An insight into the binding mechanism of Viprinin and its morpholine and piperidine derivatives with HIV-1 Vpr: molecular dynamics simulation, principal component analysis and binding free energy calculation study

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2021.1954553 ◽

2021 ◽

pp. 1-13

Author(s):

Satyabrata Majumder ◽

Kalyan Giri

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Binding Free Energy ◽

Principal Component ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Mechanism ◽

Insight Into ◽

Hiv 1

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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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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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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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Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2019.07.008 ◽

2019 ◽

Vol 92 ◽

pp. 112-122 ◽

Cited By ~ 3

Author(s):

Konda Reddy Karnati ◽

Yixuan Wang

Keyword(s):

Molecular Dynamics ◽

Principal Component Analysis ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Principal Component ◽

Component Analysis ◽

Ligand Interactions ◽

Dynamics Simulations ◽

Hiv 1

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Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with TrkA kinase

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1708798 ◽

2019 ◽

Vol 39 (1) ◽

pp. 202-208 ◽

Cited By ~ 1

Author(s):

Xiaoyun Wu ◽

Qinlan Li ◽

Shanhe Wan ◽

Jiajie Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Mechanism ◽

Allosteric Inhibitors

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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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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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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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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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Combined 3D-QSAR, Molecular Docking, Molecular Dynamics Simulation, and Binding Free Energy Calculation Studies on the 5-Hydroxy-2H-Pyridazin-3-One Derivatives as HCV NS5B Polymerase Inhibitors

Chemical Biology & Drug Design ◽

10.1111/cbdd.12203 ◽

2013 ◽

Vol 83 (1) ◽

pp. 89-105 ◽

Cited By ~ 13

Author(s):

Haijing Yu ◽

Yu Fang ◽

Xia Lu ◽

Yongjuan Liu ◽

Huabei Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Polymerase Inhibitors ◽

Hcv Ns5b ◽

Ns5b Polymerase

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