Chain-Increment Method for Free-Energy Computation of a Polymer with All-Atom Molecular Simulations

Kazuo Yamada; Nobuyuki Matubayasi

doi:10.1021/acs.macromol.9b01952

Chain-Increment Method for Free-Energy Computation of a Polymer with All-Atom Molecular Simulations

Macromolecules ◽

10.1021/acs.macromol.9b01952 ◽

2020 ◽

Vol 53 (3) ◽

pp. 775-788

Author(s):

Kazuo Yamada ◽

Nobuyuki Matubayasi

Keyword(s):

Free Energy ◽

Molecular Simulations ◽

Energy Computation ◽

Free Energy Computation

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Free Energy Computation of Particles with Membrane-Mediated Interactions Via Langevin Dynamics

SSRN Electronic Journal ◽

10.2139/ssrn.3973407 ◽

2021 ◽

Author(s):

Tobias Kies ◽

Carsten Gräser ◽

Luigi Delle Site ◽

Ralf Kornhuber

Keyword(s):

Free Energy ◽

Langevin Dynamics ◽

Energy Computation ◽

Free Energy Computation

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Approximate Optimal Controls via Instanton Expansion for Low Temperature Free Energy Computation

Multiscale Modeling and Simulation ◽

10.1137/20m1385809 ◽

2021 ◽

Vol 19 (3) ◽

pp. 1310-1332

Author(s):

Grégoire Ferré ◽

Tobias Grafke

Keyword(s):

Free Energy ◽

Low Temperature ◽

Optimal Controls ◽

Energy Computation ◽

Free Energy Computation

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Protein-drug binding free energy computation incorporating protein flexibility and its significance in predicting mutation-induced drug resistance in oncogenic kinases

10.1021/scimeetings.0c04059 ◽

2020 ◽

Author(s):

Mitsugu Araki ◽

Yasushi Okuno

Keyword(s):

Drug Resistance ◽

Free Energy ◽

Binding Free Energy ◽

Protein Flexibility ◽

Drug Binding ◽

Protein Drug ◽

Energy Computation ◽

Free Energy Computation

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Identification and characterization ofE.coliribosomal binding sites by free energy computation

Nucleic Acids Research ◽

10.1093/nar/21.17.4019 ◽

1993 ◽

Vol 21 (17) ◽

pp. 4019-4023 ◽

Cited By ~ 61

Author(s):

Tamar Schurr ◽

Eyal Nadir ◽

Hanah Margalit

Keyword(s):

Free Energy ◽

Binding Sites ◽

Energy Computation ◽

Identification And Characterization ◽

Free Energy Computation

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Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.1c00221 ◽

2021 ◽

Author(s):

Dmitrii M. Nikolaev ◽

Madushanka Manathunga ◽

Yoelvis Orozco-Gonzalez ◽

Andrey A. Shtyrov ◽

Yansel Omar Guerrero Martínez ◽

...

Keyword(s):

Free Energy ◽

Configuration Model ◽

Energy Computation ◽

Free Energy Computation

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Limits of Free Energy Computation for Protein−Ligand Interactions

Journal of Chemical Theory and Computation ◽

10.1021/ct100102q ◽

2010 ◽

Vol 6 (5) ◽

pp. 1769-1776 ◽

Cited By ~ 61

Author(s):

Kenneth M. Merz

Keyword(s):

Free Energy ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Energy Computation ◽

Free Energy Computation

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DeepBAR: A Fast and Exact Method for Binding Free Energy Computation

The Journal of Physical Chemistry Letters ◽

10.1021/acs.jpclett.1c00189 ◽

2021 ◽

Vol 12 (10) ◽

pp. 2509-2515

Author(s):

Xinqiang Ding ◽

Bin Zhang

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Exact Method ◽

Energy Computation ◽

Free Energy Computation

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Investigation of Inhibitory Potency of BHQ Derivatives as SERCA Inhibitors to use as Potential Drugs as well as Tools to Study the SERCA Function: Binding Free Energy Computation using FEP/MD Simulations

Biophysical Journal ◽

10.1016/j.bpj.2015.11.2894 ◽

2016 ◽

Vol 110 (3) ◽

pp. 540a-541a

Author(s):

Manori Jayasinghe ◽

Qi Wang ◽

Andrew Schirmer ◽

George Stan

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Md Simulations ◽

Inhibitory Potency ◽

Energy Computation ◽

Free Energy Computation

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Protein-drug binding free energy computation incorporating protein flexibility and its significance in predicting mutation-induced drug resistance in oncogenic kinases

10.1021/scimeetings.0c04058 ◽

2020 ◽

Author(s):

Mitsugu Araki ◽

Yasushi Okuno

Keyword(s):

Drug Resistance ◽

Free Energy ◽

Binding Free Energy ◽

Protein Flexibility ◽

Drug Binding ◽

Protein Drug ◽

Energy Computation ◽

Free Energy Computation

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Effect of conformational flexibility of protein-ligand binding free energy computation and its significance in predicting mutation-induced drug sensitivity changes in oncogenic kinases

10.1021/scimeetings.0c06667 ◽

2020 ◽

Author(s):

Yasushi Okuno ◽

Mitsugu Araki

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Drug Sensitivity ◽

Binding Free Energy ◽

Conformational Flexibility ◽

Sensitivity Changes ◽

Energy Computation ◽

Free Energy Computation

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