News

The San Diego Supercomputer Center (SDSC) announces the release of version 2.0 of a Microsoft Windows-based application for use in exploring the 3-D structure of biological macromolecules such as those found in the Protein Data Bank (PDB). This new version of WPDB, as the software is called, supports comparative analysis on multiple structures with emphasis on sequence alignment and structure superposition. Designed as a research and educational tool, it is free of charge to academic scientists and students. WPDB was developed by SDSC computational biologists Ilya N. Shindyalov (shindyal@sdsc.edu) and Philip E. Bourne (bourne@sdsc.edu).

WPDB comprises a set of tools to locate and analyze structures of interest from a compressed version of all or parts of the PDB. The tools include a fast but simple 3-D renderer, a contact map analyzer, a profile tool, and an alignment builder/editor.

This release includes the following databases that can be searched by the WPDB software:

• Complete PDB (dated Nov. 1, 1995-3923 structures, 110 Mbytes).
• "Unique" structures as defined by Hobohm and Sander (463 structures, 16 Mbytes).
• Test set of 100 randomly chosen structures (3 Mbytes).

Each database includes PDB REMARK records, secondary structure according to Kabsch and Sander, and exposure according to Lee and Richards.

Researchers and students can use WPDB to

• Analyze protein-protein and protein-ligand interactions.
• Analyze internal interactions in proteins to reveal different folds (e.g., helix-helix hydrophobic stacking).
• Analyze sequence-structure correlations using sequence search and static property profiles, and sequence alignment and structure superposition.
• Analyze structural and functional sites involving thermal motion profiles, secondary structure based on Kabsch and Sander assignment, and exposure according to Lee and Richards.
• Locate structures based on string searches of combinations of PDB record types and/or sequence patterns and resolution ranges.
• Perform basic molecular rendering.
• Build composite views from multiple database entries and pass them to other molecular graphics tools (e.g., Raswin).

The software and databases may be downloaded through the World Wide Web or via anonymous ftp to rosebud.sdsc.edu (refer to the directory /pub/SDSC/biology/WPDB). The WPDB manual is also available online. Printed copies may be requested by contacting the SDSC consultants at consult@sdsc.edu or 619-534-5100.

For more information and to obtain the software, refer to this URL:

http://www.sdsc.edu/CompSci/pb/Software.html and this publication:

Shindyalov, Ilya N., and Philip E. Bourne, Journal of Applied Crystallography, vol. 28, part 6, pp. 847-852.

The San Diego Supercomputer Center, a national laboratory for computational science and engineering, is sponsored by the National Science Foundation, is a subsidiary of General Atomics, and is affiliated with the University of California at San Diego. For additional information, see http://www.sdsc.edu or contact Ann Redelfs, SDSC, redelfs@sdsc.edu, 619-534-5032.