Insight into the key active sites of afChiA1 based on molecular dynamics simulations and free energy calculations

Molecular Simulation ◽

10.1080/08927022.2016.1148265 ◽

2016 ◽

Vol 42 (12) ◽

pp. 1024-1028

Author(s):

Xiao D. Niu ◽

Zhuo Lv ◽

Xin R. Zhou ◽

Hong S. Wang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Active Sites ◽

Free Energy Calculations ◽

Energy Calculations ◽

Dynamics Simulations ◽

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Gaining insight into crizotinib resistance mechanisms caused by L2026M and G2032R mutations in ROS1 via molecular dynamics simulations and free-energy calculations

Journal of Molecular Modeling ◽

10.1007/s00894-017-3314-z ◽

2017 ◽

Vol 23 (4) ◽

Author(s):

XiaoYun Wu ◽

Yu Fu ◽

YuanYuan Wang ◽

ShanHe Wan ◽

JiaJie Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Resistance Mechanisms ◽

Free Energy Calculations ◽

Energy Calculations ◽

Dynamics Simulations ◽

Insight Into ◽

Gaining Insight

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Molecular insight into the specific binding of ADP-ribose to the nsP3 macro domains of chikungunya and venezuelan equine encephalitis viruses: Molecular dynamics simulations and free energy calculations

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2010.09.010 ◽

2010 ◽

Vol 29 (3) ◽

pp. 347-353 ◽

Author(s):

Thanyada Rungrotmongkol ◽

Nadtanet Nunthaboot ◽

Maturos Malaisree ◽

Nopporn Kaiyawet ◽

Pathumwadee Yotmanee ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Specific Binding ◽

Free Energy Calculations ◽

Venezuelan Equine Encephalitis ◽

Energy Calculations ◽

Dynamics Simulations ◽

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Molecular dynamics simulations reveal insight into key structural elements of aaptamines as sortase inhibitors with free energy calculations

Chemical Physics Letters ◽

10.1016/j.cplett.2013.08.097 ◽

2013 ◽

Vol 585 ◽

pp. 171-177 ◽

Author(s):

Zhuo Lv ◽

Hong S. Wang ◽

Xiao D. Niu

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Structural Elements ◽

Energy Calculations ◽

Dynamics Simulations ◽

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Insight into binding mechanisms of EGFR allosteric inhibitors using molecular dynamics simulations and free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1552197 ◽

2019 ◽

Vol 37 (16) ◽

pp. 4384-4394 ◽

Author(s):

Shanhe Wan ◽

Ruohong Yan ◽

Ying Jiang ◽

Zhonghuang Li ◽

Jiajie Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Allosteric Inhibitors ◽

Energy Calculations ◽

Dynamics Simulations ◽

Binding Mechanisms ◽

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Insight into the structural mechanism for PKBα allosteric inhibition by molecular dynamics simulations and free energy calculations

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2013.12.002 ◽

2014 ◽

Vol 48 ◽

pp. 36-46 ◽

Author(s):

Shi-Feng Chen ◽

Yang Cao ◽

Shuang Han ◽

Jian-Zhong Chen

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Allosteric Inhibition ◽

Structural Mechanism ◽

Energy Calculations ◽

Dynamics Simulations ◽

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Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations

Journal of Chemical Information and Modeling ◽

10.1021/ci300118x ◽

2012 ◽

Vol 52 (6) ◽

pp. 1573-1582 ◽

Author(s):

Urban Bren ◽

Chris Oostenbrink

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Cytochrome P450 ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Cytochrome P450 3A4 ◽

Energy Calculations ◽

Dynamics Simulations

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Molecular Dynamics Simulations and Free Energy Calculations of a Novel Series of Protein Tyrosine Phosphatase 1B Difluoromethylenephosphonic Acid Inhibitors

Acta Physico-Chimica Sinica ◽

10.3866/pku.whxb200904271 ◽

2009 ◽

Vol 25 (04) ◽

pp. 668-676

Author(s):

CUI Wei ◽

◽

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Protein Tyrosine Phosphatase ◽

Tyrosine Phosphatase ◽

Free Energy Calculations ◽

Protein Tyrosine Phosphatase 1B ◽

Energy Calculations ◽

Protein Tyrosine ◽

Dynamics Simulations

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Targeting protein tyrosine phosphatase to unravel possible inhibitors for Streptococcus pneumoniae using molecular docking, molecular dynamics simulations coupled with free energy calculations

Life Sciences ◽

10.1016/j.lfs.2020.118621 ◽

2021 ◽

Vol 264 ◽

pp. 118621

Author(s):

Zainab Zaman ◽

Sara Khan ◽

Faisal Nouroz ◽

Umar Farooq ◽

Akasha Urooj

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Streptococcus Pneumoniae ◽

Molecular Dynamics Simulations ◽

Protein Tyrosine Phosphatase ◽

Tyrosine Phosphatase ◽

Free Energy Calculations ◽

Energy Calculations ◽

Dynamics Simulations

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Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24057 ◽

2012 ◽

Vol 80 (6) ◽

pp. 1633-1646 ◽

Author(s):

Tom Venken ◽

Dirk Daelemans ◽

Marc De Maeyer ◽

Arnout Voet

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Computational Investigation ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations ◽

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Revealing binding selectivity of ligands toward murine double minute 2 and murine double minute X based on molecular dynamics simulations and binding free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1695671 ◽

2019 ◽

Vol 38 (17) ◽

pp. 5081-5094 ◽

Author(s):

Shuhua Shi ◽

Kai Sui ◽

Weizhe Liu ◽

Yanzi Lei ◽

Shaolong Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Double Minute ◽

Murine Double Minute ◽

Binding Free Energy Calculations ◽

Dynamics Simulations

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