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WHISCY is a program to predict protein-protein interfaces. It is primarily based on conservation, but it also takes into account structural information. A sequence alignment is used to calculate a prediction score for each surface residue of your protein.

To use WHISCY, you need to supply the structure of your protein and a multiple sequence alignment of your protein sequence with homologuous sequences:

  • You need the structure of your protein as PDB file (or PDB code)
  • You need to specify the protein chain you want to predict
  • You need to specify the alignment of the protein (and the alignment file format)
Interface propensities and surface smoothing are features that are used by WHISCY to improve the predictions.

If your structure (or a close homolog) is deposited in the PDB, you can use the alignment from the HSSP database. The HSSP database contains an alignment for nearly each protein in the PDB. To use the HSSP alignment, specify the corresponding PDB code in the HSSP_ID field.

Alternatively, you can supply your own alignment. WHISCY recognizes a number of alignment formats used by major alignment programs: .aln (default output of CLUSTAL), .fasta (default output of MUSCLE), PHYLIP and MSF. Take care: WHISCY assumes that the first sequence in the alignment corresponds to the biological sequence of your protein. This can be the sequence of the PDB structure, but only if it is not engineered!

WHISCY is robust in terms of bad alignment quality, so manual correction is not essential.

Your request is expected to take a few seconds before you receive the results.

Number of successfully served jobs (since August 2019): 1357

User satisfaction rating on a scale from 1 to 5 (best):


Information about the Whiscy predictive approach can be found at the online method page.

Once you click on the button, your job will be processed.