The process of MimoPro [16] is illustrated in Figure 1b . Initially, the surface of a protein is divided into some overlapping patches and each patch is centered at atom C b of a surface residue with a radius of 15 Å . This radius allows most epitopes to be encompassed in such a patch [16] . Secondly, each surface patch is further transformed to a graph bounded by neighbor amino acids that are determined using a parameter called adaptive distance threshold (ADT). Afterwards a patch-based complete graph search algorithm is utilized to find the best alignment for each mimotope sequence in each graph. During this iteration, similarity between a path and the corresponding mimotope is rated. Finally the patch with the highest score is selected as a potential candidate for the native epitope.