Call for Papers and Posters

Session on Informatics Approaches in Structural Genomics: Modeling and Representation of Function From Macromolecular Structure

at the Pacific Symposium in Biocomputing 2005
(click for text version of this document)

As the structural genomics projects move beyond the initial implementation phase, functional assignment for Initiative targets and their homologs is an increasingly more important and frequent problem. For one Center for Structural Genomics, it has been estimated that approximately one-third of the solved structures are hypothetical proteins for which no functional information is available in sequence databases [Laskowski, R. A., J. D. Watson, et al. (2003). "From protein structure to biochemical function?" J Struct Funct Genomics 4(2-3): 167-77]. Similar estimates likely apply to other pilot centers in structural genomics. Moreover, because the core Initiative currently does not include functional characterization, there is no large-scale infrastructure to address the critical need for functional annotation of functionally uncharacterized protein structures. Thus, there is both a compelling need and an important opportunity for the biocomputing community to address the issue of modeling and representation of function from macromolecular structure. 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:

The computational problems that this session will address fall into the following three topic areas:

• 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 molecular function, and, for enzymes, chemistry.
• Examples of areas appropriate for this session include automated structure classification schemes, using sequence-structure, structure-structure alignment, and domain recognition, identification of functionally important residues, structure-based protein-protein interaction mapping and characterization
  
  
• Functional annotation and classification of structural genomics targets

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

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

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

Sean D Mooney, PhD
Indiana University School of Medicine
sdmooney@iupui.edu

Submission information

• Submissions are due July 19, 2004
  
• Decisions are announced September 8, 2004
  
• Camera ready copy due September 22, 2004
  
• Poster abstracts due November 1, 2004

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 http://psb.stanford.edu/psb-online/psb-submit/. 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.