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NetMHCpan 3.0 Server

Prediction of peptide-MHC class I binding using artificial neural networks (ANNs).

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

NetMHCpan server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). The method is trained on more than 180,000 quantitative binding data covering 172 MHC molecules from human (HLA-A, B, C, E), mouse (H-2), cattle (BoLA), primates (Patr, Mamu, Gogo) and swine (SLA). Furthermore, the user can obtain binding predictions to the any custom MHC class I molecule by uploading a full length MHC protein sequence.

Version 3.0 has been retrained on an extented data set of 8-13mer peptides using the method described in this paper

Predictions can be made for peptides of any length. Note that most HLA molecules have a strong preference for binding 9mers.

NEW: As of Oct 26th, an option to display sequence logo representations of the predicted binding motifs has been included. This option is available in the bar below as "Sequence motifs".

Link to table (tab seperated) describing the training data Training data table

Link to file with training data including partitions from 5 fold cross-validation Training data

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

Instructions Output format Article abstract Sequence motifs Download


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 (you may select multiple lengths):  

Select species/loci

Select Allele (max 20 per submission) or type allele names (ie HLA-A01:01) separated by commas (and no spaces). Max 20 alleles per submission)

For list of allowed allele names click here List of MHC allele names.

or paste a single full length MHC protein sequence in FASTA format into the field below:

or submit a file containing a full length MHC protein sequence in FASTA format directly from your local disk:

Threshold for strong binder: % Rank 
Threshold for weak binder: % Rank 

Sort by predicted affinity 

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:

  • 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
    Full text   [PDF]
  • NetMHCpan, a method for 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
    PMID: 19002680   Full text


Data resources used to develop this server was obtained from

  • IEDB database.
    • Quantitative peptide binding data were obtained from the IEDB database.
  • IMGT/HLA database. Robinson J, Malik A, Parham P, Bodmer JG, Marsh SGE: IMGT/HLA - a sequence database for the human major histocompatibility complex. Tissue Antigens (2000), 55:280-287.
    • HLA protein sequences were obtained from the IMGT/HLA database (version 3.1.0).


Would you prefer to run NetMHCpan at your own site? NetMHCpan v. 3.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms. There is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: