title: A new method for predicting binding affinity in computer-aided drug design.
abstract: 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.
authors.affiliation: Department of Molecular Biology, Uppsala University, Sweden.
authors.forename: J
authors.initials: J
authors.lastname: Aqvist
authors.forename: C
authors.initials: C
authors.lastname: Medina
authors.forename: J E
authors.initials: JE
authors.lastname: Samuelsson
mesh_terms: D016282:Aspartic Acid Endopeptidases / Q000037:antagonists & inhibitors*; D001665:Binding Sites; D003198:Computer Simulation; D015195:Drug Design; D004563:Electrochemistry; D015394:Molecular Structure; D011485:Protein Binding; D013816:Thermodynamics
chemical_list: D016282:Aspartic Acid Endopeptidases; C042466:Endothia aspartic proteinase