The use of bioinformatics for identifying class II-restricted T-cell epitopes

An important step in the design of subunit vaccines is the identification of promiscuous T helper cell epitopes in sets of disease-specific gene products. Most of the epitope prediction models are based on HLA-II peptide binding, which constitutes a major bottleneck in the natural selection of epitopes. Here we describe a computer model, TEPITOPE, that enables the systematic prediction of promiscuous peptide ligands for a broad range of HLA binding specificity. We show how to apply the TEPITOPE prediction model to identify T-cell epitopes, and provide examples of its successful application in the context of oncology, allergy, and infectious and autoimmune diseases.