Protein Engineering Design and Selection · 1994 · 1.2K citations · 0 references
PharmacyBiophysicsMedicinal ChemistryComputational ChemistryComputational ThermodynamicsDrug DesignBinding AffinityBinding Affinity PredictionBinding ThermodynamicsMolecular DynamicsMolecular Property PredictionMolecular SimulationDrug - Target Binding Affinity PredictionLinear ApproximationMolecular Dynamics Free Energy CalculationsMolecular Dynamics-based Affinity EstimationProtein-ligand Binding Affinity PredictionProtein-ligand Binding Free Energy CalculationsProtein-ligand Binding ThermodynamicsRelative Free Energy
A new semi-empirical method for calculating free energies of binding from molecular dynamics (MD) simulations is presented. It is based on standard thermodynamic cycles and on a linear approximation of polar and non-polar free energy contributions from the corresponding MD averages. The method is tested on a set of endothiapepsin inhibitors and found to give accurate results both for absolute as well as relative free energies.