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Critical Assessment of Techniques for Protein Structure Prediction

Continuous CASP Model Refinement Experiment
CASPR

Sponsored by:
the National Institute of General Medical Sciences (NIH/NIGMS), US National Library of Medicine (NIH/NLM)

News
Targets (get all)
Participants
Refinement Models

TMR01
TMR02
TMR03
TMR04
TMR05
TMR06
TMR07
Registration is closed Submission facility is closed Model Viewer

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CASPR in numbers (statistics)

Description of the experiment

Over the course of the CASP experiments, it has become clear that refinement of comparative models of protein structure is a major challenge. In spite of considerable effort, there has been little or no progress in a decade.

To increase discussion and hopefully progress as well, we are conducting a 'between-CASP's refinement experiment, using some of the models submitted in CASP6 as starting structures, and asking members for the CASP and molecular dynamics communities to test methods of refining these. The goal is to use any method you like to refine these approximate structures closer to experiment. These will not be blind predictions. We hope that any apparently successful methods will be also be used in CASP7, allowing rigorous evaluation. The idea here is to allow testing and development of methods outside of the hectic atmosphere of CASP proper, and in particular, to encourage discussion of the issues and new ideas.

Four CASP6 models were originally selected as refinement targets for this experiment. Additional 3 targets were added to the experiment on March 1 (details - in the Targets column of the table above).

The experiment is organized as follows. Using this web site you may

register as a participant (please also register at the FORCASP community site, if you have not already done so, for the discussion of the experiment details).
download starting structures
submit refined models by March 31, 2006.

All submissions and analysis will be made available through the Prediction Center website. Submissions should be in the proper format and will initially be screened in terms of Calpha RMSD of the refined structures against the experimental structures. Other CASP evaluation software will also be used. Models showing a significant improvement will be reported and discussed on the FORCASP web site.

In parallel, we encourage discussion on FORCASP of all aspects of this experiment - potential new methods, criticism of existing methods, suggestions for improving the experiment, analysis of the results once they become available.

Let us know if you have any questions. We would like to involve as many of the community as possible. So, please let your colleagues working in the relevant area know about the experiment.

Please address any questions or queries to casp@predictioncenter.org

CASP organizers 1/31/2006
Last updated 3/1/2006

Protein Structure Prediction Center