NetCTLpan 1.0 Server
NetCTLpan 1.0 server predicts CTL epitopes in protein sequences. The current version 1.0 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.
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
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
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.
Would you prefer to run NetCTLpan at your own site? NetCTLpan 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
for academic users; other users are requested to contact
CBS Software Package Manager at