3D Biomolecular structure handling for Bioperl

Eser Ayanoglu ayanoglu at cmgm.Stanford.EDU
Wed Dec 23 00:11:35 EST 1998

As some of you know, The Bioperl project (http://bio.perl.org) is a
coordinated effort to collect computational methods routinely used in
bioinformatics into a set of standard, well-documented, and freely
available Perl modules.  The latest version, bioperl-0.04.1 has recently
been made available.  Some of us are now focussing on the design of a 3D
structure object for use in Perl-based bioinformatics applications. 
Although small molecules shall be supported if/when they interact with
biological macromolecules, the main focus is on macromolecular structures. 

We would like to open the general issue to discussion, your ideas and
suggestions at this stage. Among others, we would especially like to hear
your comments on the following areas:
   - In what sort of program would you use such a module? 
   - How would you want to access the data, and what methods should be

Responses from this message will be employed to create a requirements
specification for the design of a 3D macromolecular structure object. Such
requirements will aid the design of 3D structure modules within the
Bioperl project. 

The preliminary page has been set up and an Initial Requirements List was
prepared primarily by one of us (Steve Chervitz) at:


to further compile such requirements and consolidate structure-related
issues at the moment. Any other ideas/suggestions/contributions will be
appreciated. Please direct responses to the bioperl discussion mailing
list: vsns-bcd-perl at lists.uni-bielefeld.de.  Thank you. 

Eser Ayanoglu 
Doug Brutlag Bioinformatics Group 
Dept. of Biochemistry
Stanford University

Steve Chervitz 
Bioperl Coordinator 
Neomorphic Software, Berkeley, CA

Steven Brenner 
Dept. of Structural Biology 
Stanford University

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