How are the results interpreted?
WHISCY calculates a prediction score for every surface residue in your protein that can be matched to the provided alignment. A high prediction score means a high probability of that residue to be in a protein-protein interface.
There are three files returned by WHISCY:
1. A PDB file of the protein you submitted. The prediction scores are in the column that normally contains the crystallographic B-factors (temperatures).
ATOM 125 N ASN A 17 -1.652 28.627 57.495 1.00 24.69 N
ATOM 126 CA ASN A 17 -1.282 28.264 56.130 1.00 27.68 C
ATOM 127 C ASN A 17 0.046 28.805 55.634 1.00 27.56 C
ATOM 128 O ASN A 17 0.507 28.378 54.582 1.00 28.39 O
2. A list of scores for every surface residue, sorted from high to low. You can use this list to see the top scoring residues or to find the score for a residue of interest.
3. A file containing the predicted active and passive residues for HADDOCK. This file can be opened with a text editor to list the active and passive residues, or in Rasmol to map them onto the surface. The listed residues can be directly entered in the AIR generation page on the HADDOCK website. A cutoff of 0.18 is used to define active residues and a radius of 6.5 Angstroms to define the surrounding passive residues.
Visualisation of the results
Rasmol is a good program to visualize the predictions. If you load your structure and select Colours => Temperatures, you can directly see which regions of the surface are predicted. Red means a high prediction score, whereas blue means a low prediction score.
Examples of predicted interfaces by WHISCY, viewed using Rasmol. Left: GTPase-activating domain of protein p120. The predicted interface corresponds to the interface with Ras. Right: Trypsin. The predicted interface corresponds to the interface with soybean trypsin inhibitor.
You can also use Rasmol to look at the predicted active and passive residues for HADDOCK. Load the PDB file in Rasmol and then type "script