Introduction

Methods for obtaining information about protein structure from the 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. Meeting abstracts and predictions are also available.

We now announce the second experiment. As before, the goal is to obtain an indepth 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 in advance of the meeting. Sessions will be devoted to presentation of the results and comparison with experiment, and to the description of the methods used.

Experiment:

Categories

The prediction experiment will be divided into 4 catagories, 3 as in CASP1 with one new prediction catagory:

1. Comparative modeling:
   Where there is a clear sequence relationship between the target structure and one or more known structures.

2. Fold recognition ('threading'):
   Testing a sequence for compatibility against a library of folds.

3. Ab initio structure prediction:
   Deriving structures, approximate or otherwise, from sequence.

4. Docking: (new)
   Predicting the mode of association of ligands and proteins.

Collection of Prediction Targets

As before, for the experiment to succeed, it is essential that we obtain the help of the experimental community. Therefore we would like to invite Protein crystallographers and NMR spectroscopists to provide details of structures they expect to have solved before 1st October 1996. They are also asked to notify the organizers shortly before the structure is solved.

Rules for Predictors

Participation in the experiment is open to all. In each category there will be a set of designated core targets. In order for their work to be considered part of the experiment, predictors will be required to make submissions on at last three members of that core set. A minimum amount of information about methods used will also be required from each predictor.

Target sequences for prediction can be viewed from the database here, which will be updated as sequences become available from the experimentalists.

Those interested in the prediction experiment can register and be added to a mailing list. Registered predictors will be notified of changes to the expiry dates for target sequences - all predictions must be received before the expiry date to be considered for evalution. Thus there will be no fixed time lines, each structure being available for a period dependent on the experimental situation.

Predictions will be sent to the independent assessors and evaluted according to a set of standard criteria. All prediction submission will be electronic via web forms or electronic mail and in machine readable formats which will be announced later.

Criteria for Assessing the Predictions

A team of independent assessors will evaluate the predicted structures primarily using numerical criteria that are currently being debated. Following feed back from the prediction community, software will be developed to allow these criteria to be applied to all predictions automatically. As far as possible assessments will be made from these automatic evaluations, supplemented where necessary by judgements from the assessors.

Inclusion in the Structure Prediction Databank

All predictions will be entered into the structure prediction databank currently being established and will be made public after the meeting.

Meeting:

A meeting will be held 12-16 December, 1996 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.

Program

There will be lectures by the assessors and the more successful predictors and a moderated discussion on the state of art in each category. Emphasis will be on what went right and what went wrong, and on what progress has been made since the first experiment. In particular, in what areas further effort is likely to pay off in terms of improved predictions. There will also be poster sessions and informal sessions using computer workstations. Broadly one day will be devoted to each category, depending on the levels of response.

Publication

The proceedings of the meeting will be refereed and published in Proteins.

Timetable

February 15 '96 - March 1 '96

Request for comments on draft evaluation criteria.

March 7 '96 - October 15 '96

Distribution of targets to predictors as they become available, withdrawal of structures as they are solved. Collection of predictions.

December 12 - 16 '96

Meeting, Asilomar, California

Organizing Committee

Tim Hubbard       Co-chair   Centre for Protein Engineering, Cambridge, UK
Steve Bryant      Co-chair   NCBI, National Library of Medicine, USA
John Moult        President  CARB, University of Maryland, USA
Jan T. Pedersen              CARB, University of Maryland, USA
Krzysztof Fidelis            Lawrence Livermore National Laboratory, USA
Rod Balhorn                  Lawrence Livermore National Laboratory, USA
Richard Judson               Sandia National Laboratory, USA.