Predictions 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,