Services are gradually being migrated to
Please try out the new site.

NetMHCcons 1.1 Server

NetMHCcons 1.1 server predicts binding of peptides to any known MHC class I molecule. This is a consensus method for MHC class I predictions integrating three state-of-the-art methods NetMHC, NetMHCpan and PickPocket to give the most accurate predictions. The server also allows to use each of these methods separately:

NetMHC is an artificial neural network-based (ANN) allele-specific method which has been trained using 94 MHC class I alleles. Version 3.4 is used as part of NetMHCcons-1.1.

NetMHCpan is a pan-specific ANN method trained on more than 115,000 quantitative binding data covering more than 120 different MHC molecules. Version 2.8 is used as part of NetMHCcons-1.1.

PickPocket method is matrix-based and relies on receptor-pocket similarities between MHC molecules. It has been trained on 94 different MHC alleles. In the PickPocket version 1.1, the matrices of pocket-library are generated using the SMMPMBEC method.

NetMHCcons 1.1 server can produce predictions for peptides of 8-15 amino acids in length. It also gives a possibility to choose several lengths.

Two submission types are handled - the list of peptides or a protein sequence in FASTA format. The server provides a possibility for the user to choose MHC molecule in question from a long list of alleles or alternatively upload the MHC protein sequence of interest.

The prediction values are given in nM IC50 values and as % Rank to a set of 200.000 random natural peptides. The user has a choice of setting the threshold for defining strong and weak binders based on predicted affinity (IC50) or % Rank. Strong and weak binding peptides will be indicated in the output. The output can also be sorted based on predicted binding affinity as well as filtered on the user-specified thresholds.

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


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 Method

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 strong binder (IC50) 
Threshold for weak binder (% Rank)  Threshold for weak binder (IC50) 

Filter output

Sort by affinity 

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:

  • NetMHCcons: a consensus method for the major histocompatibility complex class I predictions
    Edita Karosiene, Claus Lundegaard, Ole Lund and Morten Nielsen
    PMID: 22009319
    Full text

Other relevant publications:

  • NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MH C class I affinities for peptides of length 8-11
    Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, Nielsen M.
    Nucleic Acids Res. 1;36(Web Serve r issue):W509-12. 2008

    View the abstract.

  • NetMHCpan - MHC class I binding prediction beyond humans
    Ilka Hoof, Bjoern Peters, John Sidney, Lasse Eggers Pedersen, Ole Lund, Soren Bu us, and Morten Nielsen
    PMID: 19002680       F ull text

  • The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
    Zhang H, Lund O, Nielsen M. Bioinformatics. 2009 May 15;25(10):1293-9

    PMID: 19297351       Full text


Data resources used to develop this server was obtained from

  • IEDB database.
    • Quantitative peptide binding data were obtained from the IEDB database.


Would you prefer to run NetMHCcons at your own site? NetMHCcons v. 1.1 is also available as a stand-alone software package with the same functionality as the service above. Ready-to-ship packages exist for Linux and Darwin (MacOSX). There is a download page for academic users; other users are requested to contact


Scientific problems:        Technical problems: