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Accueil > Recherche > Equipes de recherche > Computational Molecular Systems Biology > Projects

Computational Molecular Systems Biology

CAPRI and Protein docking

Protein docking ensemble CAPRI Target 26, showing both unbound (blue, red) and bound (cyan, orange) binding partners simultaneously, as well the geometric centers of the ensemble of CAPRI docking predictions as colored spheres. Predictions nearing the native solutions are colored blue or green, depending on prediction quality.

Computational protein-protein docking is the procedure of producing a three-dimensional structure of the complex, starting from the individual structure of the interacting components. The CAPRI protein-protein docking experiment is a community-wide effort, aimed at the improvement of computational protein docking methods. It does so by working in close collaboration with experimental scientists, who make their data available to this community, in the fullest confidence and prior to publication. The number of research teams worldwide participating in the experiment lies around one hundred, of which a selection of 40 participate in any given target round. Our team is responsible for the scientific organization and evaluation of the predicted models. Our development and implementation of the assessment criteria and their application to community-wide predictions present a coherent assessment of protein docking methods and define the state of the art in computational protein docking.

The latest set of targets represented the most diverse set of complexes ever encountered in CAPRI (Lensink and Wodak, 2013). The experiment now includes the prediction of multi-component assemblies, protein-nucleic acid and protein-polysaccharide binding, but also of binding affinities and the positions of interfacial water molecules.

The CAPRI Management Committee (MC) establishes guidelines and oversees the experiment. It makes decisions concerning CAPRI targets, the protocol for evaluating models, the planning of CAPRI assessment meetings, and represents CAPRI at various scientific meetings. The current composition of the MC is as follows :

  • Alexandre Bonvin, Utrecht University, The Netherlands
  • Marc Lensink, CNRS & University Lille North of France, France
  • Michael Sternberg, Imperial College London, UK
  • Sandor Vajda, Boston University, USA
  • Ilya Vakser, University of Kansas, USA
  • Sameer Velankar, European Bioinformatics Institute, UK
  • Zhiping Weng, University of Massachussetts Medical School, USA
  • Shoshana Wodak, University of Toronto & Hospital for Sick Children, Canada

The MC has recently established a Target Committee (TC), whose responsibility it is to represent and promote CAPRI in the experimental community, and actively hunt for targets. Present members of the TC are :

  • Shoshana Wodak, University of Toronto & Hospital for Sick Children, Canada
  • Tassos Perakis, Netherlands Cancer Institute, The Netherlands
  • Vincent Villeret, CNRS & University Lille North of France, France