Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations

M. Lepšík; Z. Kříž; Z. Havlas

doi:10.1002/prot.20192

Efficiency of a second-generation HIV-1 protease inhibitor studied by molecular dynamics and absolute binding free energy calculations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20192 ◽

2004 ◽

Vol 57 (2) ◽

pp. 279-293 ◽

Cited By ~ 51

Author(s):

M. Lepšík ◽

Z. Kříž ◽

Z. Havlas

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Protease Inhibitor ◽

Second Generation ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Hiv 1 ◽

Absolute Binding Free Energy

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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 ◽

Cited By ~ 6

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 ◽

Hiv 1

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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 ◽

Cited By ~ 234

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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Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations

Journal of Molecular Modeling ◽

10.1007/s00894-006-0121-3 ◽

2006 ◽

Vol 13 (2) ◽

pp. 297-304 ◽

Cited By ~ 29

Author(s):

Heike Meiselbach ◽

Anselm H. C. Horn ◽

Thomas Harrer ◽

Heinrich Sticht

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Hiv 1

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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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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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Dual Inhibitors for Aspartic Proteases HIV-1 PR and Renin: Advancements in AIDS–Hypertension–Diabetes Linkage via Molecular Dynamics, Inhibition Assays, and Binding Free Energy Calculations

Journal of Medicinal Chemistry ◽

10.1021/jm300180r ◽

2012 ◽

Vol 55 (12) ◽

pp. 5784-5796 ◽

Cited By ~ 28

Author(s):

Haralambos Tzoupis ◽

Georgios Leonis ◽

Grigorios Megariotis ◽

Claudiu T. Supuran ◽

Thomas Mavromoustakos ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Aspartic Proteases ◽

Energy Calculations ◽

Dual Inhibitors ◽

Binding Free Energy Calculations ◽

Hiv 1

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Investigating the Selectivity of Allosteric Inhibitors for Mutant T790M EGFR over Wild Type Using Molecular Dynamics and Binding Free Energy Calculations

ACS Omega ◽

10.1021/acsomega.8b03256 ◽

2018 ◽

Vol 3 (12) ◽

pp. 16556-16562 ◽

Cited By ~ 2

Author(s):

Annachiara Tinivella ◽

Giulio Rastelli

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Wild Type ◽

Allosteric Inhibitors ◽

Energy Calculations ◽

Binding Free Energy Calculations

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Absolute Binding Free Energy Calculations to Improve the Accuracy of Near-Native Ligand Pose Predictions

Biophysical Journal ◽

10.1016/j.bpj.2011.11.3379 ◽

2012 ◽

Vol 102 (3) ◽

pp. 620a

Author(s):

Hui Sun Lee ◽

Sunhwan Jo ◽

Wonpil Im

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Native Ligand ◽

Absolute Binding Free Energy

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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 ◽

Cited By ~ 1

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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Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.0c00634 ◽

2020 ◽

Vol 16 (11) ◽

pp. 7160-7172

Author(s):

Marina Macchiagodena ◽

Marco Pagliai ◽

Maurice Karrenbrock ◽

Guido Guarnieri ◽

Francesco Iannone ◽

...

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Main Protease ◽

Double System ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

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