CFP: Informatics Applications in Structural Genomics at PSB 2004

Sean Mooney sdm at
Wed May 28 10:42:06 EST 2003

*********************Call for Papers and Posters**************************
*       Session on Informatics Approaches in Structural Genomics         *
*            at the Pacific Symposium in Biocomputing 2004               *

The goal of structural genomics is to discover and characterize the
three dimensional structure of all proteins and other macromolecules
found in nature. Currently there are ongoing efforts to develop
high-throughput methods for protein structure determination both in
industry and in academia. This session will continue to present
progress and achievements in the field through the use of
computational techniques. Topic areas included in the discussions will
be (1) Progress in projects aimed at high throughput structure
determination, (2) Structure-based functional prediction and
classification and (3) Determining, using and analyzing large datasets
of experimental and modeled proteins and nucleic acid
structures. Submitted papers are reviewed and accepted on a
competitive basis. Please note that speakers are responsible 
for their own conference registration fees and travel costs to 
and from the conference.

Potential Topics Include:

* Progress in projects aimed at high throughput structure
determination including applications developed specifically to support
the NIGMS and other structural genomics centers pipelines worldwide,
for example: 
	o Target selection strategies 
	o Improved crystallization strategies by mining failed data 
	o Computational projects aimed at determining, storing and
	annotating large numbers of theoretically and experimentally 
	determined structures 

* Structure-based functional prediction and classification 
	o Controlled vocabularies for the annotation of structure and 
	o Semi-automated/automated fold and motif determination
	o Tools and methods for the semi-automated/automated 
	characterization of a protein's structure, function, and, for 
	enzymes, chemistry. Examples are tools/methods that focus on 
	automated structure classification schemes using sequence-structure, 
	structure-structure alignment, and domain recognition
	o Methods for identification of functionally important residues
	o Structure-based drug discovery in the age of structural proteomics
	o Structure-based protein-protein interaction mapping and 
	o Applications in pharmacogenomics

* Determining, using and analyzing large datasets of experimental and
  modeled proteins and nucleic acid structures 
	o Construction and use of fold libraries in proteome
	annotation and fold recognition from sequence
	o Comparative structural proteomics - comparing the complement
	of folds present in different species
	o Visualization and analysis of structure function relationships

Other topics within the subject area are welcome. If unsure whether
your paper fits within the session, please contact one of the session

Session Co-Chairs

Sean D Mooney, PhD
Stanford University
mooney at 

Phil Bourne, PhD
University of California San Diego
bourne at

Patricia C Babbitt, PhD 
University of California San Francisco
babbitt at 

Submission information 
* Submissions are due July 14, 2003
* Decisions are announced September 8, 2003 
* Camera ready copy due September 22, 2003 
* Poster abstracts due November 1, 2003 

All papers must be submitted to russ.altman at in electronic
format. The file formats we accept are: postscript (*.ps), adobe
acrobat (*.pdf) and Microsoft Word documents (*.doc). Attached files
should be named with the last name of the first author
(e.g., altman.pdf, or altman.doc). Hardcopy submissions or
unprocessed TEX or LATEX files will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter
must state the following:
     * The email address of the corresponding author 
     * The specific PSB session that should review the paper or abstract 
     * The submitted paper contains original, unpublished results, and is
       not currently under consideration elsewhere.
     * All co-authors concur with the contents of the paper. 

Submitted papers are limited to twelve (12) pages in our publication
format. Please format your paper according to instructions found at If figures can not be
easily resised and placed precisely in the text, then it should be
clear that with appropriate modifications, the total manuscript length
would be within the page limit.


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