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NetH2pan Server

Prediction of peptide interactions with murine MHC class I (H2) molecules.

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

The NetH2pan server is a version of NetMHCpan dedicated to mouse MHC molecules.
The method was trained on binding affinity and ligand elution data from nine different H-2 class I molecules. By default it predicts LIGAND likelihood scores, but it can be toggled to return predicted BINDING AFFINITY scores.

Instructions Output format Motif viewer Article abstract Download


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 (i.e. H-2-Dq) separated by commas (and no spaces).

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 predicted affinity 

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:

  • NetH2pan: A Computational Tool to Guide MHC peptide prediction on Murine Tumors
    Christa I. DeVette, Massimo Andreatta, Wilfried Bardet, Steven J. Cate, Vanessa I. Jurtz, Kenneth W. Jackson, Alana L. Welm, Morten Nielsen, William H. Hildebrand
    Cancer Immunology Research (2018) DOI: 10.1158/2326-6066.CIR-17-0298
    Full text  
  • 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  


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.
    • MHC protein sequences were obtained from the IMGT/HLA database (version 3.1.0).


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