Call for prediction targets for CASP3

Tim Hubbard th at sanger.ac.uk
Tue Jul 7 07:58:27 EST 1998


Call for prediction targets for CASP3
=====================================

This is a call to X-ray crystallographers and NMR spectroscopists for
targets for CASP3, the third experiment in critical assessment of
techniques for protein structure prediction.

In 1994 the first protein structure prediction experiment was held to
evaluate prediction methods through blind prediction.  Details of about 33
protein sequences, which were expected to be solved before the end of 1994,
were submitted by experimentalists and this allowed 135 blind predictions
to be made by 35 different groups.  The results of the experiment are
published in the November 1995 issue of Proteins: Structure, Function, and
Genetics, volume 23, No 3.

A second meeting on the Critical Assessment of Techniques for Protein
Structure Prediction (December 1996) was a culmination of the second 9
month long,
community wide experiment.  Before that meeting, 42 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, and led to the most objective assessment of prediction methods
so far. The results are published in a special issue of Proteins:
Structure, Function and Genetics, Suppl.1, 1997.

The third experiment is now running and will culminate in a meeting in
December 1998. 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 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.

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 who expect to solve a
structure before 1st October 1998 to submit the sequence so that attempts
can be made to predict it before it is publically announced.  Each
prediction will be given a deadline  prior to the date on which the first
information about the structure is to be made public.

Targets of all sizes and types are required. Small structures (less than
100 residues) are needed to test some of the ab initio structure prediction
methods. Proteins with folds related to those of known structures are
needed to test fold identification methods.  Proteins with sequences
homologous to that of one or more known structures are needed to test
comparative modeling methods.  We would like to collect as many targets are
possible.

All that is requested is:

- the sequence or a sequence accession number of the protein

- an estimate of the likely date of public release (and updates if the work
procedes faster or slower)

- a commitment to make the coordinates available to the independent
assessors not latter than 1st October should the structure be solved by
then.

Any coordinates provided will be treated with strict confidentiality as
requested and used only to evalute the accuracy of predictions.

For further information and on-line forms and documents see:

        http://predictioncenter.llnl.gov/casp3/

A Target protein submission form is also attached to this message and can
be mailed to casp3 at predictioncenter.llnl.gov

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

CASP3 organising committee

----

Instructions for completing this form
-------------------------------------

(0) Please only use this form if you are unable to complete the WWW version at
    http://predictioncenter.llnl.gov/casp3/
(1) Save this page as a text file
(2) Complete all sections
(3) send by email to casp3 at predictioncenter.llnl.gov
(4) if you have filled out the form correctly, you should receive an
    email acknowledgement (though not necessarily immediately)



cut here
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CASP3: Third Community Wide Experiment on the Critical Assessment of
Techniques for Protein Structure Prediction

Target submission form
======================

This is the text version of the Prediction target submission form for
the Third Critical Assessment of Techniques for Protein Structure
Prediction Experiment (CASP3).

Introduction
============

Protein crystallographers and NMR spectroscopists are asked to provide
details of structures they expect to have solved before 1st September
1998 using this form.

Targets of all sizes and types are required. Small structures (less
than 100 residues) are needed to test some of the ab initio structure
prediction methods. Proteins with folds related to those of known
structures are needed to test fold recognition methods.  Proteins with
sequences homologous to that of one or more known structures are
needed to test comparative modelling methods.

To be useful to the predictors, a period of at least a month is
required before any details of the structure will be released. Please
notify us immediately when the details are going to be made public, so
that we can ask the predictors to stop work in a timely manner.  This
can be done by sending a mail to casp3 at predictioncenter.llnl.gov

In order for the predictions to be assessed in time for the meeting in
December, we will need a set of co-ordinates by the beginning of
September at the latest. If necessary, these can be for limited
distribution until the meeting.

A. Scientific information
=========================

1. [                         ] Protein Name

2. [                         ] Organism Name

3. [        ] Number of amino acids (does not need to be exact)

Please provide accession number and the name of the database of the
protein (4. and 5.) or the actual sequence (6.) (both if possible).

4. [                         ] Accession number

5. Sequence Database
   [ ] Swiss-prot  [ ] PIR  [ ] Genbank  [ ] EMBL  [ ] Other [               ]

6. Amino acid sequence











One letter code (ACEDFTK) is preferred, but three letter code (ala cys glu asp)
can also be processed.

7. Are there homologous sequences of known structure to this protein
                                                            Yes [ ] No [ ]

8. Current state of the experimental work

Please describe briefly where things are at, addressing as many of the
following points as you wish to/are relevant/can.  The more
information, the easier it is for a modeler to decide whether to
predict your structure.

Protein supply?  Crystals?  Diffraction quality?
Molecular replacement in progress?  Molecular replacement solution in hand?
Heavy atom derivative search in progress?  Heavy atom derivatives in hand?

























9. Do you already have an interpretable map?               Yes [ ] No [ ]

10. [                         ]  Estimated date of chain tracing completion.

In order to assess the predictions before the meeting, this date
should be before 1st September 1998.

11. [                         ]  Estimated date of public release of structure

12. If you have any other useful information about this sequence
family please enter it below












B. Administrative information
=============================

13. [                         ] Name

14. Mailing address:

    [                                   ] Institution
    [                                   ] Street/P.O. Box
    [                                   ] City
    [                                   ] State/Province
    [                                   ] ZIP/Postal code
    [                                   ] Country

15. [                         ] Tel

16. [                         ] Fax

17. [                         ] Email

18. How did you hear about this prediction experiment?
    [ ] Nature Add  [ ] Poster  [ ] Newsgroup  [ ] Email
    [ ] Other  [                                       ]

19. Do you wish to remain anonymous until the structure is publically
    announced?                                             Yes [ ] No [ ]

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Dr Tim Hubbard                         email: th at sanger.ac.uk
Head, Human Genome Analysis            Tel (direct): +44 1223 494983
Sanger Centre                          Tel (switch): +44 1223 834244
Wellcome Trust Genome Campus, Hinxton  Fax: +44 1223 494919
Cambridgeshire. CB10 1SA. UK.          URL: http://www.sanger.ac.uk/Users/th
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