Customized Predictions of Peptide–MHC Binding and T-Cell Epitopes Using EPIMHC

Peptide binding to major histocompatibility complex (MHC) molecules is the most selective requisite for T-cell recognition. Therefore, prediction of peptide–MHC binding is the main basis for anticipating T-cell epitopes. A very popular and accurate method to predict peptide–MHC binding is based on motif-profiles and here we show how to make them using EPIMHC (http://imed.med.ucm.es/epimhc/). EPIMHC is a database of T-cell epitopes and MHC-binding peptides that unlike any related resource provides a framework for computational vaccinology. In this chapter, we describe how to derive peptide–MHC binding motif-profiles in EPIMHC and use them to predict peptide–MHC binding and T-cell epitopes. Moreover, we show evidence that customization of peptide–MHC binding predictors can lead to enhanced epitope predictions.