An algorithmic flowchart of Pep-3D-Search. Given the 3D structure of an antigen, Pep-3D-Search identifies all the surface residues and creates a surface graph. After that, it can be used in two modes: mimotope or motif. In mimotope mode, every mimotope received as an input is aligned to the antigen surface and the epitope candidates are obtained through screening and clustering of the matched paths. In motif mode, a motif received as an input is mapped on to the antigen surface. Subsequently, the top scoring paths are output directly as the epitope candidates.