Introduction

CASP experiments aim at establishing the current state of the art in protein structure prediction, identifying what progress has been made, and highlighting where future effort may be most productively focused.

There have been three previous experiments, in 1994, 1996 and 1998. Full details of these may be found at the CASP web site, http://predictioncenter.org/, and in the special issues of the journal PROTEINS: 23(5), 1995; Suppl 1, 1997 and Suppl 3, 1999. In CASP3, 98 prediction groups from all around the world took part.

We now announce the fourth 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’ made on already known structures.

The experiment will begin in April 2000, when the first prediction targets will be made available. The prediction season will run through August. There will be a meeting at the Asilomar Conference Center in California December 3 - 7^th, to discuss the results.

Scope of CASP4 and Related Experiments

As in earlier CASPs, all types of methods for predicting protein structure will be considered, ranging from comparative modeling through fold recognition and ab initio prediction. Most emphasis will be on tertiary structure prediction but secondary structure and contact prediction methods will also be included. In addition, there will be two other experiments run in parallel with CASP4, which will extend the scope substantially:

CAFASP2: In the era of genome sequencing, rapid protein structure modeling methods have a critical role to play. This experiment, led by Dani Fischer, will evaluate automatic methods of predicting protein structure, using the CASP targets. All targets will be processed through prediction servers that register for the experiment. Models will be evaluated by the same numerical criteria as used for CASP4, and a session at the CASP4 meeting will compare performance through the servers with that obtained when full human participation is allowed. Further details of this experiment may be found at http://www.cs.bgu.ac.il/~dfischer/CAFASP2

CATFEE: Rational drug design can be greatly accelerated by identification and evaluation of potential ligands in silico. This experiment, led by Raul Cachau and Adrian Roitberg, will evaluate the state of the art in protein ligand docking, based on bona fide predictions made on specialized targets. There will be a meeting at Asilomar, immediately after the CASP4 one, to assess the results. Further details of this experiment may be found at http://uqbar.ncifcrf.gov/~catfee/

Experiment

The broad goals of the CASP4 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. Is the mapping of the target sequence onto the proposed structure (i.e. the alignment) correct?
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 from the earlier CASPs?
6. What methods are most effective?
7. Where can future effort be most productively focused?

In addition, a set of more specific goals, based on the apparent barriers to progress at CASP3, will be paid particular attention. Suggested goals are:

1. Improved refinement of comparative modeling structures.
2. Accurate comparative modeling, such that functional differences within sequence families can be deduced.
3. Improved sequence to structure alignment for all categories of model.
4. Reliable estimates of accuracy for secondary structure prediction.
5. Predictions that test hypotheses concerning the nature of the forces and folding mechanisms.
6. Bold new methods aimed at removing current bottlenecks to progress.

The exact set of specific goals has still to be finalized, following discussion with the consultancy groups. Participants are advised to check for revisions.

Collection of Prediction Targets

For the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore, starting at the beginning of April, we will invite protein crystallographers and NMR spectroscopists to provide details of structures they expect to have made public before 1st October 2000.

Participation

Participation in the experiment will be 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 date.

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 of earlier CASPs, 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 this web site, shortly before the meeting.

Meeting

A meeting will be held 3-7 December, 2000 at Asilomar, California, USA to evaluate the results of the prediction experiment. The meeting will be limited to about 200 participants and precedence will be given to active predictors. It is hoped that some financial assistance will be available for the more successful predictors. The proceedings of the meeting will be published.

Organizing Committee

John Moult, (jmoult@tunc.org), CARB, University of Maryland, USA
Tim Hubbard, (th@sanger.ac.uk), Sanger Centre, Hinxton, UK
Krzysztof Fidelis, (fidelis@llnl.gov), Lawrence Livermore National Laboratory, USA
Adam Zemla, (adamz@llnl.gov), Lawrence Livermore National Laboratory, USA

Prediction process and logistic support is provided by the Protein Structure Prediction Center run by Krzysztof Fidelis, Adam Zemla, and Ceslovas Venclovas (venclovas@llnl.gov).

Three Consultancy Groups of experienced predictors will provide advice to the Organizing Committee on the details of the experiment.

Support

The organizers gratefully acknowledge support for the CASP4 experiment from the Department of Energy. Additional support is being sought from other agencies.

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

Protein Structure Prediction Center