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In order to use the DiscoTope server for prediction of discontinuous B cell epitopes:
  1. Use one of the following three ways of submission:

    1. Write a PDB entry name and chain id(s) into the corresponding windows.

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

    3. Specify a file from your local disk, in PDB format, and chain id(s).

    Note: Chain ids should be separated by comma (,). If no chain id is specified, all chains in the file will be used for prediction.

  2. Optional: Select DiscoTope threshold score for epitope identification.

    The default value -7.7 corresponds to a specificity of 75%.
    Higher values correspond to higher specificity.

    Different thresholds for the DiscoTope score can be translated into sensitivity/specificity values. In a benchmark containing more than 75 antigen/antibody complexes, the following relations were found:

    Score Sensitivity Specificity
    > -3.1 0.16 0.95
    > -4.7 0.24 0.90
    > -6.0 0.32 0.85
    > -6.9 0.40 0.80
    > -7.7 0.47 0.75

    A specificity of 0.75 means that 25% of the nonepitope residues were predicted as part of epitopes.
    A sensitivity of 0.47 means that 47% of the epitope residues were predicted as part of epitopes.

  3. Press the "Submit sequence" button.

  4. A WWW page will return the results when the prediction is ready. Response time depends on system load.


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