NetChop 3.1 Server
The NetChop server produces neural network predictions for cleavage sites of the
NetChop has been trained on human data only, and will therefore presumably have
better performance for prediction of the cleavage sites of the human proteasome.
However, since the proteasome structure is quite conserved, we believe that the
server is able to produce reliable predictions for at least the other mammalian
This server is an update to the Netchop 2.0 server. It has been trained using
a novel sequence encoding scheme, and an improved neural network training strategy.
The Netchop 3.0 version has two different network
methods that can be used for prediction. C-term 3.0 and 20S 3.0.
View the version history of this server.
All the previous versions are available on line, for comparison and
network is trained with a database consisting of 1260 publicly available
MHC class I ligands (using only C-terminal cleavage site of the ligands). 20S
network is trained with in vitro degradation data published in
Toes, et al.
and Emmerich et al.
C-term 3.0 network performs best in predicting the boundaries of CTL
Another proteasome prediction server is available in Tubingen University:
For publication of results, please cite:
- Current version:
The role of the proteasome in generating cytotoxic T cell epitopes:
Insights obtained from improved predictions of proteasomal cleavage.
M. Nielsen, C. Lundegaard, O. Lund, and C. Kesmir.
Immunogenetics., 57(1-2):33-41, 2005.
View the abstract.
- Original paper:
Prediction of proteasome cleavage motifs by neural networks.
A. Nussbaum, Hansjorg Schild, Vincent Detours, and S. Brunak,
Prot. Eng., 15(4): 287-296, 2002.
View the abstract.
Would you prefer to run NetChop at your own site? NetChop 3.1 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 firstname.lastname@example.org.