The essential idea of graph search methods is to find a group of simple paths on a graph generated from the residues on the surface of a protein and find out some paths from the graph best matched to the query peptides derived from in vitro screening against a target antibody [6] . Searching in Pep-3D-Search [4] is achieved through an algorithm based on ant colony optimization (ACO) whereas PepSurf [6] realizes the mapping using a dynamic programming based stochastic color-coding algorithm. However, finding a simple path on a graph is computationally intractable for any large scale of searching problem. For example, PepSurf takes a few hours to get the result for a peptide of 14 or 15 amino acids.