Patent Document ID: 8140268
Application ID: 11695494
Patent Flag: 1

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, wherein said portions are putatively involved in ligand binding; (d) identifying at least one first local energy minimum for conformations of the ligand by using a computation method with a first energy model; (e) 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; (f) 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 first portion of said receptor is treated as restrained and the second portion of said receptor is treated as unrestrained; (g) computing an energy of binding, using computer hardware or software, between the ligand and the receptor, based on the first, second and third energy minima; and (h) outputting an affinity of the ligand for the receptor.