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Sakae Y , Zhang BW , Levy RM , Deng N
Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses
J Comput Chem. 2020 Jan 5;41(1) :56-68
PMID: 31621932 PMCID: PMC7140983 URL: https://www.ncbi.nlm.nih.gov/pubmed/31621932
AbstractWe propose a free energy calculation method for receptor-ligand binding, which have multiple binding poses that avoids exhaustive enumeration of the poses. For systems with multiple binding poses, the standard procedure is to enumerate orientations of the binding poses, restrain the ligand to each orientation, and then, calculate the binding free energies for each binding pose. In this study, we modify a part of the thermodynamic cycle in order to sample a broader conformational space of the ligand in the binding site. This modification leads to more accurate free energy calculation without performing separate free energy simulations for each binding pose. We applied our modification to simple model host-guest systems as a test, which have only two binding poses, by using a single decoupling method (SDM) in implicit solvent. The results showed that the binding free energies obtained from our method without knowing the two binding poses were in good agreement with the benchmark results obtained by explicit enumeration of the binding poses. Our method is applicable to other alchemical binding free energy calculation methods such as the double decoupling method (DDM) in explicit solvent. We performed a calculation for a protein-ligand system with explicit solvent using our modified thermodynamic path. The results of the free energy simulation along our modified path were in good agreement with the results of conventional DDM, which requires a separate binding free energy calculation for each of the binding poses of the example of phenol binding to T4 lysozyme in explicit solvent. (c) 2019 Wiley Periodicals, Inc.
Notes1096-987x Sakae, Yoshitake ORCID: https://orcid.org/0000-0001-7204-2021 Zhang, Bin W Levy, Ronald M Deng, Nanjie GM30580/GF/NIH HHS/United States S10-OD020095-01/GF/NIH HHS/United States Tg-mcb100145/nsf 1665032/nsf Journal Article United States J Comput Chem. 2020 Jan 5;41(1):56-68. doi: 10.1002/jcc.26078. Epub 2019 Oct 17.