Exploring the Molecular Design of Protein Interaction Sites with Molecular Dynamics Simulations and Free Energy Calculations†

Biochemistry ◽

10.1021/bi8017043 ◽

2009 ◽

Vol 48 (2) ◽

pp. 399-414 ◽

Author(s):

Shide Liang ◽

Liwei Li ◽

Wei-Lun Hsu ◽

Meaghan N. Pilcher ◽

Vladimir Uversky ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Protein Interaction ◽

Molecular Design ◽

Free Energy Calculations ◽

Energy Calculations ◽

Interaction Sites ◽

Dynamics Simulations ◽

Protein Interaction Sites

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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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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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Free Energy Calculations and Molecular Dynamics Simulations of Wild-Type and Variants of the DNA-EcoRI Complex

Biophysical Journal ◽

10.1016/s0006-3495(99)77025-6 ◽

1999 ◽

Vol 77 (4) ◽

pp. 1801-1810 ◽

Author(s):

Srikanta Sen ◽

Lennart Nilsson

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Wild Type ◽

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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Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

Biophysical Journal ◽

10.1529/biophysj.106.084301 ◽

2006 ◽

Vol 91 (8) ◽

pp. 2798-2814 ◽

Author(s):

Jiyao Wang ◽

Yuqing Deng ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations ◽

Absolute Binding Free Energy

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Theoretical studies on the selective mechanisms of GSK3β and CDK2 by molecular dynamics simulations and free energy calculations

Chemical Biology & Drug Design ◽

10.1111/cbdd.12907 ◽

2016 ◽

Vol 89 (6) ◽

pp. 846-855 ◽

Author(s):

Sufang Zhao ◽

Jingyu Zhu ◽

Lei Xu ◽

Jian Jin

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Theoretical Studies ◽

Energy Calculations ◽

Dynamics Simulations

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