title: Ligand binding affinity prediction by linear interaction energy methods.
abstract: A recent method for estimating ligand binding affinities is extended. This method employs averages of interaction potential energy terms from molecular dynamics simulations or other thermal conformational sampling techniques. Incorporation of systematic deviations from electrostatic linear response, derived from free energy perturbation studies, into the absolute binding free energy expression significantly enhances the accuracy of the approach. This type of method may be useful for computational prediction of ligand binding strengths, e.g., in drug design applications.
authors.affiliation: Department of Molecular Biology, Uppsala University, Sweden.
authors.forename: T
authors.initials: T
authors.lastname: Hansson
authors.forename: J
authors.initials: J
authors.lastname: Marelius
authors.forename: J
authors.initials: J
authors.lastname: Aqvist
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D015195:Drug Design; D066298:In Vitro Techniques; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins