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

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

Published: 2022-03-10 DOI: 10.1038/s41596-021-00676-1

protein:ligand binding

molecular dynamics

BFEE2

binding free energy

statistical mechanics

AI 解读

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Designing a reliable computational methodology to calculate protein:ligand standard binding free energies is extremely challenging. The large change in configurational enthalpy and entropy that accompanies the association of ligand and protein is notoriou
Introduction
Materials
Procedure 1: the geometric route
Procedure 2: the alchemical route
Troubleshooting
Timing
- Procedure 1: the geometrical route
- Procedure 2: the alchemical route
Anticipated results
References
ACKNOWLEDGMENTS
ACKNOWLEDGMENTS

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

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