• NetMHCpan is now trained on Mass Spectrometry Eluted Ligands (EL) data from Single Allele (SA, peptides annotated to a single MHC) and Multi Allele (MA, peptides annotated to multiple MHCs) sources. The use of EL MA data is now possible due to an upgrade NNAlign (called NNAlign_MA) which enables pseudo-labelling.
• The server returns by default the likelihood of a peptide being a natural ligand and, if selected, also the predicted binding affinity.

Publication:

• NetMHCpan-4.1: Under Review

• NetMHCpan is now trained both on affinity data and naturally eluted ligands
• The method predicts two properties: likelihood of ligand presentation and binding affinity

Publication:

• NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
  Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters and Morten Nielsen
  The Journal of Immunology (2017) ji1700893; DOI: 10.4049/jimmunol.1700893
  

• Improved algorithm implementing insertions and deletions in the alignment
• Method trained on extended data-set including peptides of length 8 to 13
• Length distribution of predicted binders that reflects the MHC molecules preferences

Publication:

• NetMHCpan-3.0: improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets
  Morten Nielsen and Massimo Andreatta
  Genome Medicine (2016): 8:33
  

• Method retrained on extented data set including 10 prevalent HLA-C and 7 prevalent BoLA MHC-I molecules.

• Method retrained on extented data set including several HLA-C allele, and two BoLA alleles.

• Method retrained on the version 2.2 data excluding data from the Mamu-A1*02601 allele due to data contamination. Also, the method has been updated to include the newest MHC allele releases from the IMGT/HLA and IPD-MHC databases (for non-human primates and pig). These updates include incoportation of the new nomemclature for HLA and Rhesus macaque (Mamu).

• Method retrained on an extented data covering more than 100 MHC alleles and more than 110,000 peptide/MHC interactions.

• Predicted binding score are shown as percent rank to a pool of 1000.000 random natural 9mer peptides. IC50 values are only shown for a set of white-listed alleles (mostly HLA-A and HLA-B alleles) where the values can be relied on.

• Binding predictions for all known MHC molecules including HLA-C, non-classical HLA (HLA-E and HLA-G), non-human primates, pig and mouse.
• Prediction of performance accuracy

Publication:

• NetMHCpan - MHC class I binding prediction beyond humans
  Ilka Hoof, Bjoern Peters, John Sidney, Lasse Eggers Pedersen, Ole Lund, Soren Buus, and Morten Nielsen
  Immunogenetics 61.1 (2009): 1-13
  

• Includes prediction of peptides length 8-11 .

Publication:

• NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence.
  Nielsen M, et al. (2007) PLoS ONE 2(8): e796. doi:10.1371/journal.pone.0000796
  View the the full text version at PLoSONE: Full text, or Full text including supplementary materials: PDF_fulltext.pdf