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NetMHCstabpan 1.0 Server

NetMHCstabpan server predicts binding stability of peptides to any known MHC molecule using artificial neural networks (ANNs). The method is trained on more than 25,000 quantitative stability data covering 75 different HLA molecules. 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 8-14 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 half life time in hours values and as %-Rank to a set of 200.000 random natural peptides.

The project is a collaboration between CBS, and IMMI.

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

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

Instructions Output format Article abstract


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 (several lengths are possible): 

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 

Include affinity predictions Sort by score  

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:

  • Pan-specific prediction of peptide-MHC-I complex stability; a correlate of T cell immunogenicity
    Michael Rasmussen, Emilio Fenoy, Mikkel Harndahl, Anne Bregnballe Kristensen, Ida Kallehauge Nielsen, Morten Nielsen, Soren Buus. Accepted for publication Journal of Immunology, June 2016


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? NetMHCstabpan v. 1.0 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: