title: NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11.
abstract: NetMHC-3.0 is trained on a large number of quantitative peptide data using both affinity data from the Immune Epitope Database and Analysis Resource (IEDB) and elution data from SYFPEITHI. The method generates high-accuracy predictions of major histocompatibility complex (MHC): peptide binding. The predictions are based on artificial neural networks trained on data from 55 MHC alleles (43 Human and 12 non-human), and position-specific scoring matrices (PSSMs) for additional 67 HLA alleles. As only the MHC class I prediction server is available, predictions are possible for peptides of length 8-11 for all 122 alleles. artificial neural network predictions are given as actual IC(50) values whereas PSSM predictions are given as a log-odds likelihood scores. The output is optionally available as download for easy post-processing. The training method underlying the server is the best available, and has been used to predict possible MHC-binding peptides in a series of pathogen viral proteomes including SARS, Influenza and HIV, resulting in an average of 75-80% confirmed MHC binders. Here, the performance is further validated and benchmarked using a large set of newly published affinity data, non-redundant to the training set. The server is free of use and available at: http://www.cbs.dtu.dk/services/NetMHC.
authors.affiliation: CBS, Department of Systems Biology, Technical University of Denmark DTU, Kemitorvet Build. 208, 2800 Lyngby, Denmark. lunde@cbc.dtu.dk
authors.forename: Claus
authors.initials: C
authors.lastname: Lundegaard
authors.forename: Kasper
authors.initials: K
authors.lastname: Lamberth
authors.forename: Mikkel
authors.initials: M
authors.lastname: Harndahl
authors.forename: Søren
authors.initials: S
authors.lastname: Buus
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.forename: Morten
authors.initials: M
authors.lastname: Nielsen
mesh_terms: D000483:Alleles; D000818:Animals; D000939:Epitopes / Q000737:chemistry; D006680:HLA Antigens / Q000235:genetics / Q000378:metabolism*; D000882:Haplorhini / Q000235:genetics; D015395:Histocompatibility Antigens Class I / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D020407:Internet; D051379:Mice; D010455:Peptides / Q000737:chemistry / Q000276:immunology*; D012984:Software
chemical_list: D000939:Epitopes; D006680:HLA Antigens; D015395:Histocompatibility Antigens Class I; D010455:Peptides