Version history

Please click on the version number to activate the corresponding server.

4.0 The current server (online since April 2020). New in this version:
  • The two output neuron architechture introduced in NetMHCpan-4.0 permits the inclusion of EL data, and the new training algorithm NNAlign_MA extends training data to ligands of ambiguous allele assignments. The model also, optionally, encodes ligand context.
Main publication:

  • Improved methods for predicting peptide binding affinity to MHC class II molecules.
    Reynisson B, Barra C, Kaabinejadian S, Hildebrand WH, Peters B, Nielsen M
    J Proteome Res 2020 Apr 30. doi: 10.1021/acs.jproteome.9b00874.
    PubMed: 32308001
3.2 (online since January 2018). New in this version:
  • Method retrained on an extensive dataset of over 100,000 datapoints, covering 36 HLA-DR, 27 HLA-DQ, 9 HLA-DP, and 8 mouse MHC-II molecules.
Main publication:

  • Improved methods for predicting peptide binding affinity to MHC class II molecules.
    Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M.
    Immunology. 2018 Jan 6. doi: 10.1111/imm.12889.
    PubMed: 29315598
3.1 (online since December 2014). New in this version:
  • Improved binding core identification by realigning individual networks in the ensemble.
  • Introduced a reliability measure on the predicted binding core (Core_Rel column).
  • Graphical representation of the binding core register and of possible multiple cores.
Main publication:

  • Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification
    Andreatta M, Karosiene E, Rasmussen M, Stryhn A, Buus S, and Nielsen M
    Immunogenetics (2015)
    PubMed: 26416257
3.0 (online since June 2013). New in this version:
  • The user can make predictions for all DR, DP and DQ molecules with known protein sequence. Likewise can the user upload full length MHC class II alpha and beta chain and have the server predict MHC restricted peptides from any given protein of interest
2.1 (online since 6 June 2011). New in this version:
  • User can upload full length MHC class II beta chain and have the server predict MHC restricted peptides from any given protein of interest.
2.0 (online since 17 Nov 2010). New in this version:
  • New concurent algorithm used to train the network.
1.1 (online since 15 April 2010). New in this version:
  • %-rank measure include for each prediction value. The %-rank score give the rank of the prediction score to a distribution of prediction scores from 200.000 natural random 15mer peptides.
1.0 Original version (online version until April 15 2010):

Main publication:

  • Quantitative predictions of peptide binding to any HLA-DR molecule of known sequence: NetMHCIIpan.
    Nielsen M, et al. (2008) PLoS Comput Biol. Jul 4;4(7):e1000107. View the full text article at PLoS Compu: Full text.