NetMHCpan 2.2 Server

NetMHCpan server predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs). The method is trained on more than 110,000 quantitative binding data covering more than 100 different MHC molecules. Predictions can be made for HLA-A, B, C, E and G alleles, as well as for non-human primates, mouse and pig. Further the user can upload full length MHC protein sequences, and have the server predict MHC restricted peptides from any given protein of interest.

Predictions can be made for 8-11 mer peptides. Note that all non 9mer predictions are made using approximations. Most HLA molecules have a strong preference for binding 9mers.

The prediction values are given in nM IC50 values and as %-Rank to a set of 1000.000 random natural peptides. For alleles distant to the MHC molecules included in the training of the method, only the Rank score is provided.

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 Evaluation Data


Paste a single sequence or several sequences in FASTA or PEPTIDE 9mer (if PEPTIDE 9mer format click the box below) format into the field below:

Submit a file in FASTA or PEPTIDE 9mer (if PEPTIDE 9mer format click the box below) format directly from your local disk:

Click if input is PEPTIDES (NOTE Peptides MUST be of equal length)  

Select species

Select Allele (max 20 per submission) or type allele names (ie HLA-A0101) 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:

Peptide length 

Threshold for presentation         Sort by affinity 

Include IC50 prediction value for all alleles (default is for white-listed alleles only)  

Save prediction 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 - MHC class I binding prediction beyond humans
    Ilka Hoof, Bjoern Peters, John Sidney, Lasse Eggers Pedersen, Ole Lund, Soren Buus, and Morten Nielsen
    PMID: 19002680
    Full text
  • NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence.
    Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roeder G, Peters B, Sette A, Lund O, Buus S.
    PMID: 17726526
    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 2.17.0).


Would you prefer to run NetMHCpan at your own site? NetMHCpan v. 2.0 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


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