NetMHC-3.0: Accurate Web Accessible Predictions of Human, Mouse and Monkey MHC Class I Affinities for Peptides of Length 8-11

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W509-12. doi: 10.1093/nar/gkn202. Epub 2008 May 7.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Alleles
  • Animals
  • Epitopes / chemistry
  • HLA Antigens / genetics
  • HLA Antigens / metabolism*
  • Haplorhini / genetics
  • Histocompatibility Antigens Class I / genetics
  • Histocompatibility Antigens Class I / metabolism*
  • Humans
  • Internet
  • Mice
  • Peptides / chemistry
  • Peptides / immunology*
  • Software*

Substances

  • Epitopes
  • HLA Antigens
  • Histocompatibility Antigens Class I
  • Peptides