The process of Pep-3D-Search has two unique features. Firstly, Pep-3D-Search is able to deal with both mimotope searching and motif mapping on the residue surface graph. Secondly, the adoption of ACO algorithm allows longer mimotopes or motifs to be processed with reasonable efficiency. The performance of Pep-3D-Search assessed by a few comparative studies [16] seems to be above the average level.