Relative binding free energy calculations of inhibitors to two mutants (Glu46— Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches

Protein Engineering Design and Selection ◽

10.1093/protein/4.3.233 ◽

1991 ◽

Vol 4 (3) ◽

pp. 233-243 ◽

Author(s):

Shuichi Hirono ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Free Energy Perturbation ◽

Ribonuclease T1 ◽

Energy Calculations ◽

Relative Binding ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.340160303 ◽

1993 ◽

Vol 16 (3) ◽

pp. 226-245 ◽

Author(s):

Shuichi Miyamoto ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Free Energy Perturbation ◽

Energy Calculations ◽

Relative Binding ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

Journal of Chemical Theory and Computation ◽

10.1021/ct1001768 ◽

2010 ◽

Vol 6 (9) ◽

pp. 2559-2565 ◽

Author(s):

Wei Jiang ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Ligand-Induced Structural Changes in TEM-1 Probed by Molecular Dynamics and Relative Binding Free Energy Calculations

Journal of Chemical Information and Modeling ◽

10.1021/ci400269d ◽

2013 ◽

Vol 53 (10) ◽

pp. 2648-2658 ◽

Author(s):

A. C. Pimenta ◽

J. M. Martins ◽

R. Fernandes ◽

I. S. Moreira

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Structural Changes ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Relative Binding ◽

Binding Free Energy Calculations

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Faculty Opinions recommendation of Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

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

10.3410/f.718636459.8572054 ◽

2011 ◽

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Faculty Opinions recommendation of Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations.

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

10.3410/f.8162956.8572054 ◽

2011 ◽

Author(s):

Martin Zacharias

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Replica Exchange ◽

Free Energy Perturbation ◽

Replica Exchange Molecular Dynamics ◽

Hamiltonian Replica Exchange ◽

Binding Free Energy Calculations ◽

Energy Perturbation

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Calculation of the relative binding free energy of 2′GMP and 2′AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches

Journal of Molecular Biology ◽

10.1016/0022-2836(90)90315-d ◽

1990 ◽

Vol 212 (1) ◽

pp. 197-209 ◽

Author(s):

Shuichi Hirono ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Perturbation ◽

Ribonuclease T1 ◽

Relative Binding ◽

Energy Perturbation

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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 ◽

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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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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Molecular dynamics guided insight, binding free energy calculations and pharmacophore-based virtual screening for the identification of potential VEGFR2 inhibitors

Journal of Receptors and Signal Transduction ◽

10.1080/10799893.2019.1690509 ◽

2019 ◽

Vol 39 (5-6) ◽

pp. 415-433

Author(s):

Ekta Rathi ◽

Avinash Kumar ◽

Suvarna G. Kini

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Virtual Screening ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations

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