Announcement: Call for prediction targets for CASP2

Tim Hubbard th at mrc-cpe.cam.ac.uk
Tue Feb 20 13:50:46 EST 1996


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 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://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.

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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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