Patent Document ID: 20090326878
Application ID: 11695494
Patent Flag: 0

Claim One:
1. A method for predicting the affinity of a ligand for a receptor comprising the steps of: a. selecting a ligand; b. selecting a receptor; c. selecting a first and a second portion of said receptor; d. selecting a third and fourth portion of said receptor; e. identifying at least one first local energy minimum for conformations of the ligand by using a computation method with a first energy model; f. identifying at least one second local energy minimum for conformations of the receptor by using a computation method with a second energy model, wherein the first portion of said receptor is treated as restrained and the second portion of said receptor is treated as unrestrained; g. identifying at least one third local energy minimum for conformations of a complex of said receptor and said ligand, wherein said receptor is complexed to said ligand, by using a computation method with a third energy model, wherein the third portion of said receptor is treated as restrained and the fourth portion of said receptor is treated as unrestrained; h. computing an energy of binding between the ligand and the receptor, based on the first, second and third energy minima; and i. outputting an affinity of the ligand for the receptor.