Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. I. Free energy perturbation and thermodynamic integration along a coupling parameter

Tatsuhiko Miyata; Yasuhiro Ikuta; Fumio Hirata

doi:10.1063/1.3462276

Free energy calculation using molecular dynamics simulation combined with the three dimensional reference interaction site model theory. I. Free energy perturbation and thermodynamic integration along a coupling parameter

The Journal of Chemical Physics ◽

10.1063/1.3462276 ◽

2010 ◽

Vol 133 (4) ◽

pp. 044114 ◽

Cited By ~ 23

Author(s):

Tatsuhiko Miyata ◽

Yasuhiro Ikuta ◽

Fumio Hirata

Keyword(s):

Free Energy ◽

Coupling Parameter ◽

Three Dimensional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Free Energy Perturbation ◽

Energy Calculation ◽

Interaction Site ◽

Site Model ◽

Energy Perturbation

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Free energy calculation using molecular dynamics simulation combined with the three-dimensional reference interaction site model theory. II. Thermodynamic integration along a spatial reaction coordinate

The Journal of Chemical Physics ◽

10.1063/1.3532078 ◽

2011 ◽

Vol 134 (4) ◽

pp. 044127 ◽

Cited By ~ 15

Author(s):

Tatsuhiko Miyata ◽

Yasuhiro Ikuta ◽

Fumio Hirata

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Model Theory ◽

Three Dimensional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Interaction Site ◽

Site Model

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Binding free energy calculation of human beta defensin 3 with negatively charged lipid bilayer using free energy perturbation method

Biophysical Chemistry ◽

10.1016/j.bpc.2021.106662 ◽

2021 ◽

pp. 106662

Author(s):

Ann Brewer ◽

Liqun Zhang

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Lipid Bilayer ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Free Energy Perturbation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Energy Perturbation

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Toward Accurate Solvation Free Energy Calculation with the Reference Interaction Site Model Self-Consistent Field: Introduction of a New Bridge Function

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.8b00314 ◽

2018 ◽

Vol 14 (6) ◽

pp. 3272-3278 ◽

Cited By ~ 8

Author(s):

D. Yokogawa

Keyword(s):

Free Energy ◽

Solvation Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Interaction Site ◽

Bridge Function ◽

Site Model ◽

Consistent Field ◽

Self Consistent ◽

Self Consistent Field

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3D-QSAR, docking, molecular dynamics simulation and free energy calculation studies of some pyrimidine derivatives as novel JAK3 inhibitors

Arabian Journal of Chemistry ◽

10.1016/j.arabjc.2017.09.009 ◽

2020 ◽

Vol 13 (1) ◽

pp. 1052-1078 ◽

Cited By ~ 9

Author(s):

Anand Balupuri ◽

Pavithra K. Balasubramanian ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Pyrimidine Derivatives

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Efficient Free-Energy Calculation of Proton Transfer by Constrained Density Functional Theory and Geometrically Restrained Molecular Dynamics Simulation

Chemistry Letters ◽

10.1246/cl.210132 ◽

2021 ◽

Author(s):

Tatsuya Joutsuka ◽

Koji Ando

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Density Functional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Functional Theory

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Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

Molecular Pharmaceutics ◽

10.1021/mp900131p ◽

2009 ◽

Vol 7 (1) ◽

pp. 75-85 ◽

Cited By ~ 57

Author(s):

Huanxiang Liu ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Influenza Virus ◽

Molecular Dynamics Simulation ◽

Molecular Basis ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Virus Rna ◽

Essential Subunit

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Insights into the mechanism of inhibition of phospholipase A2 by resveratrol: An extensive molecular dynamics simulation and binding free energy calculation

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107649 ◽

2020 ◽

Vol 100 ◽

pp. 107649

Author(s):

Sajedeh Sharifpour ◽

Sara Fakhraee ◽

Reza Behjatmanesh-Ardakani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Phospholipase A2 ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Mechanism Of Inhibition

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A relative free energy calculation method with ion screening effect using molecular dynamics simulation

Journal of Molecular Graphics ◽

10.1016/0263-7855(94)80025-1 ◽

1994 ◽

Vol 12 (1) ◽

pp. 56-57

Author(s):

K. Tazaki ◽

J. Doi

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Calculation Method ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Screening Effect ◽

Relative Free Energy

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Free Energy Calculation of Protein Conformational Changes using Parallel Cascade Selection Molecular Dynamics Simulation and Markov State Model

Biophysical Journal ◽

10.1016/j.bpj.2013.11.2300 ◽

2014 ◽

Vol 106 (2) ◽

pp. 408a

Author(s):

Yasutaka Nishihara ◽

Ryuhei Harada ◽

Akio Kitao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Conformational Changes ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Markov State Model ◽

Markov State ◽

Protein Conformational Changes

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Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory

The Journal of Chemical Physics ◽

10.1063/1.2904865 ◽

2008 ◽

Vol 128 (18) ◽

pp. 185102 ◽

Cited By ~ 12

Author(s):

Yoshiteru Yonetani ◽

Yutaka Maruyama ◽

Fumio Hirata ◽

Hidetoshi Kono

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Computational Methods ◽

Model Theory ◽

Three Dimensional ◽

Dynamics Simulation ◽

Interaction Site ◽

Site Model ◽

Dna Hydration ◽

Reference Interaction Site

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