NetCTL 1.2 Server
NetCTL 1.2 server predicts CTL epitopes in protein sequences. The current version 1.2 is an update to the version 1.0. The version 1.2 expands the MHC class I binding predicition to 12 MHC supertypes including the supertypes A26 and B39. The accuracy of the MHC class I peptide binding affinity is significantly improved compared to the earlier version. Also the prediction of proteasonal cleavage has been improved and is now identical to the predictions obtained by the NetChop-3.0 server. The updated version has been trained on a set of 886 known MHC class I ligands.
NOTE. On Aug 16 2006 a minor update to the server has been implemented improving the prediction accuracy for MHC binding. The earlier version of the NetCTL 1.2 server (1.2 beta) is available via the versions history for the server.
View the version history of this server. All the previous versions are available on line, for comparison and reference.
The method integrates prediction of peptide MHC class I binding, proteasomal C terminal cleavage and TAP transport efficiency. The server allows for predictions of CTL epitopes restricted to 12 MHC class I supertype. MHC class I binding and proteasomal cleavage is performed using artificial neural networks. TAP transport efficiency is predictied using weight matrix.
The MHC peptide binding is predicted using neural networks trained as described for the NetMHC 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.
The server includes predictions of MHC/peptide binding for 12 MHC class I supertypes. The output from the neural network predicting MHC/peptide binding is a log transformed value related to the IC50 values in nM units. For details on the transformation please see output format.
The scores from the three individual prediction methods are integrated as a weighted sum with a relative
weight on peptide/MHC binding of 1. Different thresholds for the integrated score can be translated into
sensitivity/specificity values. In a large benchmark calculate containing more than 800 known MHC class I ligands
the following relations were found
The project is collaboration between CBS and IMMI.
For publication of results, please cite:
Would you prefer to run NetCTL at your own site? NetCTL 1.2 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
for academic users; other users are requested to contact CBS Software Package
Manager at email@example.com.
Scientific problems: Technical problems: