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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 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.

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.

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 weak binder (% Rank)  

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 %Rank <   %

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


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