Call for Papers and Posters

Session on Informatics Approaches in Structural Genomics

at the Pacific Symposium in Biocomputing 2004
(click for text version of this document)

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:

• 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:
  • Target selection strategies
  • Improved crystallization strategies by mining failed data
  • Computational projects aimed at determining, storing and annotating large numbers of theoretically and experimentally determined structures

• Structure-based functional prediction and classification
  • Controlled vocabularies for the annotation of structure and function
  • Semi-automated/automated fold and motif determination
  • 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
  • Methods for identification of functionally important residues
  • Structure-based drug discovery in the age of structural proteomics
  • Structure-based protein-protein interaction mapping and characterization
  • Applications in pharmacogenomics

• Determining, using and analyzing large datasets of experimental and modeled proteins and nucleic acid structures
  • Construction and use of fold libraries in proteome annotation and fold recognition from sequence
  • Comparative structural proteomics - comparing the complement of folds present in different species
  • 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 chairs

Session Co-Chairs

Sean D Mooney, PhD
Stanford University
mooney@smi.stanford.edu

Phil Bourne, PhD
University of California San Diego
bourne@sdsc.edu

Patricia C Babbitt, PhD
University of California San Francisco
babbitt@cgl.ucsf.edu

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@stanford.edu 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.ps, 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 ftp://ftp-smi.stanford.edu/pub/altman/psb. 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.