Protein Structure Prediction Competition

Ram Samudrala ram at
Tue Sep 13 01:13:37 EST 1994

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  Meeting on the Critical assessment of Techniques for Protein 
                      Structure Prediction
  December 4 - 8 1994, Asilomar Conference Center, California,


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? The goal of the workshop is
to provide an indepth and objective assessment of our current
abilities and inabilities in this area. To this end, prediction teams
are predicting as much as possible about a set of soon to be known
structures.  Sessions at the meeting will be devoted to presentation
of the results and comparison with experiment, and to the description
of the methods used.


Prediction methods are divided into three classes:

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
with a library of folds.

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

Current Status of the Predictions:

Details of a total of 25 target structures have so far been received
from the experimentalists. Information about these can be found on the
anonymous ftp site at Not all of these structures
will be predicted, but with approximately three months prediction time
still to go, predictions have been received on eight of them. A total
of 10 groups have already made at least one prediction, and a number
of other groups have declared a serious intent to take part. The
current list is as follows:

Geoffrey Barton, Oxford University, UK
Steve Benner, ETH, Zurich, Switzerland
Tom Blundell, University of London, UK
Steve Bryant, NLM, Bethesda, USA
David Covell, NCI, Frederick, USA
Andrew Coulson, University of Edinburgh, UK
David Eisenberg, UCLA, USA
Adam Godzik, Scripps, USA
Tim Hubbard, MRC, Cambridge,UK
Rod Hubbard, MSI, USA.
Yo Matsuo, PERI, Japan
David Mosenkis, Tripos, USA
Chris Sander, EMBL, Germany
Harold Scheraga, Cornell University, USA
Manfred Sippl, University of Salzburg, Austria
Janet Thornton, University of London, UK
Gert Vriend, EMBL, Germany
Irene Weber,  Thomas Jefferson University,  USA
Peter Wolynes, University of Illinois, USA.

Prediction Arrangements:

Predictors say which category they intend to submit in, and declare a
serious intent to submit. They are provided with the sequences and
origins of the structures to be determined as they become available
from the experimentalists, and are asked to stop work on a structure
and submit their results with (hopefully) at least three weeks notice.
Predictions are sent to the independent assessors. Thus there are no
fixed time lines, each structure being available for a period dependent
on the experimental situation.

Those wishing to make predictions should contact:
John Moult     jmoult at    tel: 301-738 6241
                                             Fax: 301-738 6255
Criteria for Assessing the Predictions: 

A team of independent assessors will evaluate the predicted
structures.  As far as possible, assessments will be made objectively,
using predefined criteria, supplemented where necessary by comments
from the assessors. The primary assessors are:

Michael James, University of Alberta, Canada (Comparative modeling)
Shoshana Wodak, Free University of Brussels, Belgium (Threading)
Fred Cohen, UCSF, USA (Ab initio methods).


The proceedings of the meeting will be published, preferably in a
refereed journal. Arrangements for publication are nearing completion.

Meeting Program:

December 4:

     Afternoon : Arrival and registration
     Evening   : Dinner, Introductory lecture.

December 5, 6, 7:

One day devoted to each of the three categories of prediction:
Comparative modeling, threading and ab initio methods. Each day as

     Morning:  : Overview by the primary assessor in that area.                             
                 Lectures on the most successful and interesting
     Afternoon : Free time
                 Poster session
                 Informal session using workstations
     Evening   : Round table discussion of the implications of  the          
                 day's  results

 December 8:

     Morning    : Lectures on emerging techniques
     After lunch: End of meeting.
Those wishing to attend the meeting should fill in and return the
accompanying application form. Since space is limited applications
will be reviewed by the organizing committee. Preference will be
given to early applications.  

Organizing committee:
John Moult               CARB, University of Maryland 
Jan T. Pedersen          CARB, University of Maryland
Krzysztof Fidelis        Lawrence Livermore National Laboratory.
Rod Balhorn              Lawrence Livermore National Laboratory.
Richard  Judson          Sandia National Laboratory
Walt Stevens             National Institute of Standards and Technology

---------------------------- Cut Here -------------------
Meeting on the Critical assessment of Techniques for 
	    Protein Structure Prediction


This meeting has a limited attendence of approximately 100.
If you wish to attend, please complete the following 






Phone:_________________ FAX:________________



Student                ____

Post-doc               ____

Academic Faculty       ____

Industry               ____

Other (please specify) _______________

Please give a brief description of your research interests:




Some financial assistance (i.e. payment for lodging and meals 
and a waiver of the conference fee) will be available for 
students and post-docs. Please indicate if you wish to be 
considered for assistance: ________


Meeting:   Academics  $150
	   Others     $300

Lodging and Meals:    $250 (double occupancy)
NOTE: Most rooms are double occupancy.
      A very limited number of single rooms will be available. 
      Single room surcharge will be $100.

Check here if you are interested in a single room ______

Send application, but no money to:

Richard Judson
Sandia National Laboratories
Livermore, CA 94551-0969. 

email: rsjuds at
FAX:   (510) 294-2234
Phone  (510) 294-1438

Deadline for application:  1 October, 1994.
Preference will be given to early respondents 
Decisions on attendence will be sent out by 
October 15 at the latest.


Ram Samudrala      
ram at 

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