Free-Energy Calculation Using Nonequilibrium Simulations

Free Energy Calculation Methods of Biomolecules

ACTA BIOPHYSICA SINICA ◽

10.3724/sp.j.1260.2011.00395 ◽

2011 ◽

Vol 27 (5) ◽

pp. 395-402 ◽

Cited By ~ 1

Author(s):

Changjun CHEN ◽

Yanzhao HUANG ◽

Yi XIAO

Keyword(s):

Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Calculation Methods

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Predicting gas selectivity in organic ionic plastic crystals by free energy calculations

RSC Advances ◽

10.1039/d1ra01844b ◽

2021 ◽

Vol 11 (32) ◽

pp. 19623-19629

Author(s):

Vinay S. Kandagal ◽

Jennifer M. Pringle ◽

Maria Forsyth ◽

Fangfang Chen

Keyword(s):

Free Energy ◽

Gas Separation ◽

Free Energy Calculations ◽

Free Energy Calculation ◽

Energy Calculation ◽

Plastic Crystal ◽

Plastic Crystals ◽

New Type ◽

Gas Molecules ◽

Gas Selectivity

The free energy calculation shows the different free energy changes of the adsorption and absorption of gas molecules into an organic ionic plastic crystal, successfully predicting the gas selectivity of this new type of gas separation material.

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Free energy calculation of the effects of the fluorinated phosphorus ligands on the C–H and C–C reductive elimination from Pt(IV)

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2007.12.012 ◽

2008 ◽

Vol 852 (1-3) ◽

pp. 54-61 ◽

Cited By ~ 6

Author(s):

Carine Michel ◽

Anne Milet

Keyword(s):

Free Energy ◽

Reductive Elimination ◽

Free Energy Calculation ◽

Energy Calculation ◽

Phosphorus Ligands

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1J1015 Web application for fast solvation free energy calculation using PC cluster

Seibutsu Butsuri ◽

10.2142/biophys.42.s54_3 ◽

2002 ◽

Vol 42 (supplement2) ◽

pp. S54

Author(s):

Y. Yamashita ◽

M. Masuya

Keyword(s):

Free Energy ◽

Web Application ◽

Solvation Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Pc Cluster

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Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

The Journal of Chemical Physics ◽

10.1063/1.1590311 ◽

2003 ◽

Vol 119 (6) ◽

pp. 3559-3566 ◽

Cited By ~ 501

Author(s):

Sanghyun Park ◽

Fatemeh Khalili-Araghi ◽

Emad Tajkhorshid ◽

Klaus Schulten

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Steered Molecular Dynamics ◽

Free Energy Calculation ◽

Energy Calculation ◽

Dynamics Simulations ◽

Jarzynski’S Equality

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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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Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation

Food Science & Nutrition ◽

10.1002/fsn3.2253 ◽

2021 ◽

Author(s):

Ruiyao Chen ◽

Yulu Miao ◽

Xuan Hao ◽

Bei Gao ◽

Mingzhe Ma ◽

...

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Inhibitory Peptides ◽

Binding Free Energy Calculation ◽

Ace Inhibitory Peptides ◽

Ace Inhibitory

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MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.1c01010 ◽

2021 ◽

Author(s):

Haochuan Chen ◽

Han Liu ◽

Heying Feng ◽

Haohao Fu ◽

Wensheng Cai ◽

...

Keyword(s):

Machine Learning ◽

Free Energy ◽

Dimensionality Reduction ◽

Free Energy Calculation ◽

Energy Calculation

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2P006 Relative binding free energy calculation with a free energy variational principle and its application to FK506-binding protein inhibitors(Proteins-structure and structure-function relationship,Oral Presentations)

Seibutsu Butsuri ◽

10.2142/biophys.47.s114_3 ◽

2007 ◽

Vol 47 (supplement) ◽

pp. S114

Author(s):

Yuichi Shine ◽

Yasutomo Minami ◽

Takeshi Kikuchi

Keyword(s):

Free Energy ◽

Variational Principle ◽

Structure Function ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Fk506 Binding Protein ◽

Relative Binding ◽

Function Relationship ◽

Oral Presentations

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Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Journal of the American Chemical Society ◽

10.1021/ja512751q ◽

2015 ◽

Vol 137 (7) ◽

pp. 2695-2703 ◽

Cited By ~ 493

Author(s):

Lingle Wang ◽

Yujie Wu ◽

Yuqing Deng ◽

Byungchan Kim ◽

Levi Pierce ◽

...

Keyword(s):

Free Energy ◽

Drug Discovery ◽

Ligand Binding ◽

Force Field ◽

Free Energy Calculation ◽

Energy Calculation ◽

Reliable Prediction

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