Mimotope-Based Prediction of B-Cell Epitopes

Mimotopes are peptides mimicking epitopes on the corresponding antigen. They can be obtained via panning the phage-displayed random peptide library against the corresponding monoclonal antibody or specific sera. Besides mimotopes however, the experimental results also include all kinds of unwanted sequences called "target-unrelated peptides," which often interfere with the subsequent experimental and computational analyses. Nevertheless, the prediction of B-cell epitopes based on the experimental result of phage display has shown to be a promising and reliable strategy with acceptable precision. In this chapter, we summarize mimotope-based prediction of B-cell epitopes under three conditions and focus on protocols and tips for retrieving, cleaning, and decoding the data from phage display technology.