Perhaps the best strategy is to combine two or more methods together to deal with various cases of epitope-peptide mapping in practice. Pepitope [17] combined both PepSurf and Mapitope [1] together as a Web tool for epitope-peptide mapping so as to complement with each other. The algorithm used in PepSurf maps the affinity-selected peptides directly back to the protein surface. The most significant alignments are then clustered into a patch, from which the epitope location is inferred. In Mapitope, each peptide is first deconvoluted to amino acid pairs, and those pairs of residues that are significantly overrepresented in the panel of peptides are then identified. Epitopic regions are finally predicted through searching for a cluster of those enriched pairs on the 3D structure of the antigen.