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NetMHCIIpan 3.1 Server

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 nM IC50 values and as % Rank to a set of 200.000 random natural peptides. The user has a choice of setting the threshold for defining strong and weak binders based on predicted affinity (IC50) or % Rank. Strong and weak binding peptides will be indicated in the output. The output can also be sorted based on predicted binding affinity as well as filtered on the user-specified thresholds. 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 the previous versions are available on line, for comparison and reference.

Instructions Output format Article abstract Data sets


Hover the mouse cursor over the symbol for a short description of the options

Type of input

Paste a single sequence or several sequences in FASTA format into the field below:

or submit a file in FASTA format directly from your local disk:

Peptide length  

Select species/loci

Select Allele (max. 20 per submission)

or type a list of molecules names separated by commas (no spaces)
Max 20 alleles per submission. 

For the list of available molecule names click here: List of MHC molecule names.

Alternatively, upload full length Alpha and Beta chain protein sequences:

Definition of binding peptides:
Threshold for strong binder (% Rank)       Threshold for strong binder (IC50)   nM
Threshold for weak binder (% Rank)       Threshold for weak binder (IC50)   nM

Turn on filtering options 

Fast mode 

Print only the strongest binding core 

Sort output by affinity 

Exclude offset correction 

Graphical representation of binding registers 
for peptides with predicted affinity <   nM

Save predictions to xls file 

At most 5000 sequences per submission; each sequence not more than 20,000 amino acids and not less than 8 amino acids. Max 20 MHC alleles per submission.

The sequences are kept confidential and will be deleted after processing.


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: