Call for Papers and Participation

 

Session on BIOGEOMETRY: Applications of Computational Geometry to Molecular Structure.

 

at the Pacific Symposium in Biocomputing 2005

 

 

It is widely believed that the geometry of biomolecules plays a crucial role in defining the relationship between their structure and function. Yet geometrical methods are relatively uncommon in computational biology because several unresolved representational and algorithmic issues remain. BioGeometry is an emerging scientific discipline at the interface between computational geometry, biochemistry and biophysics, statistics, and chemistry that brings together specialists in the above disciplines to develop new computational techniques and paradigms for representing, storing, searching, simulating, analyzing, and visualizing biological structures. BioGeometry brings together ideas from a wide range of areas of computer science and mathematics, including algorithms, geometry, topology, graphics, robotics, and databases to address on of the most fundamental biological problems, i.e., structure-function relationships for biological molecules.

 

Geometric methods should be an essential component of any attempt to understand and simulate biological systems. Existing techniques in computational structural biology and bioinformatics have been developed over three decades and have their roots in methods first applied by computational chemists to much smaller molecular systems. Although there have been significant advancements in the field, a systematic solution of many of the most important biological problems is still elusive, including ab initio protein structure prediction, the protein folding process, and ligand to protein docking. It is widely believed that the geometry of molecules plays a crucial role in these processes, yet geometrical methods are relatively uncommon in computational biology because several unresolved representational and algorithmic issues remain.

 

 The new PSB session on BioGeometry will naturally complement traditional topics such as protein folding, tools for visualization, computer-aided drug design, cheminformatics  addressed in the past. It will also serve to promote a relatively new discipline of BioGeometry and thereby will uniquely enrich the diversity of computational biology topics that are included as part of the PSB

 

Submission topics can include but are not limited to:

 

á  protein folding and docking

 

á  applications of graph theory to biological systems

 

á  protein-ligand recognition

 

á  visualization of biological structures

 

á  computational geometry method development

 

 

General Information on PSB

 

The Pacific Symposium on Biocomputing (PSB 2005) 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.  PSB 2005 will be held January 4-8, 2005 at the Fairmont Orchid on the Big Island of Hawaii.  Tutorials will be offered prior to the start of the conference.

 

PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing.  For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals.  PSB sessions are targeted to provide a forum for publication and discussion of research in biocomputingÕs Òhot topicsÓ.  In this way, PSB provides an early forum for serious examination of emerging methods and approaches in a rapidly changing field.  More information on the conference can be obtained from the conference web page: http://psb.stanford.edu/.  

 

 

Submission Information

 

á  Submissions are due July 16, 2004

 

á  Decisions are announced September 8, 2004

 

á  Camera ready copy due September 22, 2004

 

á  Poster abstracts due November 1, 2004

 

 

PSB will publish accepted full papers in an archival proceedings volume indexed in MEDLINE. All submissions will be peer-reviewed.  A limited number of submissions will be selected for oral presentation.  Poster abstracts will be submitted separately from the conference proceedings.  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 (*.doc). Attached files should be names 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:

 

á  The email address of the corresponding author

 

á  The specific PSB session that should review the paper or abstract

 

á  The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.

 

á  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 resized and placed precisely in the text, then it should be clear with appropriate modifications, the total manuscript length would be within the page limit.  Color pictures can be printed at the expense of the author.  The fee is $500 per page of color pictures, and is payable at the time of camera-ready submission.

 

 

Session Co-Chairs

 

Alexander Tropsha Ð Professor, School of Pharmacy, University of North Carolina, Chapel Hill, NC 27599

alex_tropsha@unc.edu

 

Herbert Edelsbrunner - Arts and Sciences Professor of Computer Science and Mathematics, Duke University, Computer Science Department, Box 90129, Durham, NC 27708

edels@cs.duke.edu