Patent ID: RE44747

Claim:
A method for improved prediction of the region on the surface of a proteinaceous material representing a binding surface that associates with a predetermined binding molecule, comprising: (a) screening a peptide library with said predetermined binding molecule to identify a plurality of peptides that bind to said binding molecule; (b) determining the amino acid sequence of each identified peptide; (c) assigning a symbol to each class of amino acid residue represented in the library and presenting each said sequence as a string of said symbols; (d) calculating the frequency of occurrences of each tandem pair of symbols that exist in the strings of symbols presented in step (c); (e) identifying those tandem pairs of symbols, the number of occurrences of which is statistically significant; (f) mapping on a three-dimensional model of the proteinaceous material those pairs of amino acids represented by the tandem pairs of symbols identified in step (e), wherein a pair of amino acids is two amino acids, at least one of which is accessible to the surface of the proteinaceous material and whose alpha carbons are separated by no more than a predetermined distance; and (g) determining clusters of amino acid pairs mapped in (f), each amino acid pair in the cluster being topographically related to at least one other pair in the cluster, whereby each said cluster is a predicted region on the surface of the proteinaceous material representing said binding surface.