prediction-meeting

Miri Hirshberg m-hirshb at anika.nimr.mrc.ac.uk
Tue Jun 18 13:17:06 EST 1996


From: John Moult <tunc at indigo5.carb.nist.gov>
Subject: Appeal for Structure Prediction Targets
Date: Thu, 30 May 1996 15:12:38 -0400 (EDT)

Dear Macromolecular Crystallographer:

   As you may know, the second Asilomar protein structure prediction
experiment (called CASP2) is well underway, with a prediction season
running until October 1, and a meeting in December.  The goal of the
experiment is to obtain as objective a view as possible of what current
protein structure prediction methods are or are not capable of. The
method is to obtain information about soon to be solved structures from
experimentalists, to pass that on to the predictors, and to collect their
models before the structure becomes public. The first experiment, held
during 1994, produced a large amount of interesting and provocative data.
A special issue of PROTEINS (vol 23, no 3, November 1995) contains papers
describing the outcome.  We hope the second experiment will be as
informative. In particular, a big question now is the extent to which the
key problems identified have been solved in the intervening two years. 

You can find out more about the whole process, including the target
situation, from two web sites: 

http://iris4.carb.nist.gov/casp2
http://www.mrc-cpe.cam.ac.uk/casp2

If you would like to be get the mailings associated with the experiment, 
please register there as 'interested'.

So far, we have 58 groups registered as intending to make predictions. 35
teams predicted last time, so we look like on the way to doubling
participation. In contrast to this, we so far have just ten targets, and
we would like to get to around 50. 

So the purpose of this message is to ask you to help with target
provision, if you can. The rules are spelled out on the general target
request below.  We need targets in all four categories, and with expiry
dates between quite soon and October 1.  Even if you do not have any
targets available yourself, please pass this message on to other
experimentalists you think might be interested. We cannot make this
experiment work without again getting the help of the experimental
community. 


                                        John Moult.

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Announcement: Call for prediction targets for CASP2
===================================================

This is a call to X-ray crystallographers and NMR spectroscopists.

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, and led to the most objective assessment
of prediction methods so far.  The results of the experiment are published
in the November 1995 issue of Proteins: Structure, Function, and Genetics.

This is the announcement of the second prediction experiment, which will
run throughout 1996 and culminate in an evaluation meeting in December.

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 1996 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.  Protein-Protein and Protein-Ligand complexes
are required to test docking methods.

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
proceeds 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 evaluate the accuracy of predictions.

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

        http://iris4.carb.nist.gov/casp2/
        http://www.mrc-cpe.cam.ac.uk/casp2/

A Target protein submission form is also attached to this message and can
be mailed to casp2 at mrc-lmb.cam.ac.uk

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.
Richard  Judson               Sandia National Laboratory, USA.

-------------------------------------------------------------------------
CASP2: Second Meeting on the Critical Assessment of Techniques
for Protein Structure Prediction

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

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

(0) Please only use this form if you are unable to complete the WWW version at
    http://iris4.carb.nist.gov/casp2/ or http://www.mrc-cpe.cam.ac.uk/casp2/
(1) Save this page as a text file
(2) Complete all sections
(3) send by email to casp2 at mrc-lmb.cam.ac.uk
(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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CASP2: Second Meeting 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 Second Critical Assessment Techniques for Protein Structure
Prediction Experiment (CASP2).

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

Protein crystallographers and NMR spectroscopists are asked to provide
details of structures they expect to have solved before 1st October
1996 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 casp2 at mrc-lmb.cam.ac.uk.

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
October 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 database of the protein or the actual
sequence (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 October 1996.

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:

    [




                                                                      ]

15. [                         ] Tel

16. [                         ] Fax

17. [                         ] Email

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

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