Patent ID: 7702465

Claim:
A method for predicting the binding affinity of a peptide for a major histocompatibility (MHC) class I or class II molecule, the method being executed on a computer under the control of a program stored on the computer, comprising the following steps: a) receiving a representation of a complete or partial three-dimensional structure of a MHC class I or class II molecule, b) obtaining an ensemble of conformational representations of peptide backbone structures of said peptide, said conformational representations located within the binding site of said MHC molecule, c) modeling the side-chains of said peptide for each peptide backbone structure of said ensemble in relation to said MHC molecule, thereby obtaining an ensemble of modeled MHC/peptide complexes, d) evaluating the binding properties of said peptide for said MHC molecule, by using scoring function which combines at least: d1) average binding energy component obtained by evaluating one or more components of the potential energy of each complex of the ensemble of step c), d2) conformational entropy component obtained by evaluating the conformational entropy for the complete ensemble of modeled MHC/peptide complexes of step c), and e) outputting said evaluation to a user in a user-readable format.