Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations

Journal of Chemical Theory and Computation ◽

10.1021/ct500964e ◽

2015 ◽

Vol 11 (2) ◽

pp. 423-435 ◽

Author(s):

Robert B. Sandberg ◽

Martina Banchelli ◽

Carlo Guardiani ◽

Stefano Menichetti ◽

Gabriella Caminati ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free 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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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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Faculty Opinions recommendation of Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1047901.497924 ◽

2006 ◽

Author(s):

Jeffry Madura

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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Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations

PLoS ONE ◽

10.1371/journal.pone.0145219 ◽

2015 ◽

Vol 10 (12) ◽

pp. e0145219 ◽

Author(s):

Yuzhen Niu ◽

Dabo Pan ◽

Danfeng Shi ◽

Qifeng Bai ◽

Huanxiang Liu ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Inhibitory Activity ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations

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Faculty Opinions recommendation of Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1047901.501171 ◽

2006 ◽

Author(s):

Tjerk P. Straatsma

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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Resistance mechanism of the oncogenic β3-αC deletion mutation in BRAF kinase to dabrafenib and vemurafenib revealed by molecular dynamics simulations and binding free energy calculations

Chemical Biology & Drug Design ◽

10.1111/cbdd.13399 ◽

2018 ◽

Vol 93 (2) ◽

pp. 177-187

Author(s):

Yuzhen Niu ◽

Yan Zhang ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Resistance Mechanism ◽

Free Energy Calculations ◽

Deletion Mutation ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations

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Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1591304 ◽

2019 ◽

Vol 38 (4) ◽

pp. 985-996 ◽

Author(s):

Jianzhong Chen ◽

Laixue Pang ◽

Wei Wang ◽

Lifei Wang ◽

John Z. H. Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Molecular Mechanism ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations

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Insights into the binding mechanisms of inhibitors of MDM2 based on molecular dynamics simulations and binding free energy calculations

Chemical Physics Letters ◽

10.1016/j.cplett.2019.05.001 ◽

2019 ◽

Vol 728 ◽

pp. 94-101

Author(s):

Pei Zhao ◽

Huali Cao ◽

Yu Chen ◽

Tong Zhu

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations ◽

Binding Mechanisms

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Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method

Journal of Chemical Information and Modeling ◽

10.1021/ci0601214 ◽

2006 ◽

Vol 46 (5) ◽

pp. 1972-1983 ◽

Author(s):

Eva Stjernschantz ◽

John Marelius ◽

Carmen Medina ◽

Micael Jacobsson ◽

Nico P. E. Vermeulen ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Interaction Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Linear Interaction ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations

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