURNAL OF MEMBRANE BIOLOGY, 239:35-48, JAN 2011 2011
abstract, full text

Terranova, U., Bowler, D. R.
Effect of hydration of the TiO(2) anatase (101) substrate on the atomic layer deposition of alumina films
JOURNAL OF MATERIALS CHEMISTRY, 21:4197-4203, 2011 2011
abstract, full text

Burkhardt, Stephen E., Conte, Sean, Rodriguez-Calero, Gabriel G., Lowe, Michael A., Qian, Hualei, Zhou, Weidong, Gao, Jie, Hennig, Richard G., Abruna, Hector D.
Towards organic energy storage: characterization of 2,5-bis(methylthio) thieno[3,2-b]thiophene
JOURNAL OF MATERIALS CHEMISTRY, 21:9553-9563, 2011 2011
abstract, full text

Kaila, Ville R. I., Sharma, Vivek, Wikstrom, Marten
The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1807:80-84, JAN 2011 2011
abstract, full text

Zhang, Jiapu
Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing
JOURNAL OF MOLECULAR MODELING, 17:173-179, JAN 2011 2011
abstract, full text

Ghelfi, A., Gaziola, S. A., Cia, M. C., Chabregas, M., Falco, M. C., Kuser-Falcao, P. R., Azevedo, R. A.
Cloning, expression, molecular modelling and docking analysis of glutathione transferase from Saccharum officinarum
ANNALS OF APPLIED BIOLOGY, 159:267-280, 2011 2011
abstract, full text

Allison, A. B., Palacios, G., da Rosa, A. Travassos, Popov, V. L., Lu, L., Xiao, S. Y., DeToy, K., Briese, T., Lipkin, W. I., Keel, M. K., Stallknecht, D. E., Bishop, G. R., Tesh, R. B.
Characterization of Durham virus, a novel rhabdovirus that encodes both a C and SH protein
VIRUS RESEARCH, 155:112-122, JAN 2011 2011
abstract, full text

Arslan, Melis, Qin, Zhao, Buehler, Markus J.
Coiled-coil intermediate filament stutter instability and molecular unfolding
COMPUTER METHODS IN BIOMECHANICS AND BIOMEDICAL ENGINEERING, 14:483-489, 2011 2011
abstract, full text

Dong, J. Z., Shen, Y., Zhang, J., Tsomaia, N., Mierke, D. F., Taylor, J. E.
Discovery and characterization of taspoglutide, a novel analogue of human glucagon-like peptide-1, engineered for sustained therapeutic activity in type 2 diabetes
DIABETES OBESITY & METABOLISM, 13:19-25, JAN 2011 2011
abstract, full text

Canepa, Pieremanuele, Chiatti, Fabio, Corno, Marta, Sakhno, Yuriy, Martra, Gianmario, Ugliengo, Piero
Affinity of hydroxyapatite (001) and (010) surfaces to formic and alendronic acids: a quantum-mechanical and infrared study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:1099-1111, 2011 2011
abstract, full text

Weiss, Alexander K. H., Hofer, Thomas S., Randolf, Bernhard R., Bhattacharjee, Anirban, Rode, Bernd M.
Hydrogen bond formation of formamide and N-methylformamide in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD)
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:12173-12185, 2011 2011
abstract, full text

Watkins, Matthew, Berkowitz, Max L., Shluger, Alexander L.
Role of water in atomic resolution AFM in solutions
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:12584-12594, 2011 2011
abstract, full text

Farmahini, Amir Hajiahmadi, Kvamme, Bjorn, Kuznetsova, Tatiana
Molecular dynamics simulation studies of absorption in piperazine activated MDEA solution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:13070-13081, 2011 2011
abstract, full text

Kaila, Ville R. I., Hummer, Gerhard
Energetics and dynamics of proton transfer reactions along short water wires
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:13207-13215, 2011 2011
abstract, full text

Almeida, Joao A. S., Pinto, Sandra P. R., Wang, Yujie, Marques, Eduardo F., Pais, Alberto A. C. C.
Structure and order of DODAB bilayers modulated by dicationic gemini surfactants
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:13772-13782, 2011 2011
abstract, full text

Cezard, Christine, Trivelli, Xavier, Aubry, Frederic, Djedaini-Pilard, Florence, Dupradeau, Francois-Yves
Molecular dynamics studies of native and substituted cyclodextrins in different media: 1. Charge derivation and force field performances
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:15103-15121, 2011 2011
abstract, full text

Wang, Qiuming, Shah, Nilam, Zhao, Jun, Wang, Chengshan, Zhao, Chao, Liu, Lingyun, Li, Lingyan, Zhou, Feimeng, Zheng, Jie
Structural, morphological, and kinetic studies of beta-amyloid peptide aggregation on self-assembled monolayers
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:15200-15210, 2011 2011
abstract, full text

Standara, Stanislav, Bouzkova, Katerina, Straka, Michal, Zacharova, Zuzana, Hocek, Michal, Marek, Jaromir, Marek, Radek
Interpretation of substituent effects on (13)C and (15)N NMR chemical shifts in 6-substituted purines
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:15854-15864, 2011 2011
abstract, full text

Brasiello, Antonio, Crescitelli, Silvestro, Milano, Giuseppe
Development of a coarse-grained model for simulations of tridecanoin liquid-solid phase transitions
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:16618-16628, 2011 2011
abstract, full text

Brylinski, Michal, Gao, Mu, Skolnick, Jeffrey
Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:17044-17055, 2011 2011
abstract, full text

First, Eric L., Gounaris, Chrysanthos E., Wei, James, Floudas, Christodoulos A.
Computational characterization of zeolite porous networks: an automated approach
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:17339-17358, 2011 2011
abstract, full text

Rodrigo Machado, Matias, Daniel Dans, Pablo, Pantano, Sergio
A hybrid all-atom/coarse grain model for multiscale simulations of DNA
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:18134-18144, 2011 2011
abstract, full text

Ramirez, Cristina. L., Pegoraro, Cesar, Trupp, Leandro, Bruttomesso, Andrea, Amorebieta, Valentin, Vera, D. Mariano A., Parise, Alejandro R.
Charge transfer properties of Troger base derivatives
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:20076-20080, 2011 2011
abstract, full text

Manna, Moutusi, Mukhopadhyay, Chaitali
Cholesterol driven alteration of the conformation and dynamics of phospholamban in model membranes
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:20188-20198, 2011 2011
abstract, full text

Callejas-Tovar, Rafael, Balbuena, Perla B.
Molecular dynamics simulations of surface oxide-water interactions on Pt(111) and Pt/PtCo/Pt(3)Co(111)
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:20461-20470, 2011 2011
abstract, full text

Steinmann, Stephan N., Mo, Yirong, Corminboeuf, Clemence
How do electron localization functions describe pi-electron delocalization?
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:20584-20592, 2011 2011
abstract, full text

Lin, Bo-Chao, Cheng, Cheu-Pyeng, You, Zhi-Qiang, Hsu, Chao-Ping
The role of CH-pi interaction in the charge transfer properties in tris(8-hydroxyquinolinato)aluminium(III)
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:20704-20713, 2011 2011
abstract, full text

Longhi, Giovanna, Abbate, Sergio, Ceraulo, Leopoldo, Ceselli, Alberto, Fornili, Sandro L., Liveri, Vincenzo Turco
A molecular dynamics study of structure, stability and fragmentation patterns of sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates in vacuo
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:21423-21431, 2011 2011
abstract, full text

Ramos, Javier, Cruz, Victor L., Martinez-Salazar, Javier, Campillo, Nuria E., Paez, Juan A.
Dissimilar interaction of CB1/CB2 with lipid bilayers as revealed by molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:3660-3668, 2011 2011
abstract, full text

Bernini, Caterina, Pogni, Rebecca, Ruiz-Duenas, Francisco J., Martinez, Angel T., Basosia, Riccardo, Sinicropi, Adalgisa
EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:5078-5098, 2011 2011
abstract, full text

Gauden, Piotr A., Terzyk, Artur P., Pienkowski, Rafal, Furmaniak, Sylwester, Wesolowski, Radoslaw P., Kowalczyk, Piotr
Molecular dynamics of zigzag single walled carbon nanotube immersion in water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:5621-5629, 2011 2011
abstract, full text

Chen, L. Y.
Exploring the free-energy landscapes of biological systems with steered molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6176-6183, 2011 2011
abstract, full text

Salanne, Mathieu, Simon, Christian, Madden, Paul A.
Optical basicity scales in protic solvents: water, hydrogen fluoride, ammonia and their mixtures
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:6305-6308, 2011 2011
abstract, full text

Kowalczyk, Piotr, Gauden, Piotr A., Terzyk, Artur P., Furmaniak, Sylwester
Quantum fluctuations increase the self-diffusive motion of para-hydrogen in narrow carbon nanotubes
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 13:9824-9830, 2011 2011
abstract, full text

Tapia, G., Morales-Quintana, L., Inostroza, L., Acuna, H.
Molecular characterisation of Ltchi7, a gene encoding a Class III endochitinase induced by drought stress in Lotus spp
PLANT BIOLOGY, 13:69-77, JAN 2011 2011
abstract, full text

Salanne, Mathieu, Madden, Paul A.
Polarization effects in ionic solids and melts
MOLECULAR PHYSICS, 109:2299-2315, 2011 2011
abstract, full text

Fromme, Petra, Grotjohann, Ingo
Structure of Cyanobacterial Photosystems I and II
BIOENERGETIC PROCESSES OF CYANOBACTERIA: FROM EVOLUTIONARY SINGULARITY TO ECOLOGICAL DIVERSITY, 285-335, 2011 2011
full text

Gangupomu, Vamshi K., Capaldi, Franco M.
Interactions of Carbon Nanotube with Lipid Bilayer Membranes
JOURNAL OF NANOMATERIALS, Art. No. 830436, 2011 2011
abstract, full text

Offman, Marc N., Krol, Marcin, Silman, Israel, Sussman, Joel L., Futerman, Anthony H.
Molecular Basis of Reduced Glucosylceramidase Activity in the Most Common Gaucher Disease Mutant, N370S
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:42105-42114, DEC 31 2010 2010
abstract, full text

Kurisaki, Ikuo, Fukuzawa, Kaori, Nakano, Tatsuya, Mochizuki, Yuji, Watanabe, Hirofumi, Tanaka, Shigenori
Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 962:45-55, DEC 30 2010 2010
abstract, full text

Jia Xuebing, Zhang Jun, Sun Hongwei, Chen Lan, Shen Rongxin, Lai Chengming
Molecular Dynamics Simulation Study on the Interaction Mode of Auxin Perception
ACTA CHIMICA SINICA, 68:2500-2508, DEC 28 2010 2010
abstract, full text

Reeder, Philippa J., Huang, Yao-Ming, Dordick, Jonathan S., Bystroff, Christopher
A Rewired Green Fluorescent Protein: Folding and Function in a Nonsequential, Noncircular GFP Permutant
BIOCHEMISTRY, 49:10773-10779, DEC 28 2010 2010
abstract, full text

Holdbrook, Daniel A., Leung, Yuk Ming, Piggot, Thomas J., Marius, Phedra, Williamson, Philip T. F., Khalid, Syma
Stability and Membrane Orientation of the Fukutin Transmembrane Domain: A Combined Multiscale Molecular Dynamics and Circular Dichroism Study
BIOCHEMISTRY, 49:10796-10802, DEC 28 2010 2010
abstract, full text

Gao, Mu, Skolnick, Jeffrey
Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:22517-22522, DEC 28 2010 2010
abstract, full text

Jones, Martin K., Zhang, Lei, Catte, Andrea, Li, Ling, Oda, Michael N., Ren, Gang, Segrest, Jere P.
Assessment of the Validity of the Double Superhelix Model for Reconstituted High Density Lipoproteins A COMBINED COMPUTATIONAL-EXPERIMENTAL APPROACH
JOURNAL OF BIOLOGICAL CHEMISTRY, Issue 52, , DEC 24 2010 2010
abstract, full text

Yang, Huaiyu, Xu, Yechun, Gao, Zhaobing, Mao, Yanyan, Du, Yun, Jiang, Hualiang
Effects of Na(+), K(+), and Ca(2+) on the Structures of Anionic Lipid Bilayers and Biological Implication
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16978-16988, DEC 23 2010 2010
abstract, full text

Kaminski, Steve, Mroginski, Maria Andrea
Molecular Dynamics of Phycocyanobilin Binding Bacteriophytochromes: A Detailed Study of Structural and Dynamic Properties
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16677-16686, DEC 23 2010 2010
abstract, full text

Hirao, Hajime, Morokuma, Keiji
Ferric Superoxide and Ferric Hydroxide Are Used in the Catalytic Mechanism of Hydroxyethylphosphonate Dioxygenase: A Density Functional Theory Investigation
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:17901-17909, DEC 22 2010 2010
abstract, full text

Patapati, Kalliopi K., Glykos, Nicholas M.
Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study
PLOS ONE, 5: Art. No. e15290, DEC 20 2010 2010
abstract, full text

Paracuellos, Patricia, Ballandras, Allison, Robert, Xavier, Kahn, Richard, Herve, Mireille, Mengin-Lecreulx, Dominique, Cozzone, Alain J., Duclos, Bertrand, Gouet, Patrice
The Extended Conformation of the 2.9-angstrom Crystal Structure of the Three-PASTA Domain of a Ser/Thr Kinase from the Human Pathogen Staphylococcus aureus
JOURNAL OF MOLECULAR BIOLOGY, 404:847-858, DEC 17 2010 2010
abstract, full text

Kim, Taekyung, Cooper, John A., Sept, David
The Interaction of Capping Protein with the Barbed End of the Actin Filament
JOURNAL OF MOLECULAR BIOLOGY, 404:794-802, DEC 17 2010 2010
abstract, full text

DeVane, Russell, Jusufi, Arben, Shinoda, Wataru, Chiu, Chi-cheng, Nielsen, Steven O., Moore, Preston B., Klein, Michael L.
Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16364-16372, DEC 16 2010 2010
abstract, full text

Priyakumar, U. Deva, Harika, G., Suresh, G.
Molecular Simulations on the Thermal Stabilization of DNA by Hyperthermophilic Chromatin Protein Sac7d, and Associated Conformational Transitions
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16548-16557, DEC 16 2010 2010
abstract, full text

Shao, Qing, He, Yi, White, Andrew D., Jiang, Shaoyi
Difference in Hydration between Carboxybetaine and Sulfobetaine
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16625-16631, DEC 16 2010 2010
abstract, full text

Pauwels, Ewald, Declerck, Reinout, Verstraelen, Toon, De Sterck, Bart, Kay, Christopher W. M., Van Speybroeck, Veronique, Waroquier, Michel
Influence of Protein Environment on the Electron Paramagnetic Resonance Properties of Flavoprotein Radicals: A QM/MM Study
JOURNAL OF PHYSICAL CHEMISTRY B, 114:16655-16665, DEC 16 2010 2010
abstract, full text

Watanabe, Akira, Choe, Seungho, Chaptal, Vincent, Rosenberg, John M., Wright, Ernest M., Grabe, Michael, Abramson, Jeff
The mechanism of sodium and substrate release from the binding pocket of vSGLT
NATURE, 468:988-U162, DEC 16 2010 2010
abstract, full text

Huang, Xiaopeng, Wang, Xinwei, Cook, Bruce
Coherent Nanointerfaces in Thermoelectric Materials
JOURNAL OF PHYSICAL CHEMISTRY C, 114:21003-21012, DEC 16 2010 2010
abstract, full text

Kowalczyk, Piotr, Furmaniak, Sylwester, Gauden, Piotr A., Terzyk, Artur P.
Optimal Single-Walled Carbon Nanotube Vessels for Short-Term Reversible Storage of Carbon Dioxide at Ambient Temperatures
JOURNAL OF PHYSICAL CHEMISTRY C, 114:21465-21473, DEC 16 2010 2010
abstract, full text

Khandelia, Himanshu, Witzke, Sarah, Mouritsen, Ole G.
Interaction of Salicylate and a Terpenoid Plant Extract with Model Membranes: Reconciling Experiments and Simulations
BIOPHYSICAL JOURNAL, 99:3887-3894, DEC 15 2010 2010
abstract, full text

Yogurtcu, Osman N., Wolgemuth, Charles W., Sun, Sean X.
Mechanical Response and Conformational Amplification in alpha-Helical Coiled Coils
BIOPHYSICAL JOURNAL, 99:3895-3904, DEC 15 2010 2010
abstract, full text

Chen, Ke, Eargle, John, Sarkar, Krishnarjun, Gruebele, Martin, Luthey-Schulten, Zaida
Functional Role of Ribosomal Signatures
BIOPHYSICAL JOURNAL, 99:3930-3940, DEC 15 2010 2010
abstract, full text

Xu, Yechun, Colletier, Jacques-Philippe, Weik, Martin, Qin, Guangrong, Jiang, Hualiang, Silman, Israel, Sussman, Joel L.
Long Route or Shortcut? A Molecular Dynamics Study of Traffic of Thiocholine within the Active-Site Gorge of Acetylcholinesterase
BIOPHYSICAL JOURNAL, 99:4003-4011, DEC 15 2010 2010
abstract, full text

Knecht, Volker, Levine, Zachary A., Vernier, P. Thomas
Electrophoresis of neutral oil in water
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 352:223-231, DEC 15 2010 2010
abstract, full text

Kaila, Ville R. I., Johansson, Mikael P., Sundholm, Dage, Wikstroem, Marten
Interheme electron tunneling in cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:21470-21475, DEC 14 2010 2010
abstract, full text

Scrima, Mario, Di Marino, Sara, Grimaldi, Manuela, Mastrogiacomo, Antonia, Novellino, Ettore, Bifulco, Maurizio, D'Ursi, Anna Maria
Binding of the Hemopressin Peptide to the Cannabinoid CB(1) Receptor: Structural Insights
BIOCHEMISTRY, 49:10449-10457, DEC 14 2010 2010
abstract, full text

Winston, Matthew S., Bercaw, John E.
A Novel Bis(phosphido)pyridine [PNP](2-) Pincer Ligand and Its Potassium and Bis(dimethylamido)zirconium(IV) Complexes
ORGANOMETALLICS, 29:6408-6416, DEC 13 2010 2010
abstract, full text

Kim, Jun Soo, Szleifer, Igal
Depletion Effect on Polymers Induced by Small Depleting Spheres
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20864-20869, DEC 9 2010 2010
abstract, full text

Nonella, Marco, Seeger, Stefan
Monitoring peptide-surface interaction by means of molecular dynamics simulation
CHEMICAL PHYSICS, 378:73-81, DEC 9 2010 2010
abstract, full text

Witzke, Sarah, Duelund, Lars, Kongsted, Jacob, Petersen, Michael, Mouritsen, Ole G., Khandelia, Himanshu
Inclusion of Terpenoid Plant Extracts in Lipid Bilayers Investigated by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15825-15831, DEC 9 2010 2010
abstract, full text

Lin, I-Chun, Tuckerman, Mark E.
Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15935-15940, DEC 9 2010 2010
abstract, full text

Cheung, David L., Troisi, Alessandro
Theoretical Study of the Organic Photovoltaic Electron Acceptor PCBM: Morphology, Electronic Structure, and Charge Localization
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20479-20488, DEC 9 2010 2010
abstract, full text

Davis, William B., Bjorklund, Chad C., Cho, Paul S.
Hole Transport Dynamics in Mixed Sequence DNA Can Vary with Salt Concentration: An Experimental and Theoretical Analysis
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20821-20833, DEC 9 2010 2010
abstract, full text

Lue, Shouqin, Zhang, Yan, Long, Mian
Visualization of Allostery in P-Selectin Lectin Domain Using MD Simulations
PLOS ONE, 5: Art. No. e15417, DEC 8 2010 2010
abstract, full text

Reymond, Cedric, Levesque, Dominique, Bisaillon, Martin, Perreault, Jean-Pierre
Developing Three-Dimensional Models of Putative-Folding Intermediates of the HDV Ribozyme
STRUCTURE, 18:1608-1616, DEC 8 2010 2010
abstract, full text

Ranieri, Antonio, Monari, Stefano, Sola, Marco, Borsari, Marco, Battistuzzi, Gianantonio, Ringhieri, Paola, Nastri, Flavia, Pavone, Vincenzo, Lombardi, Angelina
Redox and Electrocatalytic Properties of Mimochrome VI, a Synthetic Heme Peptide Adsorbed on Gold
LANGMUIR, 26:17831-17835, DEC 7 2010 2010
abstract, full text

Chakrabarty, Suman, Bagchi, Biman
Temperature dependent free energy surface of polymer folding from equilibrium and quench studies
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 214901, DEC 7 2010 2010
abstract, full text

Keten, Sinan, Buehler, Markus J.
Nanostructure and molecular mechanics of spider dragline silk protein assemblies
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 7:1709-1721, DEC 6 2010 2010
abstract, full text

Masitas, Cesar A., Kumar, Manoj, Mashuta, Mark S., Kozlowski, Pawel M., Grapperhaus, Craig A.
Controlled Sulfur Oxygenation of the Ruthenium Dithiolate (4,7-Bis-(2 '-methyl-2 '-mercaptopropyl)-1-thia-4,7-diazacyclononane)RuPPh(3) under Limiting O(2) Conditions Yields Thiolato/Sulfinato, Sulfenato/Sulfinato, and Bis-Sulfinato Derivatives
INORGANIC CHEMISTRY, 49:10875-10881, DEC 6 2010 2010
abstract, full text

Mohan, Suma, Sheena, Aswathy, Poulose, Ninu, Anilkumar, Gopalakrishnapillai
Molecular Dynamics Simulation Studies of GLUT4: Substrate-Free and Substrate-Induced Dynamics and ATP-Mediated Glucose Transport Inhibition
PLOS ONE, 5: Art. No. e14217, DEC 3 2010 2010
abstract, full text

Sevvana, Madhumati, Kassler, Kristin, Ahnstrom, Josefin, Weiler, Sigrid, Dahlback, Bjorn, Sticht, Heinrich, Muller, Yves A.
Mouse ApoM Displays an Unprecedented Seven-Stranded Lipocalin Fold: Folding Decoy or Alternative Native Fold?
JOURNAL OF MOLECULAR BIOLOGY, 404:363-371, DEC 3 2010 2010
abstract, full text

Yu, Jin, Cheng, Wei, Bustamante, Carlos, Oster, George
Coupling Trans location with Nucleic Acid Unwinding by NS3 Helicase
JOURNAL OF MOLECULAR BIOLOGY, 404:439-455, DEC 3 2010 2010
abstract, full text

Pendse, Pushkar Y., Brooks, Bernard R., Klauda, Jeffery B.
Probing the Periplasmic-Open State of Lactose Permease in Response to Sugar Binding and Proton Trans location
JOURNAL OF MOLECULAR BIOLOGY, 404:506-521, DEC 3 2010 2010
abstract, full text

Anton, Lena, Majander, Katariina, Savilahti, Harri, Laakkonen, Liisa, Westerlund-Wikstrom, Benita
Two distinct regions in the model protein Peb1 are critical for its heterologous transport out of Escherichia coli
MICROBIAL CELL FACTORIES, 9: Art. No. 97, DEC 2 2010 2010
abstract, full text

Ratje, Andreas H., Loerke, Justus, Mikolajka, Aleksandra, Bruenner, Matthias, Hildebrand, Peter W., Starosta, Agata L., Doenhoefer, Alexandra, Connell, Sean R., Fucini, Paola, Mielke, Thorsten, Whitford, Paul C., Onuchic, Jose N., Yu, Yanan, Sanbonmatsu, Karissa Y., Hartmann, Roland K., Penczek, Pawel A., Wilson, Daniel N., Spahn, Christian M. T.
Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites
NATURE, 468:713-U143, DEC 2 2010 2010
abstract, full text

Kepczynski, Mariusz, Kumorek, Marta, Stepniewski, Michal, Rog, Tomasz, Kozik, Bartlomiej, Jamroz, Dorota, Bednar, Jan, Nowakowska, Maria
Behavior of 2,6-Bis(decyloxy)naphthalene Inside Lipid Bilayer
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15483-15494, DEC 2 2010 2010
abstract, full text

Sawada, Toshihiko, Fedorov, Dmitri G., Kitaura, Kazuo
Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15700-15705, DEC 2 2010 2010
abstract, full text

Khomenko, Alexei V., Prodanov, Nikolay V.
Study of Friction of Ag and Ni Nanoparticles: An Atomistic Approach
JOURNAL OF PHYSICAL CHEMISTRY C, 114:19958-19965, DEC 2 2010 2010
abstract, full text

O'Rourke, Conn, Bowler, David R.
Adsorption of Thiophene-Conjugated Sensitizers on TiO(2) Anatase (101)
JOURNAL OF PHYSICAL CHEMISTRY C, 114:20240-20248, DEC 2 2010 2010
abstract, full text

Binh Khanh Mai, Viet, Man Hoang, Li, Mai Suan
Top Leads for Swine Influenza A/H1N1 Virus Revealed by Steered Molecular Dynamics Approach
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:2236-2247, DEC 2010 2010
abstract, full text

Chabria, Mamta, Hertig, Samuel, Smith, Michael L., Vogel, Viola
Stretching fibronectin fibres disrupts binding of bacterial adhesins by physically destroying an epitope
NATURE COMMUNICATIONS, 1: Art. No. 135, DEC 2010 2010
abstract, full text

Holovko-Kamoshenkova, Oksana M., Kirij, Nataliia V., Boiko, Vladimir N., Rozhenko, Alexander B., Yagupolskii, Yurii L.
Stable gem-trifluoromethyl anionic sigma-complexes based on 1,3,5-tris(sulfonyl)benzene derivatives and their transformations
JOURNAL OF FLUORINE CHEMISTRY, 131:1344-1352, DEC 2010 2010
abstract, full text

Oliveira, A. F., Gemming, S., Seifert, G.
Molecular dynamics simulations of BMP-2 adsorption on a hydrophobic surface
MATERIALWISSENSCHAFT UND WERKSTOFFTECHNIK, 41:1048-1053, DEC 2010 2010
abstract, full text

Tseng, Chih-Yuan, Tuszynski, Jack A.
Using Entropy Leads to a Better Understanding of Biological Systems
ENTROPY, 12:2450-2469, DEC 2010 2010
abstract, full text

Menz, William J., Penna, Matthew J., Biggs, Mark J.
TNAMD: Implementation of TIGER2 in NAMD
COMPUTER PHYSICS COMMUNICATIONS, 181:2082-2085, DEC 2010 2010
abstract, full text

Lee, One-Sun, Schatz, George C.
Conformation of DNA Between Gold Surfaces
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 7:2568-2573, DEC 2010 2010
abstract, full text

Janosi, Lorant, Gorfe, Alemayehu A.
Segregation of Negatively Charged Phospholipids by the Polycationic and Farnesylated Membrane Anchor of Kras
BIOPHYSICAL JOURNAL, 99:3666-3674, DEC 1 2010 2010
abstract, full text

Autore, Flavia, Pagano, Bruno, Fornili, Arianna, Rittinger, Katrin, Fraternali, Franca
In Silico Phosphorylation of the Autoinhibited Form of p47(phox) Insights into the Mechanism of Activation
BIOPHYSICAL JOURNAL, 99:3716-3725, DEC 1 2010 2010
abstract, full text

Wieden, Hans Joachim, Mercier, Evan, Gray, John, Steed, Brett, Yawney, Davis
A Combined Molecular Dynamics and Rapid Kinetics Approach to Identify Conserved Three-Dimensional Communication Networks in Elongation Factor Tu
BIOPHYSICAL JOURNAL, 99:3735-3743, DEC 1 2010 2010
abstract, full text

Beckham, Gregg T., Bomble, Yannick J., Matthews, James F., Taylor, Courtney B., Resch, Michael G., Yarbrough, John M., Decker, Steve R., Bu, Lintao, Zhao, Xiongce, McCabe, Clare, Wohlert, Jakob, Bergenstrahle, Malin, Brady, John W., Adney, William S., Himmel, Michael E., Crowley, Michael F.
The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein
BIOPHYSICAL JOURNAL, 99:3773-3781, DEC 1 2010 2010
abstract, full text

Shafrir, Yinon, Durell, Stewart R., Anishkin, Andriy, Guy, H. Robert
Beta-barrel models of soluble amyloid beta oligomers and annular protofibrils
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:3458-3472, DEC 2010 2010
abstract, full text

Dominguez, M., Rezende, M. Caroli
The Cationic Halochromism of Phenolate Betaines: Molecular Dynamics and Quantum Mechanics Studies
JOURNAL OF THE IRANIAN CHEMICAL SOCIETY, 7:995-1003, DEC 2010 2010
abstract, full text

Illingworth, Christopher J. R., Furini, Simone, Domene, Carmen
Computational Studies on Polarization Effects and Selectivity in K(+) Channels
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3780-3792, DEC 2010 2010
abstract, full text

Luccarelli, James, Michel, Julien, Tirado-Rives, Julian, Jorgensen, William L.
Effects of Water Placement on Predictions of Binding Affinities for p38 alpha MAP Kinase Inhibitors
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3850-3856, DEC 2010 2010
abstract, full text

Jirasko, Vlastimil, Montserret, Roland, Lee, Ji Young, Gouttenoire, Jerome, Moradpour, Darius, Penin, Francois, Bartenschlager, Ralf
Structural and Functional Studies of Nonstructural Protein 2 of the Hepatitis C Virus Reveal Its Key Role as Organizer of Virion Assembly
PLOS PATHOGENS, 6: Art. No. e1001233, DEC 2010 2010
abstract, full text

Zhang, Dapeng, Aravind, L.
Identification of novel families and classification of the C2 domain superfamily elucidate the origin and evolution of membrane targeting activities in eukaryotes
GENE, 469:18-30, DEC 1 2010 2010
abstract, full text

Tummala, Naga Rajesh, Morrow, Brian H., Resasco, Daniel E., Striolo, Alberto
Stabilization of Aqueous Carbon Nanotube Dispersions Using Surfactants: Insights from Molecular Dynamics Simulations
ACS NANO, 4:7193-7204, DEC 2010 2010
abstract, full text

Yang, Jian, Kickhoefer, Valerie A., Ng, Benny C., Gopal, Ajaykumar, Bentolila, Laurent A., John, Scott, Tolbert, Sarah H., Rome, Leonard H.
Vaults Are Dynamically Unconstrained Cytoplasmic Nanoparticles Capable of Half Vault Exchange
ACS NANO, 4:7229-7240, DEC 2010 2010
abstract, full text

Knapp, Bernhard, Lederer, Nadja, Omasits, Ulrich, Schreiner, Wolfgang
vmdICE: A Plug-In for Rapid Evaluation of Molecular Dynamics Simulations using VMD
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:2868-2873, DEC 2010 2010
abstract, full text

Duerr, Katharina L., Seuffert, Ina, Friedrich, Thomas
Deceleration of the E(1)P-E(2)P Transition and Ion Transport by Mutation of Potentially Salt Bridge-forming Residues Lys-791 and Glu-820 in Gastric H(+)/K(+)-ATPase
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:39366-39379, DEC 2010 2010
abstract, full text

Wiesner, Jiri, Kriz, Zdenek, Kuca, Kamil, Jun, Daniel, Koca, Jaroslav
Influence of the Acetylcholinesterase Active Site Protonation on Omega Loop and Active Site Dynamics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:393-403, DEC 2010 2010
abstract, full text

Lee, Hyun Mee, Jin, Biao, Han, Sung Wook, Kim, Seog K.
Conformational Analysis of Genotoxic Benzo[a]pyrene-7,8-dione-Duplex DNA Adducts Using a Molecular Dynamics Method (II)
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:421-430, DEC 2010 2010
abstract, full text

Gong, Zhou, Zhao, Yunjie, Xiao, Yi
RNA Stability Under Different Combinations of Amber Force Fields and Solvation Models
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 28:431-441, DEC 2010 2010
abstract, full text

Magnuson, Timothy S., Swenson, Michael W., Paszczynski, Andrzej J., Deobald, Lee A., Kerk, David, Cummings, David E.
Proteogenomic and functional analysis of chromate reduction in Acidiphilium cryptum JF-5, an Fe(III)-respiring acidophile
BIOMETALS, 23:1129-1138, DEC 2010 2010
abstract, full text

Pirakitikulr, Nathan, Ostrov, Nili, Peralta-Yahya, Pamela, Cornish, Virginia W.
PCRless library mutagenesis via oligonucleotide recombination in yeast
PROTEIN SCIENCE, 19:2336-2346, DEC 2010 2010
abstract, full text

Brunetti, Lucia, Di Stefano, Michele, Ruggieri, Silverio, Cimadamore, Flavio, Magni, Giulio
Homology modeling and deletion mutants of human nicotinamide mononucleotide adenylyltransferase isozyme 2: New insights on structure and function relationship
PROTEIN SCIENCE, 19:2440-2450, DEC 2010 2010
abstract, full text

Missimer, John H., Dolenc, Jozica, Steinmetz, Michel O., van Gunsteren, Wilfred F.
Exploring the trigger sequence of the GCN4 coiled-coil: Biased molecular dynamics resolves apparent inconsistencies in NMR measurements
PROTEIN SCIENCE, 19:2462-2474, DEC 2010 2010
abstract, full text

Mulkidjanian, Armen Y.
Activated Q-cycle as a common mechanism for cytochrome bc(1) and cytochrome b(6)f complexes
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1797:1858-1868, DEC 2010 2010
abstract, full text

Di Marino, Daniele, Oteri, Francesco, della Rocca, Blasco Morozzo, Chillemi, Giovanni, Falconi, Mattia
ADP/ATP mitochondrial carrier MD simulations to shed light on the structural-dynamical events that, after an additional mutation, restore the function in a pathological single mutant
JOURNAL OF STRUCTURAL BIOLOGY, 172:225-232, DEC 2010 2010
abstract, full text

Kurisaki, Ikuo, Watanabe, Hirofumi, Tanaka, Shigenori
Spontaneous Adjustment Mechanism in an RNA-Binding Protein: Cooperation Between Energetic Stabilization and Target Search Enhancement
PROTEIN AND PEPTIDE LETTERS, 17:1547-1552, DEC 2010 2010
abstract, full text

Kamysz, Elzbieta, Sikorska, Emilia
Synthesis and conformational analysis of salivary proline-rich peptide P-B
JOURNAL OF PEPTIDE SCIENCE, 16:709-715, DEC 2010 2010
abstract, full text

Hu, Guodong, Chen, L. Y.
In silico experiments of single-chain antibody fragment against drugs of abuse
BIOPHYSICAL CHEMISTRY, 153:97-103, DEC 2010 2010
abstract, full text

Rendine, Stefano, Pieraccini, Stefano, Sironi, Maurizio
Vinblastine perturbation of tubulin protofilament structure: a computational insight
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:15530-15536, DEC 2010 2010
abstract, full text

Kaila, Ville R. I., Verkhovsky, Michael I., Wikstrom, Marten
Proton-Coupled Electron Transfer in Cytochrome Oxidase
CHEMICAL REVIEWS, 110:7062-7081, DEC 2010 2010
full text

D'Auria, Gabriella, Esposito, Carla, Falcigno, Lucia, Calvanese, Luisa, Iaccarino, Emanuela, Ruggiero, Alessia, Pedone, Carlo, Pedone, Emilia, Berisio, Rita
Dynamical properties of cold shock protein A from Mycobacterium tuberculosis
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 402:693-698, NOV 26 2010 2010
abstract, full text

Li, Jinghua, Du, Likai, Wang, Lushan
Glycosidic-Bond Hydrolysis Mechanism Catalyzed by Cellulase Cel7A from Trichoderma reesei: A Comprehensive Theoretical Study by Performing MD, QM, and QM/MM Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15261-15268, NOV 25 2010 2010
abstract, full text

Hou, Qianqian, Du, Likai, Gao, Jun, Liu, Yongjun, Liu, Chengbu
QM/MM Study on the Reaction Mechanism of O(6)-Alkylguanine-DNA Alkyltransferase
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15296-15300, NOV 25 2010 2010
abstract, full text

Wang, Wei, Castelan-Vega, Juan A., Jimenez-Alberto, Alicia, Vassell, Russell, Ye, Zhiping, Weiss, Carol D.
A mutation in the receptor binding site enhances infectivity of 2009 H1N1 influenza hemagglutinin pseudotypes without changing antigenicity
VIROLOGY, 407:374-380, NOV 25 2010 2010
abstract, full text

Salvalaglio, Matteo, Muscionico, Isabella, Cavallotti, Carlo
Determination of Energies and Sites of Binding of PFOA and PFOS to Human Serum Albumin
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14860-14874, NOV 25 2010 2010
abstract, full text

Gang, Hong-Ze, Liu, Jin-Feng, Mu, Bo-Zhong
Interfacial Behavior of Surfactin at the Decane/Water Interface: A Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14947-14954, NOV 25 2010 2010
abstract, full text

Furlan, Sara, Hureau, Christelle, Faller, Peter, La Penna, Giovanni
Modeling the Cu(+) Binding in the 1-16 Region of the Amyloid-beta Peptide Involved in Alzheimer's Disease
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15119-15133, NOV 25 2010 2010
abstract, full text

Hou, Jin-Qiang, Chen, Shuo-Bin, Tan, Jia-Heng, Ou, Tian-Miao, Luo, Hai-Bin, Li, Ding, Xu, Jun, Gu, Lian-Quan, Huang, Zhi-Shu
New Insights into the Structures of Ligand-Quadruplex Complexes from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15301-15310, NOV 25 2010 2010
abstract, full text

Stafford, Amy J., Ensign, Daniel L., Webb, Lauren J.
Vibrational Stark Effect Spectroscopy at the Interface of Ras and Rap1A Bound to the Ras Binding Domain of RalGDS Reveals an Electrostatic Mechanism for Protein-Protein Interaction
JOURNAL OF PHYSICAL CHEMISTRY B, 114:15331-15344, NOV 25 2010 2010
abstract, full text

Chandrachud, Prachi, Pujari, Bhalchandra S., Haldar, Soumyajyoti, Sanyal, Biplab, Kanhere, D. G.
A systematic study of electronic structure from graphene to graphane
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 465502, NOV 24 2010 2010
abstract, full text

McIntyre, Neil R., Lowe, Edward W., Jr., Belof, Jonathan L., Ivkovic, Milena, Shafer, Jacob, Space, Brian, Merkler, David J.
Evidence for Substrate Preorganization in the Peptidylglycine alpha-Amidating Monooxygenase Reaction Describing the Contribution of Ground State Structure to Hydrogen Tunneling
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:16393-16402, NOV 24 2010 2010
abstract, full text

Cheng, Mary Hongying, Coalson, Rob D., Tang, Pei
Molecular Dynamics and Brownian Dynamics Investigation of Ion Permeation and Anesthetic Halothane Effects on a Proton-Gated Ion Channel
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:16442-16449, NOV 24 2010 2010
abstract, full text

Selvan, Anitha, Seniya, Chandrabhan, Chandrasekaran, Srinivas Niranj, Siddharth, Nithyanand, Anishetty, Sharmila, Pennathur, Gautam
Molecular dynamics simulations of human and dog gastric lipases: Insights into domain movements
FEBS LETTERS, 584:4599-4605, NOV 19 2010 2010
abstract, full text

Kim, Youngchang, Zhou, Min, Moy, Shiu, Morales, Jennifer, Cunningham, Mark A., Joachimiak, Andrzej
High-Resolution Structure of the Nitrile Reductase QueF Combined with Molecular Simulations Provide Insight into Enzyme Mechanism
JOURNAL OF MOLECULAR BIOLOGY, 404:127-137, NOV 19 2010 2010
abstract, full text

Xu, Xinping, Vysotskaya, Zhanna V., Liu, Qinglian, Zhou, Lei
Structural Basis for the cAMP-dependent Gating in the Human HCN4 Channel
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:37082-37091, NOV 19 2010 2010
abstract, full text

Kumar, Amit, Hajjar, Eric, Ruggerone, Paolo, Ceccarelli, Matteo
Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 454125, NOV 17 2010 2010
abstract, full text

Mahendran, Kozhinjampara R., Singh, Pratik Raj, Arning, Juergen, Stolte, Stefan, Kleinekathoefer, Ulrich, Winterhalter, Mathias
Permeation through nanochannels: revealing fast kinetics
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 454131, NOV 17 2010 2010
abstract, full text

Jolley, Craig C., Douglas, Trevor
Ion Accumulation in a Protein Nanocage: Finding Noisy Temporal Sequences Using a Genetic Algorithm
BIOPHYSICAL JOURNAL, 99:3385-3393, NOV 17 2010 2010
abstract, full text

Sacquin-Mora, Sophie, Delalande, Olivier, Baaden, Marc
Functional Modes and Residue Flexibility Control the Anisotropic Response of Guanylate Kinase to Mechanical Stress
BIOPHYSICAL JOURNAL, 99:3412-3419, NOV 17 2010 2010
abstract, full text

Gangupomu, Vamshi K., Abrams, Cameron F.
All-Atom Models of the Membrane-Spanning Domain of HIV-1 gp41 from Metadynamics
BIOPHYSICAL JOURNAL, 99:3438-3444, NOV 17 2010 2010
abstract, full text

Li, Yunlang, Schlick, Tamar
Modeling DNA Polymerase mu Motions: Subtle Transitions before Chemistry
BIOPHYSICAL JOURNAL, 99:3463-3472, NOV 17 2010 2010
abstract, full text

Weis, Felix, Bron, Patrick, Giudice, Emmanuel, Rolland, Jean-Paul, Thomas, Daniel, Felden, Brice, Gillet, Reynald
tmRNA-SmpB: a journey to the centre of the bacterial ribosome
EMBO JOURNAL, 29:3810-3818, NOV 17 2010 2010
abstract, full text

Anishkin, A., Akitake, B., Kamaraju, K., Chiang, C.-.S., Sukharev, S.
Hydration properties of mechanosensitive channel pores define the energetics of gating
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 454120, NOV 17 2010 2010
abstract, full text

Marque, Gregory, Verdu, Jacques, Prunier, Valery, Brown, David
A Molecular Dynamics Simulation Study of Three Polysulfones in Dry and Hydrated States
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 48:2312-2336, NOV 15 2010 2010
abstract, full text

Margapoti, E., Alves, Fabrizio M., Mahapatra, S., Schmidt, T., Lopez-Richard, V., Destefani, C., Menendez-Proupin, E., Qu, Fanyao, Bougerol, C., Brunner, K., Forchel, A., Marques, G. E., Worschech, L.
Characterization of spin-state tuning in thermally annealed semiconductor quantum dots
PHYSICAL REVIEW B, 82: Art. No. 205318, NOV 15 2010 2010
abstract, full text

Ivanov, Igor, Heydeck, Dagmar, Hofheinz, Katharina, Roffeis, Jana, O'Donnell, Valerie B., Kuhn, Hartmut, Walther, Matthias
Molecular enzymology of lipoxygenases
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 503:161-174, NOV 15 2010 2010
abstract, full text

Berski, Slawomir, Latajka, Zdzislaw, Gordon, Agnieszka J.
Ab Initio and Quantum Chemical Topology Studies on the Isomerization of HONO to HNO(2). Effect of the Basis Set in QCT
JOURNAL OF COMPUTATIONAL CHEMISTRY, 31:2555-2567, NOV 15 2010 2010
abstract, full text

Gan, Yong, Chen, J. K.
An atomic-level study of material ablation and spallation in ultrafast laser processing of gold films
JOURNAL OF APPLIED PHYSICS, 108: Art. No. 103102, NOV 15 2010 2010
abstract, full text

Ong, Zhun-Yong, Pop, Eric
Frequency and polarization dependence of thermal coupling between carbon nanotubes and SiO(2)
JOURNAL OF APPLIED PHYSICS, 108: Art. No. 103502, NOV 15 2010 2010
abstract, full text

Li, Zhenlong, Djohari, Hadrian, Dormidontova, Elena E.
Molecular dynamics simulations of supramolecular polymer rheology
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 184904, NOV 14 2010 2010
abstract, full text

Sakuraba, Shun, Joti, Yasumasa, Kitao, Akio
Detecting coupled collective motions in protein by independent subspace analysis
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 185102, NOV 14 2010 2010
abstract, full text

Iakhiaeva, Elena, Iakhiaev, Alexei, Zwieb, Christian
Identification of amino acid residues in protein SRP72 required for binding to a kinked 5e motif of the human signal recognition particle RNA
BMC MOLECULAR BIOLOGY, 11: Art. No. 83, NOV 13 2010 2010
abstract, full text

Gonzalez-Gutierrez, Giovanni, Grosman, Claudio
Bridging the Gap between Structural Models of Nicotinic Receptor Superfamily Ion Channels and Their Corresponding Functional States
JOURNAL OF MOLECULAR BIOLOGY, 403:693-705, NOV 12 2010 2010
abstract, full text

Llop-Tous, Immaculada, Madurga, Sergio, Giralt, Ernest, Marzabal, Pablo, Torrent, Margarita, Ludevid, M. Dolors
Relevant Elements of a Maize gamma-Zein Domain Involved in Protein Body Biogenesis
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:35633-35644, NOV 12 2010 2010
abstract, full text

Leuty, Gary M., Tsige, Mesfin
Structure and Dynamics of Tetrahalomethane Adsorption on (001) Surfaces of Graphite and alpha-Quartz
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13970-13981, NOV 11 2010 2010
abstract, full text

Balamurugan, K., Gopalakrishnan, R., Raman, S. Sundar, Subramanian, V.
Exploring the Changes in the Structure of alpha-Helical Peptides Adsorbed onto a Single Walled Carbon Nanotube Using Classical Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14048-14058, NOV 11 2010 2010
abstract, full text

Ai, Yue-Jie, Liao, Rong-zhen, Chen, Shu-feng, Luo, Yi, Fang, Wei-Hai
Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
JOURNAL OF PHYSICAL CHEMISTRY B, 114:14096-14102, NOV 11 2010 2010
abstract, full text

Lim, M. C. G., Zhong, Z. W.
Atomic arrangement of copper atoms in a carbon nanotube channel under electromigration conditions
CHEMICAL PHYSICS LETTERS, 500:49-53, NOV 10 2010 2010
abstract, full text

Kim, HyeongJun, Hsin, Jen, Liu, Yanxin, Selvin, Paul R., Schulten, Klaus
Formation of Salt Bridges Mediates Internal Dimerization of Myosin VI Medial Tail Domain
STRUCTURE, 18:1443-1449, NOV 10 2010 2010
abstract, full text

Dhulesia, Anne, Cremades, Nunilo, Kumita, Janet R., Hsu, Shang-Te Danny, Mossuto, Maria F., Dumoulin, Mireille, Nietlispach, Daniel, Akke, Mikael, Salvatella, Xavier, Dobson, Christopher M.
Local Cooperativity in an Amyloidogenic State of Human Lysozyme Observed at Atomic Resolution
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:15580-15588, NOV 10 2010 2010
abstract, full text

Lorenzen, Winfried, Holst, Bastian, Redmer, Ronald
First-order liquid-liquid phase transition in dense hydrogen
PHYSICAL REVIEW B, 82: Art. No. 195107, NOV 9 2010 2010
abstract, full text

Hanasaki, Itsuo, Walther, Jens H., Kawano, Satoyuki, Koumoutsakos, Petros
Coarse-grained molecular dynamics simulations of shear-induced instabilities of lipid bilayer membranes in water
PHYSICAL REVIEW E, 82: Art. No. 051602, NOV 9 2010 2010
abstract, full text

Elliott, Ian G., Kuhl, Tonya L., Faller, Roland
Molecular Simulation Study of the Structure of High Density Polymer Brushes in Good Solvent
MACROMOLECULES, 43:9131-9138, NOV 9 2010 2010
abstract, full text

Neyertz, S., Brown, D.
A Trajectory-Extending Kinetic Monte Carlo (TEKMC) Method for Estimating Penetrant Diffusion Coefficients in Molecular Dynamics Simulations of Glassy Polymers
MACROMOLECULES, 43:9210-9214, NOV 9 2010 2010
full text

Dahse, Kirsten, Garvey, Megan, Kovermann, Michael, Vogel, Alexander, Balbach, Jlochen, Faendrich, Marcus, Fahr, Alfred
DHPC Strongly Affects the Structure and Oligomerization Propensity of Alzheimer's A beta(1-40) Peptide
JOURNAL OF MOLECULAR BIOLOGY, 403:643-659, NOV 5 2010 2010
abstract, full text

Takatani, Tait, Sears, John S., Sherrill, C. David
Assessing the Performance of Density Functional Theory For the Electronic Structure of Metal-Salens: The M06 Suite of Functionals and the d(4)-Metals
JOURNAL OF PHYSICAL CHEMISTRY A, 114:11714-11718, NOV 4 2010 2010
abstract, full text

Teague, Craig M., Dai, Sheng, Jiang, De-en
Computational Investigation of Reactive to Nonreactive Capture of Carbon Dioxide by Oxygen-Containing Lewis Bases
JOURNAL OF PHYSICAL CHEMISTRY A, 114:11761-11767, NOV 4 2010 2010
abstract, full text

von Hansen, Yann, Kalcher, Immanuel, Dzubiella, Joachim
Ion Specificity in alpha-Helical Folding Kinetics
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13815-13822, NOV 4 2010 2010
abstract, full text

Janosi, Lorant, Gorfe, Alemayehu
Importance of the Sphingosine Base Double-Bond Geometry for the Structural and Thermodynamic Properties of Sphingomyelin Bilayers
BIOPHYSICAL JOURNAL, 99:2957-2966, NOV 3 2010 2010
abstract, full text

Li, Wenfei, Takada, Shoji
Characterizing Protein Energy Landscape by Self-Learning Multiscale Simulations: Application to a Designed beta-Hairpin
BIOPHYSICAL JOURNAL, 99:3029-3037, NOV 3 2010 2010
abstract, full text

Ferguson, Andrew L., Zhang, Siyan, Dikiy, Igor, Panagiotopoulos, Athanassios Z., Debenedetti, Pablo G., Link, A. James
An Experimental and Computational Investigation of Spontaneous Lasso Formation in Microcin J25
BIOPHYSICAL JOURNAL, 99:3056-3065, NOV 3 2010 2010
abstract, full text

Watkins, Matthew, Shluger, Alexander L.
Mechanism of Contrast Formation in Atomic Force Microscopy in Water
PHYSICAL REVIEW LETTERS, 105: Art. No. 196101, NOV 2 2010 2010
abstract, full text

Li, Yang, Gu, Ning
Computer Simulation of the Inclusion of Hydrophobic Nanoparticles into a Lipid Bilayer
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 10:7616-7619, NOV 2010 2010
abstract, full text

Heruth, Daniel P., Hawkins, Troy, Logsdon, Derek P., Gibson, Margaret I., Sokolovsky, Inna V., Nsumu, Ndona N., Major, Stephanie L., Fegley, Barbara, Woods, Gerald M., Lewing, Karen B., Neville, Kathleen A., Cornetta, Kenneth, Peterson, Kenneth R., White, Robert A.
Mutation in erythroid specific transcription factor KLF1 causes Hereditary Spherocytosis in the Nan hemolytic anemia mouse model
GENOMICS, 96:303-307, NOV 2010 2010
abstract, full text

Shivange, Amol V., Schwaneberg, Ulrich, Roccatano, Danilo
Conformational Dynamics of Active Site Loop in Escherichia coli Phytase
BIOPOLYMERS, 93:994-1002, NOV 2010 2010
abstract, full text

Matthews, R., Louis, A. A., Yeomans, J. M.
Complex dynamics of knotted filaments in shear flow
EPL, 92: Art. No. 34003, NOV 2010 2010
abstract, full text

Kashif Sadiq, S., De Fabritiis, Gianni
Explicit solvent dynamics and energetics of HIV-1 protease flap opening and closing
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2873-2885, NOV 1 2010 2010
abstract, full text

Lugli, Francesca, Toschi, Francesca, Biscarini, Fabio, Zerbetto, Francesco
Electric Field Effects on Short Fibrils of A beta Amyloid Peptides
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3516-3526, NOV 2010 2010
abstract, full text

Cossio, Pilar, Trovato, Antonio, Pietrucci, Fabio, Seno, Flavio, Maritan, Amos, Laio, Alessandro
Exploring the Universe of Protein Structures beyond the Protein Data Bank
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000957, NOV 2010 2010
abstract, full text

Fatmi, M. Qaiser, Chang, Chia-en A.
The Role of Oligomerization and Cooperative Regulation in Protein Function: The Case of Tryptophan Synthase
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000994, NOV 2010 2010
abstract, full text

Gueroult, Marc, Picot, Daniel, Abi-Ghanem, Josephine, Hartmann, Brigitte, Baaden, Marc
How Cations Can Assist DNase I in DNA Binding and Hydrolysis
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1001000, NOV 2010 2010
abstract, full text

Long, Katherine S., Munck, Christian, Andersen, Theis M. B., Schaub, Maria A., Hobbie, Sven N., Boettger, Erik C., Vester, Birte
Mutations in 23S rRNA at the Peptidyl Transferase Center and Their Relationship to Linezolid Binding and Cross-Resistance
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, 54:4705-4713, NOV 2010 2010
abstract, full text

Wang, Qi, Mach, Robert H., Luedtke, Robert R., Reichert, David E.
Subtype Selectivity of Dopamine Receptor Ligands: Insights from Structure and Ligand-Based Methods
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1970-1985, NOV 2010 2010
abstract, full text

Kuhn, Misty L., Figueroa, Carlos M., Aleanzi, Mabel, Olsen, Kenneth W., Iglesias, Alberto A., Ballicora, Miguel A.
Bi-National and Interdisciplinary Course in Enzyme Engineering
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 38:370-379, NOV-DEC 2010 2010
abstract, full text

Souliere, Marie F., Perreault, Jean-Pierre, Bisaillon, Martin
Insights into the molecular determinants involved in cap recognition by the vaccinia virus D10 decapping enzyme
NUCLEIC ACIDS RESEARCH, 38:7599-7610, NOV 2010 2010
abstract, full text

Khripach, V. A., Zhabinskii, V. N., Gulyakevich, O. V., Konstantinova, O. V., Misharin, A. Yu., Mekhtiev, A. R., Timofeev, V. P., Tkachev, Ya. V.
Synthesis of secasterol and 24-episecasterol and their toxicity for MCF-7 cells
RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY, 36:746-754, NOV 2010 2010
abstract, full text

Liao, Zi-Xian, Ho, Yi-Cheng, Chen, Hsin-Lung, Peng, Shu-Fen, Hsiao, Chun-Wen, Sung, Hsing-Wen
Enhancement of efficiencies of the cellular uptake and gene silencing of chitosan/siRNA complexes via the inclusion of a negatively charged poly(gamma-glutamic acid)
BIOMATERIALS, 31:8780-8788, NOV 2010 2010
abstract, full text

Hsu, Cheng-Kuo, Park, Sheldon
Computational and mutagenesis studies of the streptavidin native dimer interface
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:295-308, NOV 2010 2010
abstract, full text

Imai, Yosuke, Liu, Xinli, Yamagishi, Junya, Mori, Kenichi, Neya, Saburo, Hoshino, Tyuji
Computational analysis of water residence on ceramide and sphingomyelin bilayer membranes
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:461-469, NOV 2010 2010
abstract, full text

Koulgi, Shruti, Sonavane, Uddhavesh, Joshi, Rajendra
Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:481-491, NOV 2010 2010
abstract, full text

Jose Valle-Delgado, Juan, Alfonso-Prieto, Mercedes, de Groot, Natalia S., Ventura, Salvador, Samitier, Josep, Rovira, Carme, Fernandez-Busquets, Xavier
Modulation of A beta(42) fibrillogenesis by glycosaminoglycan structure
FASEB JOURNAL, 24:4250-4261, NOV 2010 2010
abstract, full text

Takenoya, Mihoko, Nikolakakis, Kiel, Sagermann, Martin
Crystallographic Insights into the Pore Structures and Mechanisms of the EutL and EutM Shell Proteins of the Ethanolamine-Utilizing Microcompartment of Escherichia coli
JOURNAL OF BACTERIOLOGY, 192:6056-6063, NOV 2010 2010
abstract, full text

Rehm, Sascha, Trodler, Peter, Pleiss, Juergen
Solvent-induced lid opening in lipases: A molecular dynamics study
PROTEIN SCIENCE, 19:2122-2130, NOV 2010 2010
abstract, full text

Huber, Gary A., McCammon, J. Andrew
Browndye: A software package for Brownian dynamics
COMPUTER PHYSICS COMMUNICATIONS, 181:1896-1905, NOV 2010 2010
abstract, full text

Fu, Yi, Ding, Yanrui, Chen, Zhiguo, Sun, Jun, Fang, Wei, Xu, Wenbo
Study on the Relationship Between Cyclodextrin Glycosyltransferase Thermostability and Salt Bridge Formation by Molecular Dynamics Simulation
PROTEIN AND PEPTIDE LETTERS, 17:1403-1411, NOV 2010 2010
abstract, full text

Butu, M., Butu, A.
Parallel molecular dynamics simulation for protein sequences on PC-cluster and server
JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS, 12:2296-2300, NOV 2010 2010
abstract, full text

Almeida, Joao A. S., Marques, Eduardo F., Jurado, Amalia S., Pais, Alberto A. C. C.
The effect of cationic gemini surfactants upon lipid membranes. An experimental and molecular dynamics simulation study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:14462-14476, NOV 2010 2010
abstract, full text

Rosas-Garcia, Victor M., Lopez-Cortina, Susana T., Chavarria-Resendez, Ariadna
A computational study of axial vs. equatorial preferences of phenyl-substituted phosphorinane oxides
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 958:133-136, OCT 30 2010 2010
abstract, full text

Weinzierl, Robert O. J.
The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain
BMC BIOLOGY, 8: Art. No. 134, OCT 29 2010 2010
abstract, full text

Capriles, Priscila V. S. Z., Guimaraes, Ana C. R., Otto, Thomas D., Miranda, Antonio B., Dardenne, Laurent E., Degrave, Wim M.
Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment
BMC GENOMICS, 11: Art. No. 610, OCT 29 2010 2010
abstract, full text

Kalcher, Immanuel, Schulz, Julius C. F., Dzubiella, Joachim
Electrolytes in a nanometer slab-confinement: Ion-specific structure and solvation forces
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 164511, OCT 28 2010 2010
abstract, full text

Mueh, Frank, Madjet, Mohamed El-Amine, Renger, Thomas
Structure-Based Identification of Energy Sinks in Plant Light-Harvesting Complex II
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13517-13535, OCT 28 2010 2010
abstract, full text

Rogaski, Brent, Lim, Joseph B., Klauda, Jeffery B.
Sterol Binding and Membrane Lipid Attachment to the Osh4 Protein of Yeast
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13562-13573, OCT 28 2010 2010
abstract, full text

Kyrychenko, Alexander, Wu, Feiyue, Thummel, Randolph P., Waluk, Jacek, Ladokhin, Alexey S.
Partitioning and Localization of Environment-Sensitive 2-(2 '-Pyridyl)- and 2-(2 '-Pyrimidyl)-Indoles in Lipid Membranes: A Joint Refinement Using Fluorescence Measurements and Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:13574-13584, OCT 28 2010 2010
abstract, full text

Ando, Tadashi, Skolnick, Jeffrey
Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:18457-18462, OCT 26 2010 2010
abstract, full text

Reese, Matthew O., Nardes, Alexandre M., Rupert, Benjamin L., Larsen, Ross E., Olson, Dana C., Lloyd, Matthew T., Shaheen, Sean E., Ginley, David S., Rumbles, Garry, Kopidakis, Nikos
Photoinduced Degradation of Polymer and Polymer-Fullerene Active Layers: Experiment and Theory
ADVANCED FUNCTIONAL MATERIALS, 20:3476-3483, OCT 22 2010 2010
abstract, full text

Chetwynd, Alan, Wee, Chze Ling, Hall, Benjamin A., Sansom, Mark S. P.
The Energetics of Transmembrane Helix Insertion into a Lipid Bilayer
BIOPHYSICAL JOURNAL, 99:2534-2540, OCT 20 2010 2010
abstract, full text

Dalhaimer, Paul, Pollard, Thomas D.
Molecular Dynamics Simulations of Arp2/3 Complex Activation
BIOPHYSICAL JOURNAL, 99:2568-2576, OCT 20 2010 2010
abstract, full text

Feig, Michael, Burton, Zachary F.
RNA Polymerase II with Open and Closed Trigger Loops: Active Site Dynamics and Nucleic Acid Translocation
BIOPHYSICAL JOURNAL, 99:2577-2586, OCT 20 2010 2010
abstract, full text

Kokhan, Oleksandr, Wraight, Colin A., Tajkhorshid, Emad
The Binding Interface of Cytochrome c and Cytochrome c(1) in the bc(1) Complex: Rationalizing the Role of Key Residues
BIOPHYSICAL JOURNAL, 99:2647-2656, OCT 20 2010 2010
abstract, full text

West, Abby L., St John, Franz, Lopes, Pedro E. M., MacKerell, Alexander D., Jr., Pozharski, Edwin, Michel, Sarah L. J.
Holo-Ni(II)HpNikR Is an Asymmetric Tetramer Containing Two Different Nickel-Binding Sites
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:14447-14456, OCT 20 2010 2010
abstract, full text

Paparcone, Raffaella, Pires, Matthew A., Buehler, Markus J.
Mutations Alter the Geometry and Mechanical Properties of Alzheimer's A beta(1-40) Amyloid Fibrils
BIOCHEMISTRY, 49:8967-8977, OCT 19 2010 2010
abstract, full text

Wu, Chunya, Chen, Mingjun, Xing, Cheng
Molecular Understanding of Conformational Dynamics of a Fibronectin Module on Rutile (110) Surface
LANGMUIR, 26:15972-15981, OCT 19 2010 2010
abstract, full text

Vitalis, Andreas, Caflisch, Amedeo
Micelle-Like Architecture of the Monomer Ensemble of Alzheimer's Amyloid-beta Peptide in Aqueous Solution and Its Implications for A beta Aggregation
JOURNAL OF MOLECULAR BIOLOGY, 403:148-165, OCT 15 2010 2010
abstract, full text

Churchill, Mair E. A., Klass, Janet, Zoetewey, David L.
Structural Analysis of HMGD-DNA Complexes Reveals Influence of Intercalation on Sequence Selectivity and DNA Bending
JOURNAL OF MOLECULAR BIOLOGY, 403:88-102, OCT 15 2010 2010
abstract, full text

Iturrioz, Xavier, Gerbier, Romain, Leroux, Vincent, Alvear-Perez, Rodrigo, Maigret, Bernard, Llorens-Cortes, Catherine
By Interacting with the C-terminal Phe of Apelin, Phe(255) and Trp(259) in Helix VI of the Apelin Receptor Are Critical for Internalization
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:32627-32637, OCT 15 2010 2010
abstract, full text

Korabecny, Jan, Musilek, Kamil, Holas, Ondrej, Binder, Jiri, Zemek, Filip, Marek, Jan, Pohanka, Miroslav, Opletalova, Veronika, Dohnal, Vlastimil, Kuca, Kamil
Synthesis and in vitro evaluation of N-alkyl-7-methoxytacrine hydrochlorides as potential cholinesterase inhibitors in Alzheimer disease
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 20:6093-6095, OCT 15 2010 2010
abstract, full text

Schwardt, Oliver, Koliwer-Brandl, Hendrik, Zimmerli, Raphael, Mesch, Stefanie, Rossato, Gianluca, Spreafico, Morena, Vedani, Angelo, Kelm, Sorge, Ernst, Beat
Design, synthesis, biological evaluation, and modeling of a non-carbohydrate antagonist of the myelin-associated glycoprotein
BIOORGANIC & MEDICINAL CHEMISTRY, 18:7239-7251, OCT 15 2010 2010
abstract, full text

Olszewski, Marcin, Grot, Anna, Wojciechowski, Marek, Nowak, Marta, Mickiewicz, Malgorzata, Kur, Jozef
Characterization of exceptionally thermostable single-stranded DNA-binding proteins from Thermotoga maritima and Thermotoga neapolitana
BMC MICROBIOLOGY, 10: Art. No. 260, OCT 15 2010 2010
abstract, full text

Kalli, Antreas C., Wegener, Kate L., Goult, Benjamin T., Anthis, Nicholas J., Campbell, Iain D., Sansom, Mark S. P.
The Structure of the Talin/Integrin Complex at a Lipid Bilayer: An NMR and MD Simulation Study
STRUCTURE, 18:1280-1288, OCT 13 2010 2010
abstract, full text

Saharay, Moumita, Guo, Hong, Smith, Jeremy C.
Catalytic Mechanism of Cellulose Degradation by a Cellobiohydrolase, CelS
PLOS ONE, 5: Art. No. e12947, OCT 12 2010 2010
abstract, full text

Pielak, Gary J., Miklos, Andrew C.
Crowding and function reunite
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:17457-17458, OCT 12 2010 2010
full text

Presman, Diego M., Alvarez, Lautaro D., Levi, Valeria, Eduardo, Silvina, Digman, Michelle A., Marti, Marcelo A., Veleiro, Adriana S., Burton, Gerardo, Pecci, Adali
Insights on Glucocorticoid Receptor Activity Modulation through the Binding of Rigid Steroids
PLOS ONE, 5: Art. No. e13279, OCT 11 2010 2010
abstract, full text

Pankewitz, Tobias, Klopper, Wim
Interaction of the alcohol molecules methanol and ethanol with single-walled carbon nanotubes - A computational study
CHEMICAL PHYSICS LETTERS, 498:345-348, OCT 8 2010 2010
abstract, full text

Montserret, Roland, Saint, Nathalie, Vanbelle, Christophe, Salvay, Andres Gerardo, Simorre, Jean-Pierre, Ebel, Christine, Sapay, Nicolas, Renisio, Jean-Guillaume, Boeckmann, Anja, Steinmann, Eike, Pietschmann, Thomas, Dubuisson, Jean, Chipot, Christophe, Penin, Francois
NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:31446-31461, OCT 8 2010 2010
abstract, full text

Guo, Qinglan, Weng, Jingwei, Xu, Xiaogang, Wang, Minghua, Wang, Xiaoying, Ye, Xinyu, Wang, Wenning, Wang, Minggui
A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis
BMC STRUCTURAL BIOLOGY, 10: Art. No. 33, OCT 8 2010 2010
abstract, full text

Tian, Ye, Deutsch, Christopher, Krishnamoorthy, Bala
Scoring function to predict solubility mutagenesis
ALGORITHMS FOR MOLECULAR BIOLOGY, 5: Art. No. 33, OCT 7 2010 2010
abstract, full text

Terekhova, Irina V., Romanova, Anastasia O., Kumeev, Roman S., Fedorov, Maxim V.
Selective Na(+)/K(+) Effects on the Formation of alpha-Cyclodextrin Complexes with Aromatic Carboxylic Acids: Competition for the Guest
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12607-12613, OCT 7 2010 2010
abstract, full text

Knecht, Volker
Model Amyloid Peptide B18 Monomer and Dimer Studied by Replica Exchange Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12701-12707, OCT 7 2010 2010
abstract, full text

Karachevtsev, Victor A., Zarudnev, Evgen S., Stepanian, Stepan G., Glamazda, Alexander Yu., Karachevtsev, Maksym V., Adamowicz, Ludwik
Raman Spectroscopy and Theoretical Characterization of Nanohybrids of Porphyrins with Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY C, 114:16215-16222, OCT 7 2010 2010
abstract, full text

Burkhardt, Stephen E., Rodriguez-Calero, Gabriel G., Lowe, Michael A., Kiya, Yasuyuki, Hennig, Richard G., Abruna, Hector D.
Theoretical and Electrochemical Analysis of Poly(3,4-alkylenedioxythiophenes): Electron-Donating Effects and Onset of p-Doped Conductivity
JOURNAL OF PHYSICAL CHEMISTRY C, 114:16776-16784, OCT 7 2010 2010
abstract, full text

Jardon-Valadez, Eduardo, Bondar, Ana-Nicoleta, Tobias, Douglas J.
Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin
BIOPHYSICAL JOURNAL, 99:2200-2207, OCT 6 2010 2010
abstract, full text

Laine, Elodie, Martinez, Leandro, Blondel, Arnaud, Malliavin, Therese E.
Activation of the Edema Factor of Bacillus anthracis by Calmodulin: Evidence of an Interplay between the EF-Calmodulin Interaction and Calcium Binding
BIOPHYSICAL JOURNAL, 99:2264-2272, OCT 6 2010 2010
abstract, full text

Stanzione, Francesca, Esposito, Luciana, Paladino, Antonella, Pedone, Carlo, Morelli, Giancarlo, Vitagliano, Luigi
Role of the Conformational Versatility of the Neurotrophin N-Terminal Regions in Their Recognition by Trk Receptors
BIOPHYSICAL JOURNAL, 99:2273-2278, OCT 6 2010 2010
abstract, full text

Moreira, Pedro A. F. P., Devanathan, Ram, Weber, William J.
Atomistic simulation of track formation by energetic recoils in zircon
JOURNAL OF PHYSICS-CONDENSED MATTER, 22: Art. No. 395008, OCT 6 2010 2010
abstract, full text

Swadling, Jacob B., Coveney, Peter V., Greenwell, H. Christopher
Clay Minerals Mediate Folding and Regioselective Interactions of RNA: A Large-Scale Atomistic Simulation Study
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13750-13764, OCT 6 2010 2010
abstract, full text

Koeppen, Susan, Langel, Walter
Simulation of Adhesion Forces and Energies of Peptides on Titanium Dioxide Surfaces
LANGMUIR, 26:15248-15256, OCT 5 2010 2010
abstract, full text

Roman, Ernesto A., Rosi, Pablo, Gonzalez Lebrero, Mariano C., Wuilloud, Rodolfo, Gonzalez Flecha, F. Luis, Delfino, Jose M., Santos, Javier
Gain of local structure in an amphipathic peptide does not require a specific tertiary framework
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2757-2768, OCT 2010 2010
abstract, full text

Perrin, Bradley Scott, Jr., Ichiye, Toshiko
Fold versus sequence effects on the driving force for protein-mediated electron transfer
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2798-2808, OCT 2010 2010
abstract, full text

Fufezan, Christian
The role of Buergi-Dunitz interactions in the structural stability of proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2831-2838, OCT 2010 2010
abstract, full text

Takeda, Takako, Chang, Wenling E., Raman, E. Prabhu, Klimov, Dmitri K.
Binding of nonsteroidal anti-inflammatory drugs to A beta fibril
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2849-2860, OCT 2010 2010
abstract, full text

Seth, Ajay, Sherman, Michael, Eastman, Peter, Delp, Scott
Minimal formulation of joint motion for biomechanisms
NONLINEAR DYNAMICS, 62:291-303, OCT 2010 2010
abstract, full text

Surdutovich, E., Yakubovich, A. V., Solov'yov, A. V.
Multiscale approach to radiation damage induced by ion beams: complex DNA damage and effects of thermal spikes
EUROPEAN PHYSICAL JOURNAL D, 60:101-108, OCT 2010 2010
abstract, full text

Janosi, Lorant, Gorfe, Alemayehu A.
Simulating POPC and POPC/POPG Bilayers: Conserved Packing and Altered Surface Reactivity
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:3267-3273, OCT 2010 2010
abstract, full text

Gnanakaran, S., Daniels, Marcus G., Bhattacharya, Tanmoy, Lapedes, Alan S., Sethi, Anurag, Li, Ming, Tang, Haili, Greene, Kelli, Gao, Hongmei, Haynes, Barton F., Cohen, Myron S., Shaw, George M., Seaman, Michael S., Kumar, Amit, Gao, Feng, Montefiori, David C., Korber, Bette
Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000955, OCT 2010 2010
abstract, full text

Osolodkin, D. I., Shulga, D. A., Palyulin, V. A., Zefirov, N. S.
Interaction of manzamine A with glycogen synthase kinase 3 beta: a molecular dynamics study
RUSSIAN CHEMICAL BULLETIN, 59:1983-1993, OCT 2010 2010
abstract, full text

Yasi, Joseph A., Hector, Louis G., Jr., Trinkle, Dallas R.
First-principles data for solid-solution strengthening of magnesium: From geometry and chemistry to properties
ACTA MATERIALIA, 58:5704-5713, OCT 2010 2010
abstract, full text

Cabrera, Ricardo, Babul, Jorge, Guixe, Victoria
Ribokinase family evolution and the role of conserved residues at the active site of the PfkB subfamily representative, Pfk-2 from Escherichia coli
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 502:23-30, OCT 1 2010 2010
abstract, full text

Maccioni, E., Alcaro, S., Orallo, F., Cardia, M. C., Distinto, S., Costa, G., Yanez, M., Sanna, M. L., Vigo, S., Meleddu, R., Secci, D.
Synthesis of new 3-aryl-4,5-dihydropyrazole-1-carbothioamide derivatives. An investigation on their ability to inhibit monoamine oxidase
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 45:4490-4498, OCT 2010 2010
abstract, full text

Trabuco, Leonardo G., Schreiner, Eduard, Eargle, John, Cornish, Peter, Ha, Taekjip, Luthey-Schulten, Zaida, Schulten, Klaus
The Role of L1 Stalk-tRNA Interaction in the Ribosome Elongation Cycle
JOURNAL OF MOLECULAR BIOLOGY, 402:741-760, OCT 1 2010 2010
abstract, full text

Yang, Yuling, Li, Xiaoyi, Jiang, Jinliang, Du, Huailiang, Zhao, Lina, Zhao, Yuliang
Control Performance and Biomembrane Disturbance of Carbon Nanotube Artificial Water Channels by Nitrogen-Doping
ACS NANO, 4:5755-5762, OCT 2010 2010
abstract, full text

Besseova, Ivana, Reblova, Kamila, Leontis, Neocles B., Sponer, Jiri
Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome
NUCLEIC ACIDS RESEARCH, 38:6247-6264, OCT 2010 2010
abstract, full text

Saladin, Adrien, Amourda, Christopher, Poulain, Pierre, Ferey, Nicolas, Baaden, Marc, Zacharias, Martin, Delalande, Olivier, Prevost, Chantal
Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments
NUCLEIC ACIDS RESEARCH, 38:6313-6323, OCT 2010 2010
abstract, full text

Chan, David I., Chu, Byron C. H., Lau, Cheryl K. Y., Hunter, Howard N., Byers, David M., Vogel, Hans J.
NMR Solution Structure and Biophysical Characterization of Vibrio harveyi Acyl Carrier Protein A75H EFFECTS OF DIVALENT METAL IONS
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:30558-30566, OCT 1 2010 2010
abstract, full text

Klimacek, Mario, Nidetzky, Bernd
From Alcohol Dehydrogenase to a "One-way" Carbonyl Reductase by Active-site Redesign A MECHANISTIC STUDY OF MANNITOL 2-DEHYDROGENASE FROM PSEUDOMONAS FLUORESCENS
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:30644-30653, OCT 1 2010 2010
abstract, full text

Liu Fu-Feng, Ji Luo, Dong Xiao-Yan
Effects of Molecular Volume and Fractional Polar Surface Area of Osmolytes on the Thermal Stability of Chymotrypsin Inhibitor 2
ACTA PHYSICO-CHIMICA SINICA, 26:2813-2820, OCT 2010 2010
abstract, full text

Biasini, Marco, Mariani, Valerio, Haas, Juergen, Scheuber, Stefan, Schenk, Andreas D., Schwede, Torsten, Philippsen, Ansgar
OpenStructure: a flexible software framework for computational structural biology
BIOINFORMATICS, 26:2626-2628, OCT 2010 2010
abstract, full text

Ai, Rizi, Fatmi, M. Qaiser, Chang, Chia-en A.
T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 24:819-827, OCT 2010 2010
abstract, full text

Xu, Jiancong, Smith, Jeremy C.
Probing the mechanism of cellulosome attachment to the Clostridium thermocellum cell surface: computer simulation of the Type II cohesin-dockerin complex and its variants
PROTEIN ENGINEERING DESIGN & SELECTION, 23:759-768, OCT 2010 2010
abstract, full text

Soriano-Ursua, Marvin A., Correa-Basurto, Jose, Valencia-Hernandez, Ignacio, Amezcua-Gutierrez, Marcos A., Padilla-Martinez, Itzia I., Trujillo-Ferrara, Jose G.
Design, synthesis and in vitro evaluation of (R)-4-(2-(tert-butylamino)-1-hydroxyethyl)-2-(hydroxymethyl)phenyl hydrogen phenylboronate: A novel salbutamol derivative with high intrinsic efficacy on the beta(2) adrenoceptor
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 20:5623-5629, OCT 1 2010 2010
abstract, full text

Maass, Astrid, Tekin, Emine Deniz, Schueller, Anton, Palazoglu, Ahmet, Reith, Dirk, Faller, Roland
Folding and unfolding characteristics of short beta strand peptides under different environmental conditions and starting configurations
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1804:2003-2015, OCT 2010 2010
abstract, full text

Kolinski, Michal, Filipek, Slawomir
Study of a structurally similar kappa opioid receptor agonist and antagonist pair by molecular dynamics simulations
JOURNAL OF MOLECULAR MODELING, 16:1567-1576, OCT 2010 2010
abstract, full text

Majerfeld, Irene, Chocholousova, Jana, Malaiya, Vikas, Widmann, Jeremy, Mcdonald, Daniel, Reeder, Jens, Iyer, Matthew, Illangasekare, Mali, Yarus, Michael, Knight, Rob
Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA
RNA-A PUBLICATION OF THE RNA SOCIETY, 16:1915-1924, OCT 2010 2010
abstract, full text

Corry, Ben, Hurst, Annette C., Pal, Prithwish, Nomura, Takeshi, Rigby, Paul, Martinac, Boris
An improved open-channel structure of MscL determined from FRET confocal microscopy and simulation
JOURNAL OF GENERAL PHYSIOLOGY, 136:483-494, OCT 2010 2010
abstract, full text

Kowalczyk, Tim, Lin, Ziliang, Van Voorhis, Troy
Fluorescence Quenching by Photoinduced Electron Transfer in the Zn(2+) Sensor Zinpyr-1: A Computational Investigation
JOURNAL OF PHYSICAL CHEMISTRY A, 114:10427-10434, SEP 30 2010 2010
abstract, full text

Liu, Jian, Fan, Jianfen, Tang, Min, Cen, Min, Yan, Jianfeng, Liu, Zhao, Zhou, Weigun
Water Diffusion Behaviors and Transportation Properties in Transmembrane Cyclic Hexa-, Octa- and Decapeptide Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12183-12192, SEP 30 2010 2010
abstract, full text

Orzechowski, Marek, Meuwly, Markus
Dynamics of Water Filaments in Disordered Environments
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12203-12212, SEP 30 2010 2010
abstract, full text

Olbrich, Carsten, Kleinekathoefer, Ulrich
Time-Dependent Atomistic View on the Electronic Relaxation in Light-Harvesting System II
JOURNAL OF PHYSICAL CHEMISTRY B, 114:12427-12437, SEP 30 2010 2010
abstract, full text

Callenberg, Keith M., Choudhary, Om P., de Forest, Gabriel L., Gohara, David W., Baker, Nathan A., Grabe, Michael
APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane
PLOS ONE, 5: Art. No. e12722, SEP 29 2010 2010
abstract, full text

Foley, Meredith C., Padow, Victoria A., Schlick, Tamar
DNA Pol lambda's Extraordinary Ability To Stabilize Misaligned DNA
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13403-13416, SEP 29 2010 2010
abstract, full text

Lee, Tai-Sung, York, Darrin M.
Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:13505-13518, SEP 29 2010 2010
abstract, full text

Neyertz, S., Brown, D., Pandiyan, S., van der Vegt, N. F. A.
Carbon Dioxide Diffusion and Plasticization in Fluorinated Polyimides
MACROMOLECULES, 43:7813-7827, SEP 28 2010 2010
abstract, full text

Mullinax, J. W., Noid, W. G.
Reference state for the generalized Yvon-Born-Green theory: Application for coarse-grained model of hydrophobic hydration
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 124107, SEP 28 2010 2010
abstract, full text

Walter, Jonathan, Ermatchkov, Viktor, Vrabec, Jadran, Hasse, Hans
Molecular dynamics and experimental study of conformation change of poly(N-isopropylacrylamide) hydrogels in water
FLUID PHASE EQUILIBRIA, 296:164-172, SEP 25 2010 2010
abstract, full text

Priet, Stephane, Zlatev, Ivan, Barvik, Ivan, Jr., Geerts, Katrien, Leyssen, Pieter, Neyts, Johan, Dutartre, Helene, Canard, Bruno, Vasseur, Jean-Jacques, Morvan, Francois, Alvarez, Karine
3 '-Deoxy Phosphoramidate Dinucleosides as Improved Inhibitors of Hepatitis C Virus Subgenomic Replicon and NS5B Polymerase Activity
JOURNAL OF MEDICINAL CHEMISTRY, 53:6608-6617, SEP 23 2010 2010
abstract, full text

Dalvi, Vishwanath Haily, Srinivasan, Vibha, Rossky, Peter J.
Understanding the Effectiveness of Fluorocarbon Ligands in Dispersing Nanoparticles in Supercritical Carbon Dioxide
JOURNAL OF PHYSICAL CHEMISTRY C, 114:15553-15561, SEP 23 2010 2010
abstract, full text

Dalvi, Vishwanath Haily, Srinivasan, Vibha, Rossky, Peter J.
Understanding the Relative Effectiveness of Alkanethiol Ligands in Dispersing Nanoparticles in Supercritical Carbon Dioxide and Ethane
JOURNAL OF PHYSICAL CHEMISTRY C, 114:15562-15573, SEP 23 2010 2010
abstract, full text

Hilder, Tamsyn A., Gordon, Dan, Chung, Shin-Ho
Synthetic Chloride-Selective Carbon Nanotubes Examined by Using Molecular and Stochastic Dynamics
BIOPHYSICAL JOURNAL, 99:1734-1742, SEP 22 2010 2010
abstract, full text

Lyman, Edward, Cui, Haosheng, Voth, Gregory A.
Water under the BAR
BIOPHYSICAL JOURNAL, 99:1783-1790, SEP 22 2010 2010
abstract, full text

Chen, Qiang, Cheng, Mary Hongying, Xu, Yan, Tang, Pei
Anesthetic Binding in a Pentameric Ligand-Gated Ion Channel: GLIC
BIOPHYSICAL JOURNAL, 99:1801-1809, SEP 22 2010 2010
abstract, full text

Khandelia, Himanshu, Duelund, Lars, Pakkanen, Kirsi I., Ipsen, John H.
Triglyceride Blisters in Lipid Bilayers: Implications for Lipid Droplet Biogenesis and the Mobile Lipid Signal in Cancer Cell Membranes
PLOS ONE, 5: Art. No. e12811, SEP 22 2010 2010
abstract, full text

Wei, Shuai, Knotts, Thomas A.
Predicting stability of alpha-helical, orthogonal-bundle proteins on surfaces
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 115102, SEP 21 2010 2010
abstract, full text

Hamacher, K.
Efficient perturbation analysis of elastic network models - Application to acetylcholinesterase of T. californica
JOURNAL OF COMPUTATIONAL PHYSICS, 229:7309-7316, SEP 20 2010 2010
abstract, full text

Garcia-Mata, Carlos, Wang, Jianwen, Gajdanowicz, Pawel, Gonzalez, Wendy, Hills, Adrian, Donald, Naomi, Riedelsberger, Janin, Amtmann, Anna, Dreyer, Ingo, Blatt, Michael R.
A Minimal Cysteine Motif Required to Activate the SKOR K(+) Channel of Arabidopsis by the Reactive Oxygen Species H(2)O(2)
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:29286-29294, SEP 17 2010 2010
abstract, full text

Nygaard, Thomas P., Alfonso-Prieto, Mercedes, Peters, Gunther H., Jensen, Morten O., Rovira, Carme
Substrate Recognition in the Escherichia coli Ammonia Channel AmtB: A QM/MM Investigation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11859-11865, SEP 16 2010 2010
abstract, full text

Aliaga, Carolina, Briones, Luis, Caroli Rezende, Marcos, Tirapegui, Cristian
The thermochromism of the E(T)(30) betaine in a micro-heterogeneous medium: A spectral and dynamics simulation study
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 349:565-570, SEP 15 2010 2010
abstract, full text

Chen, Dong-Hui, Raskind, Wendy H., Parson, William W., Sonnen, Joshua A., Vu, Tiffany, Zheng, YunLin, Matsushita, Mark, Wolff, John, Lipe, Hillary, Bird, Thomas D.
A novel mutation in FHL1 in a family with X-linked scapuloperoneal myopathy: Phenotypic spectrum and structural study of FHL1 mutations
JOURNAL OF THE NEUROLOGICAL SCIENCES, 296:22-29, SEP 15 2010 2010
abstract, full text

Filomia, Federico, De Rienzo, Francesca, Menziani, M. Cristina
Insights into MAPK p38 alpha DFG flip mechanism by accelerated molecular dynamics
BIOORGANIC & MEDICINAL CHEMISTRY, 18:6805-6812, SEP 15 2010 2010
abstract, full text

Berezniak, Tomasz, Zahran, Mai, Imhof, Petra, Jaeschke, Andres, Smith, Jeremy C.
Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:12587-12596, SEP 15 2010 2010
abstract, full text

Zhang, Andrew X., Murelli, Ryan P., Barinka, Cyril, Michel, Julien, Cocleaza, Alexandra, Jorgensen, William L., Lubkowski, Jacek, Spiegel, David A.
A Remote Arene-Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:12711-12716, SEP 15 2010 2010
abstract, full text

Pemmaraju, C. D., Rungger, I., Chen, X., Rocha, A. R., Sanvito, S.
Ab initio study of electron transport in dry poly(G)-poly(C) A-DNA strands
PHYSICAL REVIEW B, 82: Art. No. 125426, SEP 14 2010 2010
abstract, full text

Shang, Zhiguo, Mao, Yanli, Tero, Ryugo, Liu, Xinli, Hoshino, Tyuji, Tanaka, Motohiko, Urisu, Tsuneo
Clustering effects of GM1 and formation mechanisms of interdigitated liquid disordered domains in GM1/SM/CHOL-supported planar bilayers on mica surfaces
CHEMICAL PHYSICS LETTERS, 497:108-114, SEP 10 2010 2010
abstract, full text

Veeraraghavan, Narayanan, Bevilacqua, Philip C., Hammes-Schiffer, Sharon
Long-Distance Communication in the HDV Ribozyme: Insights from Molecular Dynamics and Experiments
JOURNAL OF MOLECULAR BIOLOGY, 402:278-291, SEP 10 2010 2010
abstract, full text

Tsai, C.h.i.n.g.-.W., Liu, C.h.i.h.-.I., Chan, Y.i.n.g.-.C., Tsai, Hui-H G., Ruaan, R.u.o.h.-.C.
Study of Conformation Effects on the Retention of Small Peptides in Reversed-Phase Chromatography by Thermodynamic Analysis and Molecular Dynamics Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11620-11627, SEP 9 2010 2010
abstract, full text

Hesske, Holger, Urakawa, Atsushi, VandeVondele, Joost, Baiker, Alfons
Insight into Fundamental, Overtone, and Combination IR Bands of Surface and Bulk Ba(NO(3))(2) by Ab Initio Molecular Dynamics
JOURNAL OF PHYSICAL CHEMISTRY C, 114:15042-15048, SEP 9 2010 2010
abstract, full text

Fenley, Andrew T., Adams, David A., Onufriev, Alexey V.
Charge State of the Globular Histone Core Controls Stability of the Nucleosome
BIOPHYSICAL JOURNAL, 99:1577-1585, SEP 8 2010 2010
abstract, full text

Thompson, Matthew K., Davis, Michael F., de Serrano, Vesna, Nicoletti, Francesco P., Howes, Barry D., Smulevich, Giulietta, Franzen, Stefan
Internal Binding of Halogenated Phenols in Dehaloperoxidase-Hemoglobin Inhibits Peroxidase Function
BIOPHYSICAL JOURNAL, 99:1586-1595, SEP 8 2010 2010
abstract, full text

Yoda, Takao, Sugita, Yuji, Okamoto, Yuko
Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations
BIOPHYSICAL JOURNAL, 99:1637-1644, SEP 8 2010 2010
abstract, full text

Sparapani, Silvia, Haider, Shozeb M., Doria, Filippo, Gunaratnam, Mekala, Neidle, Stephen
Rational Design of Acridine-Based Ligands with Selectivity for Human Telomeric Quadruplexes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:12263-12272, SEP 8 2010 2010
abstract, full text

Anselmi, Claudio, Grininger, Martin, Gipson, Preeti, Faraldo-Gomez, Jose D.
Mechanism of Substrate Shuttling by the Acyl-Carrier Protein within the Fatty Acid Mega-Synthase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:12357-12364, SEP 8 2010 2010
abstract, full text

Wang, Zun-Jing, Deserno, Markus
Systematic implicit solvent coarse-graining of bilayer membranes: lipid and phase transferability of the force field
NEW JOURNAL OF PHYSICS, 12: Art. No. 095004, SEP 8 2010 2010
abstract, full text

Sapay, Nicolas, Bennett, W. F. Drew, Tieleman, D. Peter
Molecular Simulations of Lipid Flip-Flop in the Presence of Model Transmembrane Helices
BIOCHEMISTRY, 49:7665-7673, SEP 7 2010 2010
abstract, full text

Jakab, Zsolt, Mandi, Attila, Borbas, Aniko, Benyei, Attila, Komaromi, Istvan, Lazar, Laszlo, Antus, Sandor, Liptak, Andras
Synthesis, regioselective hydrogenolysis, partial hydrogenation, and conformational study of dioxane and dioxolane-type (9 '-anthracenyl)methylene acetals of sugars
CARBOHYDRATE RESEARCH, 344:2444-2453, DEC 14 2009 2009
abstract, full text

Salvalaglio, Matteo, Zamolo, Laura, Busini, Valentina, Moscatelli, Davide, Cavallotti, Carlo
Molecular modeling of Protein A affinity chromatography
JOURNAL OF CHROMATOGRAPHY A, 1216:8678-8686, DEC 11 2009 2009
abstract, full text

Murelli, Ryan P., Zhang, Andrew X., Michel, Julien, Jorgensen, William L., Spiegel, David A.
Chemical Control over Immune Recognition: A Class of Antibody-Recruiting Small Molecules That Target Prostate Cancer
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:17090-+, DEC 2 2009 2009
abstract, full text

Kar, Gozde, Gursoy, Attila, Keskin, Ozlem
Human Cancer Protein-Protein Interaction Network: A Structural Perspective
PLOS COMPUTATIONAL BIOLOGY, 5: Art. No. e1000601, DEC 2009 2009
abstract, full text

D'Annessa, Ilda, Chillemi, Giovanni, Desideri, Alessandro
Structural-Dynamical Properties of the Deinococcus Radiodurans Topoisomerase IB in Absence of DNA: Correlation with the Human Enzyme
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 27:307-317, DEC 2009 2009
abstract, full text

Barros, Pedro R., Stassen, Hubert, Freitas, Monica S., Carlini, Celia R., Nascimento, Marco A. C., Follmer, Cristian
Membrane-disruptive properties of the bioinsecticide Jaburetox-2Ec: Implications to the mechanism of the action of insecticidal peptides derived from ureases
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1794:1848-1854, DEC 2009 2009
abstract, full text

Xu, Guohua, Wu, Min, Wang, Lin, Zhang, Xu, Cao, Shufen, Liu, Maili, Cui, Yanfang
Conformational and dynamics simulation study of antimicrobial peptide hedistin-heterogeneity of its helix-turn-helix motif
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1788:2497-2508, DEC 2009 2009
abstract, full text

Zhou, Junpei, Huang, Huoqing, Meng, Kun, Shi, Pengjun, Wang, Yaru, Luo, Huiying, Yang, Peilong, Bai, Yingguo, Zhou, Zhigang, Yao, Bin
Molecular and biochemical characterization of a novel xylanase from the symbiotic Sphingobacterium sp TN19
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, 85:323-333, NOV 2009 2009
abstract, full text

Trylska, Joanna
Simulating activity of the bacterial ribosome
QUARTERLY REVIEWS OF BIOPHYSICS, 42:301-316, NOV 2009 2009
abstract, full text

Tarrago, Teresa, Martin-Benito, Jaime, Sabido, Eduard, Claasen, Birgit, Madurga, Sergio, Gairi, Margarida, Valpuesta, Jose M., Giralt, Ernest
A new side opening on prolyl oligopeptidase revealed by electron microscopy
FEBS LETTERS, 583:3344-3348, OCT 20 2009 2009
abstract, full text

Stradomska, Anna, Knoester, Jasper
Shape of the Q band in the absorption spectra of porphyrin nanotubes: Vibronic coupling or exciton effects?
JOURNAL OF CHEMICAL PHYSICS, 133: Art. No. 094701, SEP 7 2010 2010
abstract, full text

Hildenbrand, Zacariah L., Molugu, Sudheer K., Stock, Daniela, Bernal, Ricardo A.
The C-H Peripheral Stalk Base: A Novel Component in V(1)-ATPase Assembly
PLOS ONE, 5: Art. No. e12588, SEP 3 2010 2010
abstract, full text

Egwolf, Bernhard, Roux, Benoit
Ion Selectivity of the KcsA Channel: A Perspective from Multi-Ion Free Energy Landscapes
JOURNAL OF MOLECULAR BIOLOGY, 401:831-842, SEP 3 2010 2010
abstract, full text

Pol-Fachin, Laercio, Serrato, Rodrigo V., Verli, Hugo
Solution conformation and dynamics of exopolysaccharides from Burkholderia species
CARBOHYDRATE RESEARCH, 345:1922-1931, SEP 3 2010 2010
abstract, full text

Dolenc, Jozica, Gerster, Sarah, van Gunsteren, Wilfred F.
Molecular Dynamics Simulations Shed Light on the Enthalpic and Entropic Driving Forces That Govern the Sequence Specific Recognition between Netropsin and DNA
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11164-11172, SEP 2 2010 2010
abstract, full text

Miao, Yinglong, Johnson, John E., Ortoleva, Peter J.
All-Atom Multiscale Simulation of Cowpea Chlorotic Mottle Virus Capsid Swelling
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11181-11195, SEP 2 2010 2010
abstract, full text

Wang, Zun-Jing, Deserno, Markus
A Systematically Coarse-Grained Solvent-Free Model for Quantitative Phospholipid Bilayer Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:11207-11220, SEP 2 2010 2010
abstract, full text

Kang, Yu, Li, Xin, Tu, Yaoquan, Wang, Qi, Agren, Hans
On the Mechanism of Protein Adsorption onto Hydroxylated and Nonhydroxylated TiO(2) Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 114:14496-14502, SEP 2 2010 2010
abstract, full text

Kulkarni, Anant D., Wang, Lin-Lin, Johnson, Duane D., Sholl, David S., Johnson, J. Karl
First-Principles Characterization of Amorphous Phases of MB(12)H(12), M = Mg, Ca
JOURNAL OF PHYSICAL CHEMISTRY C, 114:14601-14605, SEP 2 2010 2010
abstract, full text

Tamamis, Phanourios, Morikis, Dimitrios, Floudas, Christodoulos A., Archontis, Georgios
Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2655-2667, SEP 2010 2010
abstract, full text

Chiappori, Federica, Merelli, Ivan, Milanesi, Luciano, Rovida, Ermanna
Exploring the role of the phospholipid ligand in endothelial protein C receptor: A molecular dynamics study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2679-2690, SEP 2010 2010
abstract, full text

Popovic, D. M., Leontyev, I. V., Beech, D. G., Stuchebrukhov, A. A.
Similarity of cytochrome c oxidases in different organisms
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2691-2698, SEP 2010 2010
abstract, full text

Ivetac, Anthony, McCammon, J. Andrew
Mapping the Druggable Allosteric Space of G-Protein Coupled Receptors: a Fragment-Based Molecular Dynamics Approach
CHEMICAL BIOLOGY & DRUG DESIGN, 76:201-217, SEP 2010 2010
abstract, full text

Paliy, Maxim, Melnik, Roderick, Shapiro, Bruce A.
Coarse-graining RNA nanostructures for molecular dynamics simulations
PHYSICAL BIOLOGY, 7: Art. No. 036001, SEP 2010 2010
abstract, full text

Morra, Giulia, Neves, Marco A. C., Plescia, Christopher J., Tsustsumi, Shinji, Neckers, Len, Verkhivker, Gennady, Altieri, Dario C., Colombo, Giorgio
Dynamics-Based Discovery of Allosteric Inhibitors: Selection of New Ligands for the C-terminal Domain of Hsp90
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2978-2989, SEP 2010 2010
abstract, full text

Zhang, Zhiyong, Voth, Gregory A.
Coarse-Grained Representations of Large Biomolecular Complexes from Low-Resolution Structural Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6:2990-3002, SEP 2010 2010
abstract, full text

Le, Ly, Lee, Eric H., Hardy, David J., Truong, Thanh N., Schulten, Klaus
Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases
PLOS COMPUTATIONAL BIOLOGY, 6: Art. No. e1000939, SEP 2010 2010
abstract, full text

Cheng, Shu, Niv, Masha Y.
Molecular Dynamics Simulations and Elastic Network Analysis of Protein Kinase B (Akt/PKB) Inactivation
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1602-1610, SEP 2010 2010
abstract, full text

Ghysels, An, Verstraelen, Toon, Hemelsoet, Karen, Waroquier, Michel, Van Speybroeck, Veronique
TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 50:1736-1750, SEP 2010 2010
abstract, full text

Yancey, Jeremy A., Vellore, Nadeem A., Collier, Galen, Stuart, Steven J., Latour, Robert A.
Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms
BIOINTERPHASES, 5:85-95, SEP 2010 2010
abstract, full text

Xiao, Jie, Huang, Yinlun, Manke, Charles W.
Computational Design of Polymer Nanocomposite Coatings: A Multiscale Hierarchical Approach for Barrier Property Prediction
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH, 49:7718-7727, SEP 1 2010 2010
abstract, full text

Todokoro, Yasuto, Kobayashi, Masatoshi, Sato, Takeshi, Kawakami, Toru, Yumen, Ikuko, Aimoto, Saburo, Fujiwara, Toshimichi, Akutsu, Hideo
Structure analysis of membrane-reconstituted subunit c-ring of E. coli H(+)-ATP synthase by solid-state NMR
JOURNAL OF BIOMOLECULAR NMR, 48:1-11, SEP 2010 2010
abstract, full text

Sikorska, Emilia, Kwiatkowska, Anna, Sobolewski, Dariusz, Slusarz, Rafal, Slusarz, Magdalena J.
Influence of bulky 3,3 '-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 45:4065-4073, SEP 2010 2010
abstract, full text

Moules, V., Ferraris, O., Terrier, O., Giudice, E., Yver, M., Rolland, J. P., Bouscambert-Duchamp, M., Bergeron, C., Ottmann, M., Fournier, E., Traversier, A., Boule, C., Rivoire, A., Lin, Y., Hay, A., Valette, M., Marquet, R., Rosa-Calatrava, M., Naffakh, N., Schoehn, G., Thomas, D., Lina, B.
In vitro characterization of naturally occurring influenza H3NA-viruses lacking the NA gene segment: Toward a new mechanism of viral resistance?
VIROLOGY, 404:215-224, SEP 1 2010 2010
abstract, full text

Thakkar, Foram M., Ayappa, K. G.
Investigations on the melting and bending modulus of polymer grafted bilayers using dissipative particle dynamics
BIOMICROFLUIDICS, 4: Art. No. 032203, SEP 2010 2010
abstract, full text

Collie, Gavin W., Haider, Shozeb M., Neidle, Stephen, Parkinson, Gary N.
A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex
NUCLEIC ACIDS RESEARCH, 38:5569-5580, SEP 2010 2010
abstract, full text

Stone, John E., Hardy, David J., Ufimtsev, Ivan S., Schulten, Klaus
GPU-accelerated molecular modeling coming of age
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:116-125, SEP 2010 2010
abstract, full text

Soares, Rosemberg O., Batista, Paulo R., Costa, Mauricio G. S., Dardenne, Laurent E., Pascutti, Pedro G., Soares, Marcelo A.
Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:137-147, SEP 2010 2010
abstract, full text

Cheng, Yuan, Li, Dechang, Ji, Baohua, Shi, Xinghua, Gao, Huajian
Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: Atomistic and coarse-grained simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 29:171-177, SEP 2010 2010
abstract, full text

Gao, Mu, Skolnick, Jeffrey
iAlign: a method for the structural comparison of protein-protein interfaces
BIOINFORMATICS, 26:2259-2265, SEP 2010 2010
abstract, full text

Panek, Jaroslaw J., Ward, Thomas R., Jezierska-Mazzarello, Aneta, Novic, Marjana
Flexibility of a biotinylated ligand in artificial metalloenzymes based on streptavidin-an insight from molecular dynamics simulations with classical and ab initio force fields
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 24:719-732, SEP 2010 2010
abstract, full text

Abroshan, Hadi, Akbarzadeh, Hamed, Parsafar, Golam Abbas
Molecular dynamics simulation and MM-PBSA calculations of sickle cell hemoglobin in dimer form with Val, Trp, or Phe at the lateral contact
JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, 23:866-877, SEP 2010 2010
abstract, full text

Haiko, Johanna, Laakkonen, Liisa, Juuti, Katri, Kalkkinen, Nisse, Korhonen, Timo K.
The Omptins of Yersinia pestis and Salmonella enterica Cleave the Reactive Center Loop of Plasminogen Activator Inhibitor 1
JOURNAL OF BACTERIOLOGY, 192:4553-4561, SEP 2010 2010
abstract, full text

Lee, Hsiau-Wei, Wylie, Greg, Bansal, Sonal, Wang, Xu, Barb, Adam W., Macnaughtan, Megan A., Ertekin, Asli, Montelione, Gaetano T., Prestegard, James H.
Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping
PROTEIN SCIENCE, 19:1673-1685, SEP 2010 2010
abstract, full text

Pierri, Ciro Leonardo, Parisi, Giovanni, Porcelli, Vito
Computational approaches for protein function prediction: A combined strategy from multiple sequence alignment to molecular docking-based virtual screening
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1804:1695-1712, SEP 2010 2010
abstract, full text

Barucha-Kraszewska, Justyna, Kraszewski, Sebastian, Jurkiewicz, Piotr, Ramseyer, Christophe, Hof, Martin
Numerical studies of the membrane fluorescent dyes dynamics in ground and excited states
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1798:1724-1734, SEP 2010 2010
abstract, full text

Kumar, Nigam, Kishore, Raghuvansh
Determination of an unusual secondary structural element in the immunostimulating tetrapeptide rigin in aqueous environments: insights via MD simulations, (1)H NMR and CD spectroscopic studies
JOURNAL OF PEPTIDE SCIENCE, 16:456-464, SEP 2010 2010
abstract, full text

Karabencheva, Tatyana, Donev, Rossen, Balali-Mood, Kia, Christov, Christo
Individual contributions of the aromatic chromophores to the near-UV Circular Dichroism in class A beta-lactamases: A comparative computational analysis
BIOPHYSICAL CHEMISTRY, 151:39-45, SEP 2010 2010
abstract, full text

Lindgren, Matteus, Westlund, Per-Olof
The affect of urea on the kinetics of local unfolding processes in chymotrypsin inhibitor 2
BIOPHYSICAL CHEMISTRY, 151:46-53, SEP 2010 2010
abstract, full text

Srinivasan, Maya, Uzel, Sebastien G. M., Gautieri, Alfonso, Keten, Sinan, Buehler, Markus J.
Linking Genetics and Mechanics in Structural Protein Materials: A Case Study of an Alport Syndrome Mutation in Tropocollagen
MATHEMATICS AND MECHANICS OF SOLIDS, 15:755-770, SEP 2010 2010
abstract, full text

Ozbabacan, Saliha Ece Acuner, Gursoy, Attila, Keskin, Ozlem, Nussinov, Ruth
Conformational ensembles, signal transduction and residue hot spots: Application to drug discovery
CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT, 13:527-537, SEP 2010 2010
abstract, full text

Jiang, Jin-Wu, Wang, Jian-Sheng
Self-repairing in single-walled carbon nanotubes by heat treatment
JOURNAL OF APPLIED PHYSICS, 108: Art. No. 054303, SEP 1 2010 2010
abstract, full text

Duverna, R., Ablordeppey, S. Y., Lamango, N. S.
Biochemical and Docking Analysis of Substrate Interactions with Polyisoprenylated Methylated Protein Methyl Esterase
CURRENT CANCER DRUG TARGETS, 10:634-648, SEP 2010 2010
abstract, full text

Mehtiev, A. R., Fedchenko, V. I., Tkachev, Ya V., Timofeev, V. P., Misharin, A. Yu
REGULATION OF CHOLESTEROL BIOSYNTHESIS AND METABOLISM IN Hep G2 CELLS BY Delta 8(14)-15-KETOERGOSTANE DERIVATIVES
Biomeditsinskaya Khimiya, 56:576-586, SEP-OCT 2010 2010
abstract, full text

Noel, Jeffrey K., Sulkowska, Joanna I., Onuchic, Jose N.
Slipknotting upon native-like loop formation in a trefoil knot protein
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:15403-15408, AUG 31 2010 2010
abstract, full text

Wang Hongyin, Lin Dongqiang, Yao Shanjing, Yun Junxian, Yao Kejian
Molecular Simulation of the Interactions between 4-Mercaptoethyl-pyridine Ligand and IgG
ACTA CHIMICA SINICA, 68:1597-1602, AUG 28 2010 2010
abstract, full text

Stabenfeldt, Sarah E., Gossett, J. Jared, Barker, Thomas H.
Building better fibrin knob mimics: an investigation of synthetic fibrin knob peptide structures in solution and their dynamic binding with fibrinogen/fibrin holes
BLOOD, 116:1352-1359, AUG 26 2010 2010
abstract, full text

Bora, Ram Prasad, Barman, Arghya, Zhu, Xiaoxia, Ozbil, Mehmet, Prabhakar, Rajeev
Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis?
JOURNAL OF PHYSICAL CHEMISTRY B, 114:10860-10875, AUG 26 2010 2010
abstract, full text

Acharya, Rudresh, Carnevale, Vincenzo, Fiorin, Giacomo, Levine, Benjamin G., Polishchuk, Alexei L., Balannik, Victoria, Samish, Ilan, Lamb, Robert A., Pinto, Lawrence H., DeGrado, William F., Klein, Michael L.
Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:15075-15080, AUG 24 2010 2010
abstract, full text

DeWitt, W., Chu, K.
Imaging Protein Statistical Substate Occupancy in a Spectrum-Function Phase Space
PHYSICAL REVIEW LETTERS, 105: Art. No. 098101, AUG 24 2010 2010
abstract, full text

Londero, Elisa, Schroder, Elsebeth
Role of van der Waals bonding in the layered oxide V(2)O(5): First-principles density-functional calculations
PHYSICAL REVIEW B, 82: Art. No. 054116, AUG 23 2010 2010
abstract, full text

Sorkin, V., Zhang, Y. W.
Rotation-dependent epitaxial relations between graphene and the Si-terminated SiC substrate
PHYSICAL REVIEW B, 82: Art. No. 085434, AUG 23 2010 2010
abstract, full text

Frolov, Andrey I., Rozhin, Alex G., Fedorov, Maxim V.
Ion Interactions with the Carbon Nanotube Surface in Aqueous Solutions: Understanding the Molecular Mechanisms
CHEMPHYSCHEM, 11:2612-2616, AUG 23 2010 2010
abstract, full text

Perera, S. Ajith, McLaurin, Patrick M., Grimes, Thomas V., Morales, Jorge A.
Time-dependent density-functional theory method in the electron nuclear dynamics framework
CHEMICAL PHYSICS LETTERS, 496:188-195, AUG 20 2010 2010
abstract, full text

Lee, Lawrence K., Ginsburg, Michael A., Crovace, Claudia, Donohoe, Mhairi, Stock, Daniela
Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching
NATURE, 466:996-U129, AUG 19 2010 2010
abstract, full text

Callahan, Karen M., Casillas-Ituarte, Nadia N., Xu, Man, Roeselova, Martina, Allen, Heather C., Tobias, Douglas J.
Effect of Magnesium Cation on the Interfacial Properties of Aqueous Salt Solutions
JOURNAL OF PHYSICAL CHEMISTRY A, 114:8359-8368, AUG 19 2010 2010
abstract, full text

Spackova, Nad'a, Reblova, Kamila, Sponer, Jiri
Structural Dynamics of the Box C/D RNA Kink-Turn and Its Complex with Proteins: The Role of the A-Minor 0 Interaction, Long-Residency Water Bridges, and Structural Ion-Binding Sites Revealed by Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 114:10581-10593, AUG 19 2010 2010
abstract, full text

Elgeti, Jens, Kaupp, U. Benjamin, Gompper, Gerhard
Hydrodynamics of Sperm Cells near Surfaces
BIOPHYSICAL JOURNAL, 99:1018-1026, AUG 18 2010 2010
abstract, full text

Golji, Javad, Mofrad, Mohammad R. K.
A Molecular Dynamics Investigation of Vinculin Activation
BIOPHYSICAL JOURNAL, 99:1073-1081, AUG 18 2010 2010
abstract, full text

Roos, W. H., Gibbons, M. M., Arkhipov, A., Uetrecht, C., Watts, N. R., Wingfield, P. T., Steven, A. C., Heck, A. J. R., Schulten, K., Klug, W. S., Wuite, G. J. L.
Squeezing Protein Shells: How Continuum Elastic Models, Molecular Dynamics Simulations, and Experiments Coalesce at the Nanoscale
BIOPHYSICAL JOURNAL, 99:1175-1181, AUG 18 2010 2010
abstract, full text

Zou, Xueqing, Liu, Yanxin, Chen, Zhongzhou, Ines Cardenas-Jiron, Gloria, Schulten, Klaus
Flow-Induced beta-Hairpin Folding of the Glycoprotein Ib alpha beta-Switch
BIOPHYSICAL JOURNAL, 99:1182-1191, AUG 18 2010 2010
abstract, full text

Tseng, Chih-Yuan, Yu, Chun-Ping, Lee, H. C.
From laws of inference to protein folding dynamics
PHYSICAL REVIEW E, 82: Art. No. 021914, AUG 18 2010 2010
abstract, full text

Liu, Ningning, Peng, Bo, Lin, Yuan, Su, Zhaohui, Niu, Zhongwei, Wang, Qian, Zhang, Wenke, Li, Hongbin, Shen, Jiacong
Pulling Genetic RNA out of Tobacco Mosaic Virus Using Single-Molecule Force Spectroscopy
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:11036-11038, AUG 18 2010 2010
abstract, full text

Ward, Joshua M., Gorenstein, Nina M., Tian, Jianhua, Martin, Stephen F., Post, Carol Beth
Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy-Entropy Compensation in SH2-Ligand Binding
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:11058-11070, AUG 18 2010 2010
abstract, full text

Shinobu, Ai, Palm, Gottfried J., Schierbeek, Abraham J., Agmon, Noam
Visualizing Proton Antenna in a High-Resolution Green Fluorescent Protein Structure
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:11093-11102, AUG 18 2010 2010
abstract, full text

Ahadi, Elias, Konermann, Lars
Surface Charge of Electrosprayed Water Nanodroplets: A Molecular Dynamics Study
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 132:11270-11277, AUG 18 2010 2010
abstract, full text

Allison, Jane R., Moll, Gian-Peider, van Gunsteren, Wilfred F.
Investigation of Stability and Disulfide Bond Shuffling of Lipid Transfer Proteins by Molecular Dynamics Simulation
BIOCHEMISTRY, 49:6916-6927, AUG 17 2010 2010
abstract, full text

Illingworth, Christopher J. R., Loenarz, Christoph, Schofield, Christopher J., Domene, Carmen
Chemical Basis for the Selectivity of the von Hippel Lindau Tumor Suppressor pVHL for Prolyl-Hydroxylated HIF-1 alpha
BIOCHEMISTRY, 49:6936-6944, AUG 17 2010 2010
abstract, full text

Marcos, Enrique, Field, Martin J., Crehuet, Ramon
Pentacoordinated phosphorus revisited by high-level QM/MM calculations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2405-2411, AUG 15 2010 2010
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Lawrenz, Morgan, Wereszczynski, Jeff, Amaro, Rommie, Walker, Ross, Roitberg, Adrian, McCammon, J. Andrew
Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2523-2532, AUG 15 2010 2010
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Peng, Ping, Liao, Guanglan, Shi, Tielin, Tang, Zirong, Gao, Yang
Molecular dynamic simulations of nanoindentation in aluminum thin film on silicon substrate
APPLIED SURFACE SCIENCE, 256:6284-6290, AUG 15 2010 2010
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Anderson, J. A., Sknepnek, R., Travesset, A.
Design of polymer nanocomposites in solution by polymer functionalization
PHYSICAL REVIEW E, 82: Art. No. 021803, AUG 13 2010 2010
abstract, full text

Harris, Sarah A., Kendon, Vivien M.
Quantum-assisted biomolecular modelling
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 368:3581-3592, AUG 13 2010 2010
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Hartmann, C., Mueller, N., Blaukat, A., Koch, J., Benhar, I., Wels, W. S.
Peptide mimotopes recognized by antibodies cetuximab and matuzumab induce a functionally equivalent anti-EGFR immune response
ONCOGENE, 29:4517-4527, AUG 12 2010 2010
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Hsin, J., Struempfer, J., Sener, M., Qian, P., Hunter, C. N., Schulten, K.
Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane
NEW JOURNAL OF PHYSICS, 12: Art. No. 085005, AUG 11 2010 2010
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Negri, Matthias, Recanatini, Maurizio, Hartmann, Rolf W.
Insights in 17 beta-HSD1 Enzyme Kinetics and Ligand Binding by Dynamic Motion Investigation
PLOS ONE, 5: Art. No. e12026, AUG 10 2010 2010
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Saam, Jan, Rosini, Elena, Molla, Gianluca, Schulten, Klaus, Pollegioni, Loredano, Ghisla, Sandro
O(2) Reactivity of Flavoproteins DYNAMIC ACCESS OF DIOXYGEN TO THE ACTIVE SITE AND ROLE OF A H(+) RELAY SYSTEM IN D-AMINO ACID OXIDASE
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:24439-24446, AUG 6 2010 2010
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Daiho, Takashi, Danko, Stefania, Yamasaki, Kazuo, Suzuki, Hiroshi
Stable Structural Analog of Ca(2+)-ATPase ADP-insensitive Phosphoenzyme with Occluded Ca(2+) Formed by Elongation of A-domain/M1 '-linker and Beryllium Fluoride Binding
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:24538-24547, AUG 6 2010 2010
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Trajtenberg, Felipe, Grana, Martin, Ruetalo, Natalia, Botti, Horacio, Buschiazzo, Alejandro
Structural and Enzymatic Insights into the ATP Binding and Autophosphorylation Mechanism of a Sensor Histidine Kinase
JOURNAL OF BIOLOGICAL CHEMISTRY, 285:24892-24903, AUG 6 2010 2010
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Barnaby, Omar S., Wa, Chunling, Cerny, Ronald L., Clarke, William, Hage, David S.
Quantitative analysis of glycation sites on human serum albumin using (16)O/(18)O-labeling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
CLINICA CHIMICA ACTA, 411:1102-1110, AUG 5 2010 2010
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Priyakumar, U. Deva
Atomistic Details of the Ligand Discrimination Mechanism of S(MK)/SAM-III Riboswitch
JOURNAL OF PHYSICAL CHEMISTRY B, 114:9920-9925, AUG 5 2010 2010
abstract, full text

Liu, Jin, Nussinov, Ruth
Rbx1 Flexible Linker Facilitates Cullin-RING Ligase Function Before Neddylation and After Deneddylation
BIOPHYSICAL JOURNAL, 99:736-744, AUG 4 2010 2010
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Piechowiak, M. A., Videcoq, A., Rossignol, F., Pagnoux, C., Carrion, C., Cerbelaud, M., Ferrando, R.
Oppositely Charged Model Ceramic Colloids: Numerical Predictions and Experimental Observations by Confocal Laser Scanning Microscopy
LANGMUIR, 26:12540-12547, AUG 3 2010 2010
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Lee, Wen-Jay, Chang, Jee-Gong, Ju, Shin-Pon
Hydrogen-Bond Structure at the Interfaces between Water/Poly(methyl methacrylate), Water/Poly(methacrylic acid), and Water/Poly(2-aminoethylmethacrylamide)
LANGMUIR, 26:12640-12647, AUG 3 2010 2010
abstract, full text

Wang, Qiuming, Zhao, Jun, Yu, Xiang, Zhao, Chao, Li, Lingyan, Zheng, Jie
Alzheimer A beta(1-42) Monomer Adsorbed on the Self-Assembled Monolayers
LANGMUIR, 26:12722-12732, AUG 3 2010 2010
abstract, full text

Ferguson, Andrew L., Panagiotopoulos, Athanassios Z., Debenedetti, Pablo G., Kevrekidis, Ioannis G.
Systematic determination of order parameters for chain dynamics using diffusion maps
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:13597-13602, AUG 3 2010 2010
abstract, full text

Dalvi, Vishwanath H., Rossky, Peter J.
Molecular origins of fluorocarbon hydrophobicity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:13603-13607, AUG 3 2010 2010
abstract, full text

Leonard, Effendi, Ajikumar, Parayil Kumaran, Thayer, Kelly, Xiao, Wen-Hai, Mo, Jeffrey D., Tidor, Bruce, Stephanopoulos, Gregory, Prather, Kristala L. J.
Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107:13654-13659, AUG 3 2010 2010
abstract, full text

Morris, John H., Meng, Elaine C., Ferrin, Thomas E.
Computational Tools for the Interactive Exploration of Proteomic and Structural Data
MOLECULAR & CELLULAR PROTEOMICS, 9:1703-1715, AUG 2010 2010
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Tsang, Casey, Malik, Huma, Nassman, Deana, Huang, Antony, Tariq, Fayha, Oelschlaeger, Peter, Stathopoulos, Christos
Intramolecular Interactions between the Protease and Structural Domains Are Important for the Functions of Serine Protease Autotransporters
INFECTION AND IMMUNITY, 78:3335-3345, AUG 2010 2010
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Yang, Mingjun, Zhang, Xin, Han, Keli
Molecular dynamics simulation of SRP GTPases: Towards an understanding of the complex formation from equilibrium fluctuations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 78:2222-2237, AUG 1 2010 2010
abstract,