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Molecular dynamics

Molecular Dynamics Simulations to Investigate the Influences of Amino Acid Mutations on Protein Three-Dimensional Structures of Cytochrome P450 2D6.1, 2, 10, 14A, 51, and 62

Shuichi Fukuyoshi, Masaharu Kometani, Yurie Watanabe, Masahiro Hiratsuka, Noriyuki Yamaotsu, Shuichi Hirono, Noriyoshi Manabe, Ohgi Takahashi, Akifumi Oda

published 05 Apr 2016

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CASP11 – An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline

Axel W. Fischer, Sten Heinze, Daniel K. Putnam, Bian Li, James C. Pino, Yan Xia, Carlos F. Lopez, Jens Meiler

published 05 Apr 2016

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Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies

Matias Fuentealba, Rodrigo Muñoz, Pablo Maturana, Adriana Krapp, Ricardo Cabrera

published 24 Mar 2016

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On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion

Àlex L. González, Jordi Teixidó, José I. Borrell, Roger Estrada-Tejedor

published 24 Mar 2016

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The Hinge Region Strengthens the Nonspecific Interaction between Lac-Repressor and DNA: A Computer Simulation Study

Lili Sun, Marcin Tabaka, Sen Hou, Lin Li, Krzysztof Burdzy, Aleksei Aksimentiev, Christopher Maffeo, Xuzhu Zhang, Robert Holyst

published 23 Mar 2016

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GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential

Wenduo Chen, Youliang Zhu, Fengchao Cui, Lunyang Liu, Zhaoyan Sun, Jizhong Chen, Yunqi Li

published 17 Mar 2016

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Structural Characterization of the Loop at the Alpha-Subunit C-Terminus of the Mixed Lineage Leukemia Protein Activating Protease Taspase1

Johannes van den Boom, Franziska Trusch, Lukas Hoppstock, Christine Beuck, Peter Bayer

published 14 Mar 2016

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Ion Concentration- and Voltage-Dependent Push and Pull Mechanisms of Potassium Channel Ion Conduction

Kota Kasahara, Matsuyuki Shirota, Kengo Kinoshita

published 07 Mar 2016

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Molecular Probing of the HPV-16 E6 Protein Alpha Helix Binding Groove with Small Molecule Inhibitors

Anne Rietz, Dino P. Petrov, Matthew Bartolowits, Marsha DeSmet, V. Jo Davisson, Elliot J. Androphy

published 25 Feb 2016

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Computing Molecular Devices in L.major through Transcriptome Analysis: Structured Simulation Approach

Pruthvi Raj Bejugam, Shailza Singh

published 22 Feb 2016

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Energetics of Transport through the Nuclear Pore Complex

Ali Ghavami, Erik van der Giessen, Patrick R. Onck

published 19 Feb 2016

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Structural Study of Cell Attachment Peptide Derived from Laminin by Molecular Dynamics Simulation

Hironao Yamada, Sakiko Mori, Takeshi Miyakawa, Ryota Morikawa, Fumihiko Katagiri, Kentaro Hozumi, Yamato Kikkawa, Motoyoshi Nomizu, Masako Takasu

published 18 Feb 2016

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Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations

Sharad Verma, Sonam Grover, Chetna Tyagi, Sukriti Goyal, Salma Jamal, Aditi Singh, Abhinav Grover

published 10 Feb 2016

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