Understanding the structural and energetic basis of inhibitor and substrate bound to the full-length NS3/4A: insights from molecular dynamics simulation, binding free energy calculation and network analysis

Weiwei Xue; Meixia Wang; Xiaojie Jin; Huanxiang Liu; Xiaojun Yao

doi:10.1039/c2mb25157d

Understanding the structural and energetic basis of inhibitor and substrate bound to the full-length NS3/4A: insights from molecular dynamics simulation, binding free energy calculation and network analysis

Molecular BioSystems ◽

10.1039/c2mb25157d ◽

2012 ◽

Vol 8 (10) ◽

pp. 2753 ◽

Cited By ~ 22

Author(s):

Weiwei Xue ◽

Meixia Wang ◽

Xiaojie Jin ◽

Huanxiang Liu ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Network Analysis ◽

Binding Free Energy ◽

Full Length ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation

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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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3D-QSAR-aided design of potent c-Met inhibitors using molecular dynamics simulation and binding free energy calculation

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1479309 ◽

2018 ◽

Vol 37 (8) ◽

pp. 2165-2178 ◽

Cited By ~ 4

Author(s):

Pavithra K. Balasubramanian ◽

Anand Balupuri ◽

Swapnil P. Bhujbal ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Aided Design

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Precise design of highly isoform-selective p21-activated kinase 4 inhibitors: computational insights into the selectivity mechanism through molecular dynamics simulation and binding free energy calculation

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1664330 ◽

2019 ◽

Vol 38 (13) ◽

pp. 3825-3837 ◽

Cited By ~ 1

Author(s):

Yuan Su ◽

Peilu Song ◽

Hanxun Wang ◽

Baichun Hu ◽

Jian Wang ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

P21 Activated Kinase

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Identification of potential inhibitors of coronavirus hemagglutinin-esterase using molecular docking, molecular dynamics simulation and binding free energy calculation

Molecular Diversity ◽

10.1007/s11030-020-10135-w ◽

2020 ◽

Author(s):

Chirag N. Patel ◽

Sivakumar Prasanth Kumar ◽

Himanshu A. Pandya ◽

Rakesh M. Rawal

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Potential Inhibitors

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Synthesis, molecular docking, binding free energy calculation and molecular dynamics simulation studies of benzothiazol-2-ylcarbamodithioates as Staphylococcus aureus MurD inhibitors

Journal of Receptors and Signal Transduction ◽

10.1080/10799893.2019.1663538 ◽

2019 ◽

Vol 39 (3) ◽

pp. 283-293

Author(s):

Srikanth Jupudi ◽

Mohammed Afzal Azam ◽

Ashish Wadhwani

Keyword(s):

Molecular Dynamics ◽

Staphylococcus Aureus ◽

Free Energy ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Simulation Studies

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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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Molecular dynamics simulation, binding free energy calculation and unbinding pathway analysis on selectivity difference between FKBP51 and FKBP52: Insight into the molecular mechanism of isoform selectivity

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.25401 ◽

2017 ◽

Vol 86 (1) ◽

pp. 43-56 ◽

Cited By ~ 25

Author(s):

Danfeng Shi ◽

Qifeng Bai ◽

Shuangyan Zhou ◽

Xuewei Liu ◽

Huanxiang Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Pathway Analysis ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Isoform Selectivity ◽

Insight Into

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Molecular Dynamics Simulation and Binding Free Energy Calculation of the Conformational Transition of Amyloid Peptide 42 Inhibited by Peptide Inhibitors

Acta Physico-Chimica Sinica ◽

10.3866/pku.whxb201207162 ◽

2012 ◽

Vol 28 (11) ◽

pp. 2735-2744 ◽

Cited By ~ 4

Author(s):

DONG Xiao-Yan ◽

◽

DU Wen-Jie ◽

LIU Fu-Feng

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Conformational Transition ◽

Binding Free Energy ◽

Peptide Inhibitors ◽

Amyloid Peptide ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation

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Molecular dynamics simulation, binding free energy calculation and molecular docking of human D-amino acid oxidase (DAAO) with its inhibitors

Molecular Simulation ◽

10.1080/08927022.2013.854892 ◽

2014 ◽

Vol 40 (14) ◽

pp. 1167-1189 ◽

Cited By ~ 5

Author(s):

Kanin Wichapong ◽

Arthit Nueangaudom ◽

Somsak Pianwanit ◽

Fumio Tanaka ◽

Sirirat Kokpol

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Acid Oxidase ◽

Amino Acid Oxidase

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Sterenin M as a potential inhibitor of SARS-CoV-2 main protease identified from MeFSAT database using molecular docking, molecular dynamics simulation and binding free energy calculation

Computers in Biology and Medicine ◽

10.1016/j.compbiomed.2021.104568 ◽

2021 ◽

pp. 104568

Author(s):

Jignesh Prajapati ◽

Rohit Patel ◽

Dweipayan Goswami ◽

Meenu Saraf ◽

Rakesh M. Rawal

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Potential Inhibitor ◽

Main Protease

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