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DiscoTope 1.1 Server

DiscoTope 1.1 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.

Instructions Output format Article abstract


Please choose one of the following three submission methods:

  1. A single chain in an existing PDB entry:

    Entry name (in four letter code):     Chain:       (both must be specified)

  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:              (both file name and chain must be specified)

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:

Prediction of residues in discontinuous B cell epitopes using protein 3D structures
Pernille Haste Andersen, Morten Nielsen and Ole Lund
Protein Science, 15:2558-2567, 2006


Would you prefer to run DiscoTope at your own site? DiscoTope 1.1 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: