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

Hosted By EMBL/EBI-MSD Group

Fourth CAPRI Evaluation Meeting, Barcelona Dec. 9-11, 2009

The 4th CAPRI meeting will be organised in Barcelona (9-11 Dec 09) . The program and registration details can be found on the following web page:

http://mmb.pcb.ub.es/capri2009/

ROUND 19 ANNOUNCEMENT

ROUND 19

To download the target coordinates you must agree to the following conditions at the time of download.

Agreement (pdf)

To Register please email

Joel Janin, joel.janin@u-psud.fr, Sameer Velankar sameer@ebi.ac.uk

Send

Team Leader Name:

e-Mail Address:

Staff Position At your Institute:

If a Team is submitting

For each member please send Name: & email:

ROUND 19 Timeline

Target T41 - protein-protein complex (unbound/unbound)

Target T42 - protein-protein complex (unbound)

31st Aug 2009 - Round 19 opens - prediction of T41 and T42

20th Sept 2009 - Deadline for submitting models of T41 and T42

24th Sept 2009 - Scoring Starts

27th Sept 2009 - Deadline for Scoring submissions

Protein-protein interactions and other interactions between macromolecules are essential to all aspects of biology and medical sciences, and a number of methods have been developed to predict them. CAPRI is a community wide experiment designed to assess those that are based on structure. If we know the 3D structure of two components of a complex and build a model of their assembly, how reliable and accurate is that model likely to be?

CAPRI is a blind prediction experiment managed by capri management . Its targets are unpublished crystal or NMR structures of complexes, communicated on a confidential basis by their authors to the CAPRI management. Participant predictor groups are given the atomic coordinates of two proteins that make biologically relevant interactions. They model the target complex with the help of the coordinates and other publicly available data (sequence, mutations etc~), and submit sets of ten models for assessment on the CAPRI Web site. In addition, the predictors are invited to upload larger sets that are communicated to scorer groups who evaluate and rank them, and make a separate ten-model submission. After the prediction round is completed, the CAPRI assessors compare the submissions to the experimental structure, et evaluate the models on criteria that depend on the geometry and biological relevance of the predicted interactions.

Since CAPRI began in 2001, the experiment has had two to four prediction rounds each year, with one or a few targets per round. Each round is announced a week in advance, it lasts 3-6 weeks, and the results are known in the following weeks. To be on the mailing list, please send a message to Sameer Velankar.

Structural biologists and scientists actively engaged in the study macromolecular interactions are invited to participate:

by offering targets -more information

by registering prediction rounds as predictors and/or scorers

Please read and observe the rules of the experiment and the confidentiality agreement that all CAPRI participants must sign.

Information on targets of past CAPRI rounds is available here

Capri Target Publications

Publications on past CAPRI rounds:

From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent , Proteins: Structure, Function, and Bioinformatics, Volume 69, Issue 4, 2007. 697-872

Special Issue: Second Meeting on the Critical Assessment of PRedicted InteractionsProteins: Structure, Function, and Bioinformatics,Volume 60, Issue 2, 2005. 1-323

Special Issue: CAPRI - Critical Assessment of PRedicted InteractionSpecial Issue: CAPRI - Critical Assessment of PRedicted Interaction, Volume 52, Issue 1, 2003. 1-122

Other publications:

Welcome to CAPRI: A Critical Assessment of PRedicted Interactions Jol Janin, Proteins: Structure, Function, and Genetics Volume 47, Issue 3, 2002. Pages: 257 ( Local Copy: Call For Targets )

Meeting Report. Modeling of protein interactions in genomes Sandor Vajda, Ilya A. Vakser, Michael J.E. Sternberg, Joel Janin, Proteins: Structure, Function, and Genetics Volume 47, Issue 4, 2002. Pages: 444-446 ( Local Copy: Meeting Report )

Assessing predictions of protein-protein interaction: The CAPRI Experiment. J Janin (2005) Protein Sci. 14:278-283.

The Third CAPRI Assessment Meeting, Toronto, Canada, April 20-21, 2007. J. Janin, SJ Wodak (2007) Structure 15, 755-759.

Email Problems or Queries to Sameer Velankar