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DiscoTope 2.0 Server

DiscoTope server predicts discontinuous B cell epitopes from protein three dimensional structures. The method utilizes calculation of surface accessibility (estimated in terms of contact numbers) and a novel epitope propensity amino acid score. The final scores are calculated by combining the propensity scores of residues in spatial proximity and the contact numbers.

New in the DiscoTope version 2.0: Novel definition of the spatial neighborhood used to sum propensity scores and half-sphere exposure as a surface measure.

Note: The DiscoTope server has been up-dated to improve the user-friendliness. The server now predicts epitopes in complexes of multiple chains. Also, DiscoTope output files are now easily downloaded and imported in spreadsheets. Futhermore, we have facilitated the visualization of prediction results.

Instructions Output format Article abstract


Please choose one of the following three submission methods:

  1. Chain(s) in an existing PDB entry. Use comma for separation of chain ids. If this box is unspecified,
    the prediction will be done using all chains in the pdb file.

    PDB code:     Chain(s):      

  2. A file from your local disk containing a list of existing PDB entries with specified chain ID, one per line,
    in the format 'entryname_chain' e.g. 1zz6_B:

    File name:

  3. A file from your local disk containing your own structure in PDB format (not necessarily present in PDB):

    File name:  

    Chain(s):          (if chain id is unspecified, all chains in the structure will be used for prediction.)

Specify the threshold for epitope identification:     (see Instructions)

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


For publication of results, please cite:

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, and Morten Nielsen
Plos Computational Biology, 2012
Link to Paper


Would you prefer to run DiscoTope at your own site? The DiscoTope 2.0 software package is in preparation; in the meanwhile an earlier version (1.1) is available as a stand-alone software package, with the same functionality as the DiscoTope 1.1 server online. 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: