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NetMHCstab 1.0 Server

NetMHCstab-1.0 predicts the stability of peptide binding to a number of different MHC molecules using artificial neural networks (ANNs).

ANNs have been trained for 13 different Human MHC (HLA) alleles representing 11 of the 12 common HLA A and B Supertypes as defined by Lund et al. (2004).

Prediction values are given in hours (half-life).

Predictions of lengths 8-14: Predictions can be made for lengths between 8 and 14 for all alleles using an approximation algorithm using ANNs trained on 9mer peptides. Caution should be taken for 8mer predictions as some alleles might not bind 8mers to any significant extend.

Highly and weakly stable binding peptides are indicated in the output.

The project is a collaboration between CBS and IMMI.

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 loci/species

Select Allele(s) or type allele names (ie HLA-A01:01) separated by commas (and no spaces).

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

Threshold for highly stable binder (hours):  
Threshold for weakly stable binder (hours):  

Include affinity predictions   Relative weight of affinity prediction: 

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.

The sequences are kept confidential and will be deleted after processing.


For publication of results, please cite:

  • NetMHCstab - predicting stability of peptide:MHC-I complexes; impacts for CTL epitope discovery
    Kasper W. Joergensen, Michael Rasmussen, Soren Buus, and Morten Nielsen
    Immunology. 2013 Aug 8. doi: 10.1111/imm.12160. [Epub ahead of print] 23927693


Would you prefer to run NetMHCstab at your own site? NetMHCstab 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


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