The main goal of CASP is to obtain an in-depth and objective assessment of our current abilities and inabilities in the area of protein structure prediction. 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’ made on already known structures.

CASP7 will particularly address the following questions:

Are the models produced similar to the corresponding experimental structure?
Is the mapping of the target sequence onto the proposed structure (i.e. the alignment) correct?
Have similar structures that a model can be based on been identified?
Are comparative models more accurate than can be obtained by simply copying the best template?
Has there been progress from the earlier CASPs?
What methods are most effective?
Where can future effort be most productively focused?

Scope

Tertiary structure predictions. For CASP7, categories have been redefined to reflect developments in methods. The 'Template based modeling' category will include all former comparative modeling, homologous fold based models and some analogous fold based models. As in CASP6, the 'Template free modeling' category will include models of proteins with previously unseen folds and hard analogous fold based models.

High resolution models. This new category will include a subset of tertiary structure models where the backbone is sufficiently accurate that the details of side chains, loops, and active sites can be meaningfully assessed. Particular attention will be paid to success in refining these models beyond the quality obtained by simply copying a best template. A separate assessor will judge these high accuracy modeling cases.

Other predictions. As in previous CASPs, we will be assessing the ability of predictors to define boundaries of structural domains, detect residue-residue contacts and identify disordered regions in target proteins. Function prediction, a new category introduced in CASP6, will again be assessed in CASP7. As suggested at the CASP6 meeting, we will also evaluate ability of predictors to judge on quality of models (without knowing native structures) and reliability of predicting certain residues in the structure. Because of its importance in producing high accuracy models, in CASP7 special attention will also be given to model refinement.

Related Experiments

There will be additional activities included in or related to CASP7, which extend its scope.

Large scaling benchmarking: It is hoped that the results of well run benchmarking experiments such as EVA and LIVEBENCH will also be discussed at the CASP meeting.
SAC-CASP7: Alike to 2002 and 2004, the CASP meeting will be joined by the Student Addendum Conference. SAC-CASP7 will use the same conference facilities as CASP7. It will start (tentatively) the day before CASP7 and will last one day. Details about this Conference can be found at SAC-CASP7 web page.

Timetable

Registration for the experiment starts in April. The first targets are expected to be available at the beginning of May. The prediction season will run for approximately three months from May through July. (for detailed CASP7 prediction season timeframe check April 26 announcement in News) . The CASP meeting will take place at the end of November, and approximately one month before that, groups with the most accurate and interesting predictions will receive invitations to give talks. There will also be discussion of predictions and methods on the FORCASP web site.

Participation

Participation is open to all. Intending participants, and those interested in receiving mailings concerning progress of the experiment should register for the experiment. The predictors with servers are requested to register immediately as we are planning on having a dry run for servers in mid-April.

Targets

For the experiment to succeed, it is essential that we obtain the help of the experimental community. As in previous CASPs, we will invite protein crystallographers and NMR spectroscopists to provide details of structures they expect to have made public before September 1, 2006. A target submission form will be available at this web site in mid-April. Prediction targets will be made available through this web site. All targets will be assigned an expiry date, and predictions must be received and accepted before that expiration date.

Submission of Predictions

Predictions must be submitted to this web site in CASP format. For 3D coordinate predictions, this is a simple PDB-like file with consecutive numbering of residues 1 -> N and a small number of required headers.

Assessment of Predictions

As in previous CASPs, independent assessors will evaluate the predictions. Assessors will be provided with the results of numerical evaluation of the predictions, and will judge the results primarily on that basis. They will be asked to focus particularly on the effectiveness of different methods. Numerical evaluation criteria will as far as possible be similar to those used in previous CASPs, although the assessors may be permitted to introduce some additional ones.

There are four assessors, representing expertise in the template-based modeling, template-free modeling, high accuracy modeling and function prediction:
       Torsten Schwede (SIB & University of Basel, Switzerland) - for template based modeling
       Neil Clarke (Genome Institute of Singapore) - for template free modeling
       Randy Read (University of Cambridge, UK) - for high resolution modeling
       Alfonso Valencia (CNB, Madrid) - for function prediction

In accordance with CASP policy, assessors are not directly involved in the organization of the experiment, nor can they take part in the experiment as predictors. Predictors must not contact assessors directly with queries, but rather these should be sent to the email address. Click here for the list of previous CASP assessors.

Results and Publication

All CASP predictions and evaluations will be made available through this web site shortly before the meeting. The proceedings of the meeting will be published. All participants will also be encouraged to fully report their results and methods on the FORCASP web site. Contributions to the site will be discussed and scored by other predictors, and this material will be taken into account in choosing some presentations at the meeting.

Meeting

A meeting to evaluate the results of the prediction experiment will be held at the Asilomar Conference Center (Pacific Grove, California, USA) on November 26-30, 2006. The meeting will be limited to about 200 participants and precedence will be given to active predictors. Some financial assistance will be available for the most successful predictors.

Organizing Committee

John Moult, CARB, University of Maryland, USA

       Krzysztof Fidelis, University of California, Davis, USA
       Tim Hubbard, Welcome Trust Sanger Institute, Hinxton, UK
       Andriy Kryshtafovych, University of California, Davis, USA
       Burkhard Rost, Columbia University, New York, USA
       Anna Tramontano, University of Rome, Italy

Please address any questions or queries to

Protein Structure Prediction Center