RT Journal Article
SR Electronic
T1 NetMHCpan 4.0: Improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 149518
DO 10.1101/149518
A1 Vanessa Jurtz
A1 Sinu Paul
A1 Massimo Andreatta
A1 Paolo Marcatili
A1 Bjoern Peters
A1 Morten Nielsen
YR 2017
UL http://biorxiv.org/content/early/2017/09/13/149518.abstract
AB 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 (major histocompatibility complex) class I molecules. Peptide binding to MHC molecules is the single most selective step in the antigen presentation pathway. On the quest for T cell epitopes, the prediction of peptide binding to MHC molecules has therefore attracted large attention.In the past, predictors of peptide-MHC interaction have in most cases been trained on binding affinity data. Recently an increasing amount of MHC presented peptides identified by mass spectrometry has been published containing information about peptide processing steps in the presentation pathway and the length distribution of naturally presented peptides. Here, we present NetMHCpan-4.0, a method trained on both binding affinity and eluted ligand data leveraging the information from both data types. Large-scale benchmarking of the method demonstrates an increased predictive performance compared to state-of-the-art when it comes to identification of naturally processed ligands, cancer neoantigens, and T cell epitopes.