biostudies-literatureGe YXtalPi Inc.PfizerNational Institute of General Medical SciencesNIGMS NIH HHS6482-6499https://www.ebi.ac.uk/biostudies/studies/S-EPMC9873352biostudies-literatureUnknown18(11)Water often plays a key role in mediating protein-ligand interactions. Understanding contributions from active-site water molecules to binding thermodynamics of a ligand is important in predicting binding free energies for ligand optimization. In this work, we tested a non-equilibrium switching method for absolute binding free energy calculations on water molecules in binding sites of 13 systems. We discuss the lessons we learned about identified issues that affected our calculations and ways to address them. This work fits with our larger focus on how to do accurate ligand binding free energy calculations when water rearrangements are very slow, such as rearrangements due to ligand modification (as in relative free energy calculations) or ligand binding (as in absolute free energy calculations). The method studied in this work can potentially be used to account for limited water sampling via providing endpoint corrections to free energy calculations using our calculated binding free energy of water.Journal of chemical theory and computationAbsolute Binding Free Energy Calculations for Buried Water Molecules.PMC9873352R01 GM124270R01 GM1088891R01GM124270-01A11R01GM108889-01Mobley DLGe YBaumann HMfalseAbsolute Binding Free Energy Calculations for Buried Water Molecules.Water often plays a key role in mediating protein-ligand interactions. Understanding contributions from active-site water molecules to binding thermodynamics of a ligand is important in predicting binding free energies for ligand optimization. In this work, we tested a non-equilibrium switching method for absolute binding free energy calculations on water molecules in binding sites of 13 systems. We discuss the lessons we learned about identified issues that affected our calculations and ways to address them. This work fits with our larger focus on how to do accurate ligand binding free energy calculations when water rearrangements are very slow, such as rearrangements due to ligand modification (as in relative free energy calculations) or ligand binding (as in absolute free energy calculations). The method studied in this work can potentially be used to account for limited water sampling via providing endpoint corrections to free energy calculations using our calculated binding free energy of water.2022-01-01T00:00:00Z2022 Nov2026-05-28T02:06:31.914Z2025-04-19T20:16:55.436ZS-EPMC98733523619745110.1021/acs.jctc.2c00658