Improved methods for predicting peptide binding affinity to MHC class II molecules.
Major histocompatibility complex class II (MHC-II) molecules are expressed on the surface of professional antigen-presenting cells where they display peptides to T helper cells, which orchestrate the onset and outcome of many host immune responses. Understanding which peptides will be presented by the MHC-II molecule is therefore important for understanding the activation of T helper cells and can be used to identify T-cell epitopes. We here present updated versions of two MHC-II-peptide binding affinity prediction methods, NetMHCII and NetMHCIIpan. These were constructed using an extended data set of quantitative MHC-peptide binding affinity data obtained from the Immune Epitope Database covering HLA-DR, HLA-DQ, HLA-DP and H-2 mouse molecules. We show that training with this extended data set improved the performance for peptide binding predictions for both methods. Both methods are publicly available at www.cbs.dtu.dk/services/NetMHCII-2.3 and www.cbs.dtu.dk/services/NetMHCIIpan-3.2.
['Jensen|Kamilla Kjaergaard|KK|0000-0001-9217-7142', 'Andreatta|Massimo|M|0000-0002-8036-2647', 'Marcatili|Paolo|P|', 'Buus|Søren|S|', 'Greenbaum|Jason A|JA|', 'Yan|Zhen|Z|', 'Sette|Alessandro|A|', 'Peters|Bjoern|B|', 'Nielsen|Morten|M|0000-0001-7885-4311']
D000595:Amino Acid Sequence D019295:Computational Biology D030562:Databases, Protein D018604:Epitope Mapping D000939:Epitopes D018984:Epitopes, T-Lymphocyte D000949:Histocompatibility Antigens Class II D006801:Humans D009842:Oligopeptides D011485:Protein Binding D015203:Reproducibility of Results
T-cell epitope affinity predictions MHC binding specificity immunogenic peptides peptide-MHC binding