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

Pavithra K. Balasubramanian; Anand Balupuri; Swapnil P. Bhujbal; Seung Joo Cho

doi:10.1080/07391102.2018.1479309

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 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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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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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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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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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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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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Theoretical Exploring Selective-Binding Mechanisms of JAK3 by 3D-QSAR, Molecular Dynamics Simulation and Free Energy Calculation

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2020.00083 ◽

2020 ◽

Vol 7 ◽

Author(s):

Jingyu Zhu ◽

Qianqian Yu ◽

Yanfei Cai ◽

Yun Chen ◽

Hui Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Selective Binding ◽

Binding Mechanisms

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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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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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