Netmhcpan-4.0: Improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data
- Danmarks Tekniske Universitet
- La Jolla Institute for Allergy and Immunology
- Instituto de Investigaciones Biotecnologicas - Instituto Tecnologico Chascomus
Fecha de publicación: Nov. 1, 2017
Copyright © 2017 by The American Association of Immunologists, Inc. Cytotoxic T cells are of central importance in the immune system's response to disease. They recognize defective cells by binding to peptides presented on the cell surface by MHC class I molecules. Peptide binding to MHC molecules is the single most selective step in the Ag-presentation pathway. Therefore, in the quest for T cell epitopes, the prediction of peptide binding to MHC molecules has attracted widespread attention. In the past, predictors of peptide-MHC interactions have primarily been trained on binding affinity data. Recently, an increasing number of MHC-presented peptides identified by mass spectrometry have been reported containing information about peptide-processing steps in the presentation pathway and the length distribution of naturally presented peptides. In this article, we present NetMHCpan-4.0, a method trained on binding affinity and eluted ligand data leveraging the information from both data types. Large-scale benchmarking of the method demonstrates an increase in predictive performance compared with state-of-the-art methods when it comes to identification of naturally processed ligands, cancer neoantigens, and T cell epitopes.