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NetChop 3.1 Server

The NetChop server produces neural network predictions for cleavage sites of the human proteasome.

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 proteasomes.

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 reference.

C-term 3.0 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 epitopes.

Another proteasome prediction server is available in Tubingen University: PAProc

Instructions Output format Article abstract


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:

Prediction method  


Short output (default is long) 

At most 100 sequences and 100,000 amino acids per submission;

The sequences are kept confidential and will be deleted after processing.


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.
    C. Kesmir, 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 is a download page for academic users; other users are requested to contact CBS Software Package Manager at


Scientific problems:        Technical problems: