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NetMHCIIpan 3.2 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.

The project is a collaboration between CBS, IMMI, and LIAI.

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

< BACK Instructions Output format Motif viewer Article abstract Data sets

Select MHC locus

Select Allele



For publication of results, please cite:

  • 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


Benchmark data used to develop this server were obtained from:


Would you prefer to run NetMHCIIpan at your own site? NetMHCIIpan 3.2 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


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