Journal article
NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
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.
Language: | English |
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Publisher: | The American Association of Immunologists, Inc. |
Year: | 2017 |
Pages: | 3360-3368 |
ISSN: | 15506606 and 00221767 |
Types: | Journal article |
DOI: | 10.4049/jimmunol.1700893 |
ORCIDs: | 0000-0002-8964-0244 , 0000-0002-8036-2647 , Marcatili, Paolo , 0000-0002-8457-6693 and Nielsen, Morten |