CASP3 general announcement

PREDICTION CENTER CASP3 casp3 at sb7.llnl.gov
Tue May 19 00:10:04 EST 1998





Announcing the Third Community Wide Experiment on the 
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          Critical Assessment of  Techniques 
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          for Protein Structure Prediction    
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Introduction
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Methods for obtaining information about protein structure from
amino acid sequence have apparently been advancing rapidly. But
just what can these methods currently deliver?

A first large scale experiment aimed at beginning to answer these
questions was conducted in 1994, and culminated in a meeting at
Asilomar, California at the end of that year. Some 135
predictions were made by 35 different groups. The results are
published in a special issue of Proteins: Structure, Function and
Genetics, volume 23, No 3, November 1995.

A second meeting in December 1996 was the culmination of a 9
month long, community wide experiment. Forty-two structural
targets provided by crystallographers and NMR spectroscopists
were made available to the prediction community. Prior to the
public release of structures, more than 900 predictions by
approximately 70 research groups world wide were collected. The
results are published in a special issue of Proteins:
Structure, Function and Genetics, Suppl.1, 1997.

Details of the predictions from both experiments and full
analysis of CASP2 prediction data are available at
http://PredictionCenter.llnl.gov/.

We now announce the third experiment. As before, the goal is to
obtain an in-depth and objective assessment of our current
abilities and inabilities in this area. To this end, participants
will predict as much as possible about a set of soon to be known
structures. These will be true predictions, not 'post-dictions'.

Experiment
----------

The broad goals of the experiment are to address the following
questions about the current state of the art in protein structure
prediction:

       1. Are the models produced similar to the corresponding
     experimental structure?
       2. Are the models correctly aligned with the experimental
     structures?
       3. Have similar structures that a model can be based on been
     identified?
  4. Are the details of the models correct?
  5. Has there been progress between CASP2 and CASP3?
  6. What methods are most effective?
  7. Where can future effort must be productively be focused?

As in CASP2, all types of methods for predicting protein
structure will be considered. However, docking predictions will
not be included in CASP3, since a separate experiment is being
planned to evaluate this area.

Collection of Prediction Targets
--------------------------------

For the experiment to succeed, it is essential that we obtain the
help of the experimental community. Therefore we invite Protein
crystallographers and NMR spectroscopists to provide details of
structures they expect to have made public before 1st October
1998, using the target submission form available at
http://PredictionCenter.llnl.gov/casp3.

Participation
-------------

Participation in the experiment is open to all. Intending
predictors must register at the web site. Those interested in
receiving mailings concerning progress of the experiment may also
register as 'observers' . Prediction targets will be made
available through the web site. All targets will be assigned an
expiry date, and predictions must be received and accepted before
that expiration.

Assessment of Predictions
-------------------------

As in previous CASPs, independent assessors will evaluate the
predictions. There will be three assessors, representing
expertise in the comparative modeling, fold recognition and ab
initio prediction areas.  Assessors will be provided with the
results of numerical evaluation of the predictions, and will
judge the results primarily on that basis. Numerical evaluation
criteria have been revised from those used in CASP2, and are now
being finalized, in consultation with the prediction community.
The assessors will be asked to focus particularly on the
effectiveness of different methods.

Release of Results
------------------

All predictions and prediction evaluations will be made available
through the web site, shortly before the meeting.

Meeting
-------

A meeting will be held 13-17 December, 1998 at Asilomar,
California, USA to evaluate the results of the prediction
experiment. The meeting will be limited to about 170 participants
and precedence will be given to active predictors. It is
anticipated that some financial assistance will be available for
the more successful predictors. The proceedings of the meeting
will be published.

Organizing Committee
--------------------

John Moult            CARB, University of Maryland, USA
Tim Hubbard           Sanger Centre, Hinxton, UK
Jan Pedersen          Acadia Pharmaceuticals, Denmark
Krzysztof Fidelis     Lawrence Livermore National Laboratory, USA

Support
-------

The organizers gratefully acknowledge support for the CASP3
experiment from the Department of Energy, the National Library of
Medicine and the National Institute of Standards and Technology.

Queries
-------

Further details are available at the web site
(http://PredictionCenter.llnl.gov/casp3)
Please address any questions or queries to
casp3 at PredictionCenter.llnl.gov







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