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NetMHCpan 4.0 Server

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

New in this version: the method is trained on naturally eluted ligands AND on binding affinity data. It returns two properties: either the likelihood of a peptide becoming a natural ligands, or the predicted binding affinity.

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 a combinatino of more than 180,000 quantitative binding data and MS derived MHC eluted ligands. The binding affinity data covers 172 MHC molecules from human (HLA-A, B, C, E), mouse (H-2), cattle (BoLA), primates (Patr, Mamu, Gogo) and swine (SLA). The MS eluted ligand data covers 55 HLA and mouse allelee. Furthermore, the user can obtain redictions to the any custom MHC class I molecule by uploading a full length MHC protein sequence.

Predictions can be made for peptides of any length.

11-03-2019: Server updated to have precalculated percentile rank values and binding motifs for all HLA alleles included in the latest IMGT HLA release

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

Link to the training data

Instructions Output format Motif viewer Article abstract


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 

Make BA predictions  

Sort by prediction score 

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-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
    Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters and Morten Nielsen
    The Journal of Immunology (2017) ji1700893; DOI: 10.4049/jimmunol.1700893
    Full text   [PDF]
  • 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. 4.0 is available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for UNIX and DARWIN platforms. To download the packages, academic users can go to NetMHCpan-4.0, and click on the "Downloads tab"; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: