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NetMHCIIpan 3.1 server predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2).

Submission is accepted in two formats - as a list of peptides or as a protein sequence in FASTA format. A comprehensive list of MHC molecules is available for prediction, alternatively the user can upload their MHC protein sequence of interest.

The prediction values are given in IC50 values (in nanoMolars) and as %Rank. The percentile rank for a peptide is generated by comparing its score against the scores of 200,000 random natural peptides of the same length of the query peptide. For example, if a peptide is assigned a rank of 1%, it means that its predicted affinity is among the top 1% scores for the specified molecule.
Strong and weak binding peptides are identified based on %Rank, with customizable thresholds. You may sort the output based on predicted binding affinity and filter out non-binders. Refer to the instructions page for more details.

View the version history of this server. All previous versions are available online, for comparison and reference.

UPDATE July 2016: strong and weak binders are now defined ONLY in terms of %Rank. Previous versions used a combination of percentile rank and IC50 binding affinity thresholds. Because the peptide-MHC affinity may vary widely for different MHC molecules, the %Rank is generally considered a better measure to define binding peptides.

NEW: visualize sequence motifs of the molecules in the NetMHCIIpan library with the Motif viewer

< BACK Instructions Output format Motif viewer Article abstract Data sets

Select MHC locus

Select Allele



For publication of results, please cite:

  • 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   [PDF]


Benchmark data used to develop this server were obtained from:


Would you prefer to run NetMHCIIpan at your own site? NetMHCIIpan 3.1 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for Linux and MacOSX. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: