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NetCTLpan 1.1 Server

NetCTLpan 1.1 server predicts CTL epitopes in protein sequences. The current version 1.1 is an update to the original NetCTL server that allows for prediction of CTL epitope with restriction to any MHC molecules of known protein sequence.

NOTE. New in this version. The method has been updated to include the newest MHC allele releases from the IMGT/HLA and IPD-MHC databases (for non-human primates and pig). This includes adaptation of the new nomenclature for HLA and Rhesus macaque (Mamu) alleles. The MHC binding predictions has been updated to NetMHCpan version 2.3.

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

The method integrates prediction of peptide MHC class I binding, proteasomal C terminal cleavage and TAP transport efficiency. MHC class I binding and proteasomal cleavage is performed using artificial neural networks. TAP transport efficiency is predicted using weight matrix.

The prediction values are calculated as a weighted average of the MHC, TAP and C terminal cleavage scores. and as %-Rank to a set of 200.000 random natural peptides.

The MHC peptide binding is predicted using neural networks trained as described for the NetMHCpan server. The proteasome cleavage event is predicted using the version of the NetChop neural networks trained on C terminals of known CTL epitopes as describe for the NetChop-3.0 server. The TAP transport efficiency is predicted using the weight matrix based method describe by Peters et al., 2003

Species Warning. Note, that both the proteasome and TAP predictions were developed using experimental data for human versions of the molecule. At least for TAP molecules, there are known to be some species dependent differences in specificity. Therefore, using these predictions for eptitope processing in non-human cells should only be done with extra caution in interpreting results.

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

Instructions Output format Article abstract Training and Evaluation Data


Paste a single sequence or several sequences in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

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 showing predictions  

Weight on C terminal cleavage         Weight on TAP transport efficiency         Threshold for epitope identification        

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:

  • NetCTLpan - Pan-specific MHC class I epitope predictions
    Stranzl T., Larsen M. V., Lundegaard C., Nielsen M.
    Immunogenetics. 2010 Apr 9. [Epub ahead of print]
  • PMID: 20379710
  • Full text


Data resources used to develop this server was obtained from

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


Scientific problems:        Technical problems: