Searching and mapping of T-cell epitopes, MHC binders, and TAP binders

Abstract

This chapter describes searching and mapping tools of MHCBN database, which is a curated database. It comprises over 23,000 peptide sequences, whose binding affinity with major histocompatibility complex (MHC) or transporter associated with antigen processing (TAP) molecules has been assayed experimentally. Each entry of the database provides full information (such as sequence, its MHC- or TAP-binding specificity, and source protein) about peptide whose binding affinity (IC50) and T-cell activity is experimentally determined. MHCBN has number of web-based tools for analyzing and retrieving information. In this chapter, we describe how to use web tools integrated in MHCBN that include (i) mapping of experimentally determined antigenic regions on the query sequence, (ii) creation of allele-specific peptide data set, and (iii) BLAST search against MHC or antigen databases.