Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.22687 ◽

2010 ◽

pp. NA-NA ◽

Cited By ~ 36

Author(s):

Nidhi Singh ◽

Arieh Warshel

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

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Absolute Binding Free Energy Calculations to Improve the Accuracy of Near-Native Ligand Pose Predictions

Biophysical Journal ◽

10.1016/j.bpj.2011.11.3379 ◽

2012 ◽

Vol 102 (3) ◽

pp. 620a

Author(s):

Hui Sun Lee ◽

Sunhwan Jo ◽

Wonpil Im

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Native Ligand ◽

Absolute Binding Free Energy

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Virtual Double-System Single-Box: A Nonequilibrium Alchemical Technique for Absolute Binding Free Energy Calculations: Application to Ligands of the SARS-CoV-2 Main Protease

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.0c00634 ◽

2020 ◽

Vol 16 (11) ◽

pp. 7160-7172

Author(s):

Marina Macchiagodena ◽

Marco Pagliai ◽

Maurice Karrenbrock ◽

Guido Guarnieri ◽

Francesco Iannone ◽

...

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Main Protease ◽

Double System ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

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Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-016-9968-2 ◽

2016 ◽

Vol 31 (1) ◽

pp. 71-85 ◽

Cited By ~ 6

Author(s):

Juyong Lee ◽

Florentina Tofoleanu ◽

Frank C. Pickard ◽

Gerhard König ◽

Jing Huang ◽

...

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Blind Challenge ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

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Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

Biophysical Journal ◽

10.1529/biophysj.106.084301 ◽

2006 ◽

Vol 91 (8) ◽

pp. 2798-2814 ◽

Cited By ~ 234

Author(s):

Jiyao Wang ◽

Yuqing Deng ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations ◽

Absolute Binding Free Energy

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A Thermodynamic Discrimination of Efficacy of GPCR Ligands using Absolute Binding Free Energy Calculations

Biophysical Journal ◽

10.1016/j.bpj.2013.11.4410 ◽

2014 ◽

Vol 106 (2) ◽

pp. 804a

Author(s):

Hui Sun Lee ◽

Wonpil Im

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

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Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

Journal of Chemical Theory and Computation ◽

10.1021/ct200684b ◽

2011 ◽

Vol 8 (1) ◽

pp. 47-60 ◽

Cited By ~ 46

Author(s):

Mauro Lapelosa ◽

Emilio Gallicchio ◽

Ronald M. Levy

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Conformational Transitions ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

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Faculty Opinions recommendation of Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

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

10.3410/f.1047901.497924 ◽

2006 ◽

Author(s):

Jeffry Madura

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Dynamics Simulations ◽

Absolute Binding Free Energy

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Binding free energy calculations of galectin-3–ligand interactions

Protein Engineering Design and Selection ◽

10.1093/protein/15.12.979 ◽

2002 ◽

Vol 15 (12) ◽

pp. 979-986 ◽

Cited By ~ 8

Author(s):

Tarun K. Mandal ◽

Chaitali Mukhopadhyay

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Ligand Interactions ◽

Galectin 3 ◽

Binding Free Energy Calculations

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Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome

The Journal of Physical Chemistry B ◽

10.1021/jp100579y ◽

2010 ◽

Vol 114 (29) ◽

pp. 9525-9539 ◽

Cited By ~ 43

Author(s):

Xiaoxia Ge ◽

Benoît Roux

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Bacterial Ribosome ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

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CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

Journal of Chemical Information and Modeling ◽

10.1021/ci300505n ◽

2012 ◽

Vol 53 (1) ◽

pp. 267-277 ◽

Cited By ~ 35

Author(s):

Sunhwan Jo ◽

Wei Jiang ◽

Hui Sun Lee ◽

Benoı̂t Roux ◽

Wonpil Im

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Energy Calculations ◽

Binding Free Energy Calculations ◽

Absolute Binding Free Energy

Download Full-text