Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation

William E. Harte; David L. Beveridge

doi:10.1021/ja00063a005

Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation

Journal of the American Chemical Society ◽

10.1021/ja00063a005 ◽

1993 ◽

Vol 115 (10) ◽

pp. 3883-3886 ◽

Cited By ~ 40

Author(s):

William E. Harte ◽

David L. Beveridge

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Protease Inhibitor ◽

Active Site ◽

Dynamics Simulation ◽

Protonation State ◽

Hiv 1

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Determination of the Active Site Protonation State of β-Secretase from Molecular Dynamics Simulation and Docking Experiment: Implications for Structure-Based Inhibitor Design

Journal of the American Chemical Society ◽

10.1021/ja0304493 ◽

2003 ◽

Vol 125 (52) ◽

pp. 16416-16422 ◽

Cited By ~ 60

Author(s):

Hwangseo Park ◽

Sangyoub Lee

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Active Site ◽

Dynamics Simulation ◽

Inhibitor Design ◽

Protonation State ◽

Docking Experiment

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Molecular Docking and Molecular Dynamics Simulation Based Approach to Explore the Dual Inhibitor Against HIV-1 Reverse Transcriptase and Integrase

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207320666170615104703 ◽

2017 ◽

Vol 20 (8) ◽

Cited By ~ 11

Author(s):

Subhash Chander ◽

Rajan Kumar Pandey ◽

Ashok Penta ◽

Bhanwar Singh Choudhary ◽

Manish Sharma ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Reverse Transcriptase ◽

Dynamics Simulation ◽

Dual Inhibitor ◽

Simulation Based ◽

Hiv 1

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Three-dimensional structure of HIV-1 VIF constructed by comparative modeling and the function characterization analyzed by molecular dynamics simulation

Organic & Biomolecular Chemistry ◽

10.1039/b612050d ◽

2007 ◽

Vol 5 (4) ◽

pp. 617 ◽

Cited By ~ 21

Author(s):

Wei Lv ◽

Zhenming Liu ◽

Hongwei Jin ◽

Xianghui Yu ◽

Liangren Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Three Dimensional ◽

Comparative Modeling ◽

Dynamics Simulation ◽

Dimensional Structure ◽

Three Dimensional Structure ◽

Function Characterization ◽

Hiv 1

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Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution. [Erratum to document cited in CA118(21):208404x]

Biochemistry ◽

10.1021/bi00063a035 ◽

1993 ◽

Vol 32 (12) ◽

pp. 3196-3196 ◽

Cited By ~ 2

Author(s):

D. M. York ◽

T. A. Darden ◽

L. G. Pedersen ◽

M. W. Anderson

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Crystalline Environment ◽

Hiv 1

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Insights of inhibition mechanism of sifuvirtide and MT-sifuvirtide against wild and mutant HIV-1 envelope glycoprotein41: a molecular dynamics simulation and binding free energy study

Molecular Simulation ◽

10.1080/08927022.2020.1716978 ◽

2020 ◽

Vol 46 (6) ◽

pp. 429-439

Author(s):

Iruthayaraj Ancy ◽

Magudeeswaran Sivanandam ◽

Raju Kalaivani ◽

Poomani Kumaradhas

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Inhibition Mechanism ◽

Hiv 1

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Binding modes of diketo-acid inhibitors of HIV-1 integrase: A comparative molecular dynamics simulation study

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2011.04.002 ◽

2011 ◽

Vol 29 (7) ◽

pp. 956-964 ◽

Cited By ~ 25

Author(s):

Meilan Huang ◽

Guy H. Grant ◽

W. Graham Richards

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Dynamics Simulation ◽

Binding Modes ◽

Hiv 1

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Molecular Dynamics Simulation of HIV-1 gp41 and the N554D/S649A Double Mutation for Drug Resistance to Enfuvirtide

2009 3rd International Conference on Bioinformatics and Biomedical Engineering ◽

10.1109/icbbe.2009.5163084 ◽

2009 ◽

Author(s):

Jian Jun Tan ◽

Ting Guang Sun ◽

Wei Zu Chen ◽

Cun Xin Wang

Keyword(s):

Molecular Dynamics ◽

Drug Resistance ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Double Mutation ◽

Hiv 1

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New 1(2H)-phthalazinone derivatives as potent nonpeptidic HIV-1 protease inhibitors: molecular docking studies, molecular dynamics simulation, oral bioavailability and ADME prediction

Molecular Simulation ◽

10.1080/08927022.2015.1067808 ◽

2015 ◽

Vol 42 (8) ◽

pp. 628-641 ◽

Cited By ~ 2

Author(s):

Dariusz Sroczyński ◽

Zbigniew Malinowski ◽

Aleksandra K. Szcześniak ◽

Wanda Pakulska

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamics Simulation ◽

Protease Inhibitors ◽

Oral Bioavailability ◽

Docking Studies ◽

Dynamics Simulation ◽

Molecular Docking Studies ◽

Adme Prediction ◽

Hiv 1

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Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase

BMC Structural Biology ◽

10.1186/s12900-017-0075-y ◽

2017 ◽

Vol 17 (1) ◽

Cited By ~ 5

Author(s):

Alexander V. Popov ◽

Anton V. Endutkin ◽

Yuri N. Vorobjev ◽

Dmitry O. Zharkov

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Active Site ◽

Dynamics Simulation ◽

Dna Glycosylase

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Anti-HIV-1 Activity Prediction of Novel Gp41 Inhibitors Using Structure-Based Virtual Screening and Molecular Dynamics Simulation

Molecular Informatics ◽

10.1002/minf.201600060 ◽

2016 ◽

Vol 36 (3) ◽

pp. 1600060 ◽

Cited By ~ 7

Author(s):

Saghi Sepehri ◽

Lotfollah Saghaie ◽

Afshin Fassihi

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Virtual Screening ◽

Dynamics Simulation ◽

Activity Prediction ◽

Anti Hiv ◽

Hiv 1

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