biostudies-literatureMingione VRNCI NIH HHSNIH HHSNIGMS NIH HHS167628https://www.ebi.ac.uk/biostudies/studies/S-EPMC9713948biostudies-literatureUnknown434(17)Allostery plays a primary role in regulating protein activity, making it an important mechanism in human disease and drug discovery. Identifying allosteric regulatory sites to explore their biological significance and therapeutic potential is invaluable to drug discovery; however, identification remains a challenge. Allosteric sites are often "cryptic" without clear geometric or chemical features. Since allosteric regulatory sites are often less conserved in protein kinases than the orthosteric ATP binding site, allosteric ligands are commonly more specific than ATP competitive inhibitors. We present a generalizable computational protocol to predict allosteric ligand binding sites based on unbiased ligand binding simulation trajectories. We demonstrate the feasibility of this protocol by rJournal of molecular biologyValidation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations.PMC9713948T32 GM008444T32 GM127253R35 GM119437S10 OD028478F30 CA260771Shan YFoda ZHSeeliger MAMingione VRRangwala AMPaung YPhilipose HfalseValidation of an Allosteric Binding Site of Src Kinase Identified by Unbiased Ligand Binding Simulations.Allostery plays a primary role in regulating protein activity, making it an important mechanism in human disease and drug discovery. Identifying allosteric regulatory sites to explore their biological significance and therapeutic potential is invaluable to drug discovery; however, identification remains a challenge. Allosteric sites are often "cryptic" without clear geometric or chemical features. Since allosteric regulatory sites are often less conserved in protein kinases than the orthosteric ATP binding site, allosteric ligands are commonly more specific than ATP competitive inhibitors. We present a generalizable computational protocol to predict allosteric ligand binding sites based on unbiased ligand binding simulation trajectories. We demonstrate the feasibility of this protocol by r2022-01-01T00:00:00Z2022 Sep2026-05-28T09:39:33.405Z2025-04-07T06:22:06.105ZS-EPMC97139483559516910.1016/j.jmb.2022.167628