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Modern Concepts in Macromolecular Modeling (Call for Papers)

Teri Klein klein at cgl.ucsf.EDU
Thu Mar 21 22:37:24 EST 1996

			      Call for Papers

		  Modern Concepts in Macromolecular Modeling

                         Pacific Symposium on Biocomputing
			 Ritz-Carlton Kapalua, Maui, Hawaii
				January 6-9, 1997

Co-chairs Chairs:   Jurgen Bajorath, Bristol-Myers Squibb Research Institute
		    Teri E. Klein, University of California, San Francisco

The Pacific Symposium on Biocomputing (PSB-97) is an international,
multidisciplinary conference for the presentation and discussion of current
research in the theory and application of computational methods in problems
of biological significance.

We are currently soliciting manuscripts for a highly interactive workshop-like 
session "Modern Concepts in Macromolecular Modeling" and/or abstracts for an
accompanying poster session. The session will assess state-of-the-art
approaches in the area of macromolecular modeling, in particular protein
modeling, to highlight their opportunities, caveats, and limitations.
Contributions which introduce or illustrate novel computational methods and
which present contemporary applications are equally encouraged.

Scientific focal points include:

 * the development and application of various energy functions for

	- analysis of the energetics and dynamics of macromolecular
	  structures and their interactions

	- protein fold recognition 
	- ab initio folding of proteins on the computer

	- evaluation and assessment of molecular models

 * techniques to construct protein models in the presence of "twilight zone" 
	sequence similarities such as

	- analysis of multiple sequences and/or structures

	- generation of sequence-structure alignments

	- interactive or automated computer modeling programs

Scientific context:

While the use of predictive methods to generate and analyze three-dimensional 
models is increasing, the objectives of such modeling and the problems 
involved are changing. Classical homology modeling on the basis of significant
sequence similarity has more or less introduced macromolecular modeling at  
times when only a rather limited number of experimentally determined protein 
structures were available. The scenario has changed dramatically. Many more
structures have been determined, and it is a significant task in itself to
compare, analyze, and classify these structures. It has become possible to
study many intra- and intermolecular interactions in detail, and much effort
is currently being spent to understand such interactions in more quantitative
energetic terms; be it on the basis of various (free) energy calculations
or automated docking procedures. Implications of these studies for drug or
protein design are evident. 

Sequence databases grow at even much faster pace than structural databases, 
and this is considered a major reason for the increasing interest in modeling. 
However, popular targets of protein modeling attempts often display, if at all,
low or barely detectable sequence similarities to known structures. In these
cases, it is difficult to establish structural relationships, even if they 
exist, and to identify structural templates for modeling. The advent of 
inverse folding and fold recognition methods has changed the approach to some 
of these problems. Nevertheless, to apply the results of a fold recognition
study, to generate a precise and global sequence-structure alignment, and to 
actually build a model remains difficult and still requires many subjective 
decisions. In parallel to novel structure-based or comparative approaches,
computational ab initio folding of (small) proteins is, for the first time,
successfully performed, albeit at still limited resolution.


PSB '97 will publish peer-reviewed full papers in an archival proceedings.  
Each accepted paper will be allocated 12 pages in the proceedings volume.  
Manuscripts adhering to the guidelines set forth on the the PSB web pages
will be accepted. Full papers must not have been previously presented or 
published, nor currently submitted for journal publication.  Once accepted to 
the conference, a paper may be submitted for journal publication. Each 
manuscript will be refereed by at least four reviewers. 

  Due dates
  May       15, 1996	     300 word abstract to bajorath at protos.bms.com
  June      15, 1996         Five copies of the manuscript
  August    15, 1996         Notification of accepted papers
  September 15, 1996         Accepted camera ready manuscripts 

Five copies of all full papers must be submitted to: 
	         c/o Section on Medical Informatics
	         Stanford University Medical School, MSOB X215
	         Stanford, CA 94305-5479  USA

Authors who do not wish to submit a full paper are welcome to submit 1-2 page 
abstract adhering to the guidelines set forth on the PSB web pages, which will 
be distributed at the meeting separately from the archival proceedings. 

  Due dates
  May       15, 1996	     300 word abstract to bajorath at protos.bms.com
  August    15, 1996         Notification of accepted abstract/poster
  September 15, 1996         Accepted camera ready abstract 

Please send abstracts and questions regarding this session to:

Jurgen Bajorath			
Bristol-Myers Squibb Res. Inst.        
3005 First Avenue                    
Seattle, WA 98121                   
bajorath at protos.bms.com           
klein at cgl.ucsf.edu
Tel  (206) 727-3612             
Fax  (206) 727-3602           

For more information on the Pacific Symposium on Biocomputing, please see
our web site at http://cgl.ucsf.edu/psb or contact: 

Ms. Sharon Surles
PSB Coordinator
Interactive Simulations, Inc.
5330 Carroll Canyon Road, Suite 203
San Diego, CA  92121
psb at intsim.com
Phone: +1 (619) 658-9782
FAX:   +1 (619) 658-9463

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