Critical Assessment of Predicted Interactions - Wodak Lab

capri imagePredictions for Target 21 (CAPRI Round 7): the complex of Yeast Orc1-BAH and Sir1p OIR Domains (PDB code: 1ZHI). The receptor molecule (Orc1-BAH) is depicted by its molecular envelope; the ligand molecule is depicted by its ribbon diagram (unbound (blue) bound version (light blue). Small spheres represent the center of mass of ligands in the structure of complexes predicted by groups participating in the CAPRI experiment.

CAPRI is a community wide experiment tailored after CASP (Critical Assessment of Structure Predictions), which deals with the assessment of protein-protein docking methods. Crystallographers provide the atomic coordinates of protein complexes prior to publication, and registered predictor groups predict the 3D structure of the complex starting from the known structure of the components (usually in the unbound form), without any knowledge of the correct answer.

Shoshana Wodak serves on the CAPRI Management Committee, and works with Dr. Marc Lensink (Université Libre de Bruxelles, Belgium) on the assessment of the CAPRI predictions. The last CAPRI evaluation meeting was held in April 2007 in Toronto. For more information on the CAPRI experiment please consult the official CAPRI Web-site, and the following published accounts of the CAPRI experiments:

The CAPRI Management Committee is actively looking for new targets for the CAPRI experiment. Structural biologists ( crystallographers and NMR experts) interested in submitting targets should contact Shoshana Wodak, or Joel Janin

List of CAPRI related publications...

  • Wodak SJ. No Abstract From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent. Proteins. 2007 Dec 1;69(4):697-8. No abstract available.
  • Janin J, Wodak S. The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. Structure. 2007 Jul;15(7):755-9.
  • Lensink MF, Méndez R, Wodak SJ. Abstract Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins. 2007 Dec 1;69(4):704-18.
  • Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ; Critical Assessment of PRedicted Interactions. Abstract CAPRI: a Critical Assessment of PRedicted Interactions. Proteins. 2003 Jul 1;52(1):2-9.
  • Méndez R, Leplae R, Lensink MF, Wodak SJ. Abstract Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins. 2005 Aug 1;60(2):150-69.
  • S. Wodak & R. Mendez (2004) Predictions of Protein-Protein Interactions: The CAPRI Experiment, Its Evaluation and Implications Curr. Opin. Struct. Biol. Apr;14(2):242-249
  • R. Mendez, R. Leplae, S. Wodak (2003) Assessment of blind predictions: current status of docking methods Proteins Struct. Func. & Bioinfo. 52: 51-67
  • S. Wodak & J. Janin (2002) The Structural Basis of Macromolecular recognition, Adv. In Protein Chemistry, 61, 9-73,
Wodak Lab:
Critical Assessment of Predicted Interactions