The process of Pep-3D-Search [4] is illustrated in Figure 1a . Given a 3D structure of an antigen, Pep-3D-Search identifies all the surface residues and creates a surface graph using those residues. An ACO algorithm is then used to search the matched paths on the antigen surface with respect to the query peptides or motif. Each matched path is then rated by its P-value score [4] . A set of highly rated paths are selected to create a weighted graph of resultant paths. The Depth-First Search (DFS) algorithm is finally used to screen and cluster this weighted graph to define the candidate epitopes.