Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations-Reference-Cited by-同舟云学术

Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations

Published:2022-03-11 Issue:4 Volume:17 Page:1114-1141
ISSN:1754-2189
Container-title:Nature Protocols
language:en
Short-container-title:Nat Protoc

Author:

Fu Haohao,Chen Haochuan^ORCID,Blazhynska Marharyta^ORCID,Goulard Coderc de Lacam Emma,Szczepaniak Florence,Pavlova Anna,Shao Xueguang,Gumbart James C.,Dehez François,Roux Benoît,Cai Wensheng^ORCID,Chipot Christophe

Funder

Agence Nationale de la Recherche

U.S. Department of Health & Human Services | National Institutes of Health

National Natural Science Foundation of China

National Science Foundation

Publisher

Springer Science and Business Media LLC

Subject

General Biochemistry, Genetics and Molecular Biology

Link

https://www.nature.com/articles/s41596-021-00676-1.pdf

Reference80 articles.

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2. Chodera, J. D. & Mobley, D. L. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu. Rev. Biophys. 42, 121–142 (2013).

3. Li, A. & Gilson, M. K. Protein-ligand binding enthalpies from near-millisecond simulations: analysis of a preorganization paradox. J. Chem. Phys. 149, 72311 (2018).

4. de Ruiter, A. & Oostenbrink, C. Advances in the calculation of binding free energies. Curr. Opin. Struct. Biol. 61, 207–212 (2020).

5. Chipot, C. Frontiers in free-energy calculations of biological systems. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 71–89 (2014).

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