Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation

Qifeng Bai; Yang Zhang; Xiaomeng Li; Wenbo Chen; Huanxiang Liu; Xiaojun Yao

doi:10.1039/c4cp03331k

Computational study on the interaction between CCR5 and HIV-1 entry inhibitor maraviroc: insight from accelerated molecular dynamics simulation and free energy calculation

Physical Chemistry Chemical Physics ◽

10.1039/c4cp03331k ◽

2014 ◽

Vol 16 (44) ◽

pp. 24332-24338 ◽

Cited By ~ 19

Author(s):

Qifeng Bai ◽

Yang Zhang ◽

Xiaomeng Li ◽

Wenbo Chen ◽

Huanxiang Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Computational Study ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Entry Inhibitor ◽

Energy Calculation ◽

Accelerated Molecular Dynamics ◽

Hiv 1

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Investigation about the Inhibition of HIV-1 Gp41 Fusion via Andrographis Paniculata: Virtual Screening, Molecular Dynamics Simulation and Free Energy Calculation

American Journal of Biomedical Sciences ◽

10.5099/aj200300191 ◽

2020 ◽

pp. 191-205

Author(s):

Ancy Iruthayaraj ◽

Poomani Kumaradhas

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Virtual Screening ◽

Andrographis Paniculata ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Hiv 1

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Insights into the interactions between HIV-1 integrase and human LEDGF/p75 by molecular dynamics simulation and free energy calculation

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21955 ◽

2008 ◽

Vol 72 (2) ◽

pp. 635-645 ◽

Cited By ~ 22

Author(s):

Yaxue Zhao ◽

Weihua Li ◽

Juan Zeng ◽

Guixia Liu ◽

Yun Tang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Hiv 1

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Computational study on the inhibition mechanism of a cyclic peptide MaD5 to PfMATE: Insight from molecular dynamics simulation, free energy calculation and dynamical network analysis

Chemometrics and Intelligent Laboratory Systems ◽

10.1016/j.chemolab.2015.10.013 ◽

2015 ◽

Vol 149 ◽

pp. 81-88

Author(s):

Xiaojie Jin ◽

Qifeng Bai ◽

Weiwei Xue ◽

Huanxiang Liu ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Network Analysis ◽

Cyclic Peptide ◽

Computational Study ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Inhibition Mechanism ◽

Energy Calculation

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3D-QSAR, docking, molecular dynamics simulation and free energy calculation studies of some pyrimidine derivatives as novel JAK3 inhibitors

Arabian Journal of Chemistry ◽

10.1016/j.arabjc.2017.09.009 ◽

2020 ◽

Vol 13 (1) ◽

pp. 1052-1078 ◽

Cited By ~ 9

Author(s):

Anand Balupuri ◽

Pavithra K. Balasubramanian ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Pyrimidine Derivatives

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Efficient Free-Energy Calculation of Proton Transfer by Constrained Density Functional Theory and Geometrically Restrained Molecular Dynamics Simulation

Chemistry Letters ◽

10.1246/cl.210132 ◽

2021 ◽

Author(s):

Tatsuya Joutsuka ◽

Koji Ando

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Density Functional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Functional Theory

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Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

Molecular Pharmaceutics ◽

10.1021/mp900131p ◽

2009 ◽

Vol 7 (1) ◽

pp. 75-85 ◽

Cited By ~ 57

Author(s):

Huanxiang Liu ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Influenza Virus ◽

Molecular Dynamics Simulation ◽

Molecular Basis ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Virus Rna ◽

Essential Subunit

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Insights into the mechanism of inhibition of phospholipase A2 by resveratrol: An extensive molecular dynamics simulation and binding free energy calculation

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107649 ◽

2020 ◽

Vol 100 ◽

pp. 107649

Author(s):

Sajedeh Sharifpour ◽

Sara Fakhraee ◽

Reza Behjatmanesh-Ardakani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Phospholipase A2 ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Mechanism Of Inhibition

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A relative free energy calculation method with ion screening effect using molecular dynamics simulation

Journal of Molecular Graphics ◽

10.1016/0263-7855(94)80025-1 ◽

1994 ◽

Vol 12 (1) ◽

pp. 56-57

Author(s):

K. Tazaki ◽

J. Doi

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Calculation Method ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Screening Effect ◽

Relative Free Energy

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Free Energy Calculation of Protein Conformational Changes using Parallel Cascade Selection Molecular Dynamics Simulation and Markov State Model

Biophysical Journal ◽

10.1016/j.bpj.2013.11.2300 ◽

2014 ◽

Vol 106 (2) ◽

pp. 408a

Author(s):

Yasutaka Nishihara ◽

Ryuhei Harada ◽

Akio Kitao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Conformational Changes ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Markov State Model ◽

Markov State ◽

Protein Conformational Changes

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Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors

Journal of Chemical Information and Modeling ◽

10.1021/ci100427j ◽

2011 ◽

Vol 51 (3) ◽

pp. 680-692 ◽

Cited By ~ 61

Author(s):

Ying Yang ◽

Jin Qin ◽

Huanxiang Liu ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Kinase Inhibitors ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Qsar Studies ◽

Raf Kinase

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