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CAPRI: Critical Assessment of PRediction of Interactions
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 MSD  CAPRI: Critical Assessment of PRediction of Interactions

First community wide experiment on the comparative evaluation of protein-protein docking for structure prediction

Hosted By EMBL/EBI-MSD Group

Target 01 Evaluation

Raul Mendez, Leonardo De Maria and Shoshana J. Wodak have now completed the evaluation of CAPRI Target_01.

The report is available as a HTML version report.html


In all the evaluation notes the entries are labelled with a unique identifier, e.g. in files such as T01_P34.8.A.fitting.summary. The identifier P34 is the identifier given to the Shoshana's group and is NOT the same as the identifier given to each participant.

For example the identifiers given in the Final Summary Do not match the Identifiers given to the participants.


The results are organised in a summary sheet, as well as more detailed data, organised in directories.

In brief they computed for each predicted interface:

  • 1. The contacts ratio
  • 2. The fraction of correctly predicted interface residues for the Hpr and Kinase subunits, respectively,
  • 3. The rigid-body rotation angle that needs to be applied to the predicted Hpr subunit, in order to superimpose it onto the Hpr in the target, once the predicted and target kinase subunits have been superimposed,
  • 4. The distance between the geometric centers of the subunits,
  • 5. The number of close contacts in each predicted interface.
  • 6. We also provide the PDB files, with the predicted complex superimposed onto the target complex. The superposition was performed only on the kinase subunits, so that the difference between the Hpr positions , between the predicted and target complexes should be clearly visible, using rasmol, for example, provided adequate colouring is used.

    The best predictions are those that have a high contacts ratio, a small rigid body rotation angle,  a small distance between the geometric centres, and a low number of close contacts.

    Only a few predictions satisfy these criteria, but the highest contact ratios are as low as 12-17/52-59 or so.  This is nevertheless very encouraging, given that the bound and unbound kinase molecules, have different conformations, making correct predictions of the interaction interface nearly impossible, using procedures that do not incorporate conformational changes.  Not only does the subunit change conformation (backbone rms 1.96Ć), but the monomers also move relative to one another (when dimers are superimposed the backbone rms is 2.42Å). These changes seem to result mainly from the movement of  the C-terminal helix ( from residue 287 on).

    When this helix is not used in the superposition of the kinase monmers, the backbone rms drops to 1.248Å.

    We do not provide at this stage, an appreciation  or ranking of the predictions. This will come later. 

    Also we do have more data (for example rms values) which we did not include.

    Email Problems or Queries to Kim Henrick, John Tate