Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation

Jianfeng Pei; Qi Wang; Jiaju Zhou; Luhua Lai

doi:10.1002/prot.20198

Estimating protein-ligand binding free energy: Atomic solvation parameters for partition coefficient and solvation free energy calculation

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20198 ◽

2004 ◽

Vol 57 (4) ◽

pp. 651-664 ◽

Cited By ~ 39

Author(s):

Jianfeng Pei ◽

Qi Wang ◽

Jiaju Zhou ◽

Luhua Lai

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Partition Coefficient ◽

Binding Free Energy ◽

Solvation Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Solvation Parameters

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Protein−Ligand Binding Free Energy Calculation by the Smooth Reaction Path Generation (SRPG) Method

Journal of Chemical Information and Modeling ◽

10.1021/ci9002156 ◽

2009 ◽

Vol 49 (8) ◽

pp. 1944-1951 ◽

Cited By ~ 17

Author(s):

Yoshifumi Fukunishi ◽

Daisuke Mitomo ◽

Haruki Nakamura

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Reaction Path ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Path Generation ◽

Binding Free Energy Calculation

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Trypsin-ligand binding free energy calculation with AMOEBA

10.1109/iembs.2009.5335108 ◽

2009 ◽

Cited By ~ 3

Author(s):

Yue Shi ◽

Dian Jiao ◽

M.J. Schnieders ◽

Pengyu Ren

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation

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A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1–Ligand Binding Free Energy Calculation

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b00609 ◽

2019 ◽

Vol 59 (9) ◽

pp. 4018-4033 ◽

Cited By ~ 5

Author(s):

Eko Aditya Rifai ◽

Marc van Dijk ◽

Nico P. E. Vermeulen ◽

Arry Yanuar ◽

Daan P. Geerke

Keyword(s):

Free Energy ◽

Ligand Binding ◽

Interaction Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Linear Interaction ◽

Linear Interaction Energy ◽

Binding Free Energy Calculation

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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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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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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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Membrane Permeability from Solvation Free Energy Calculation of Cyclic Dipeptide (CDP)

Journal of Computer Chemistry Japan ◽

10.2477/jccj.2021-0008 ◽

2020 ◽

Vol 19 (4) ◽

pp. 125-127

Author(s):

Kohki YANAGI ◽

Ryuhei HARADA ◽

Yuki MITSUTA ◽

Yasuteru SHIGETA

Keyword(s):

Free Energy ◽

Membrane Permeability ◽

Solvation Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Cyclic Dipeptide

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Protein-Protein Interactions: Interface Analysis, Binding Free Energy Calculation and Interaction Design

Acta Physico-Chimica Sinica ◽

10.3866/pku.whxb20100725 ◽

2010 ◽

Vol 26 (07) ◽

pp. 1988-1997

Author(s):

BAI Hong-Jun ◽

◽

LAI Lu-Hua ◽

◽

...

Keyword(s):

Free Energy ◽

Protein Interactions ◽

Interaction Design ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Protein Protein Interactions ◽

Interface Analysis ◽

Binding Free Energy Calculation

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