WPDB is a software package for maintaining a database of macromolecular structures derived from the PDB and exploring those structures with a variety of supplied tools. WPDB is available for all Intel processors running a version of the Microsoft Windows operating system (Windows 3.1, Win95, and Win98 Wintel platforms). A comprehensive description of WPDB can be found on the Web at http://www.sdsc.edu/pb/wpdb/. This article intends simply to introduce those not familiar with WPDB to the available features, indicate how to obtain a copy of WPDB, and to provide existing users with an update on WPDB developments.
WPDB is not new - it was first described in Shindyalov and Bourne (1995) J. Appl. Cryst. 28(6) 847-852. Over 2,000 copies have been distributed and feedback indicates it is used most in education at the undergraduate level. Central to WPDB is a database of structures in compressed form. Three databases are available: the complete PDB of currently 10,000 structures (300MB); a unique set of structures defined by Holbohm and Sander based on sequence identity (20MB); and 100 randomly selected structures (2MB). Users can increment these databases or create their own with the supplied loader program (WPDBL) which loads PDB files into a database. Complete documentation is available both online and in a printed manual.
Simple queries permit locating a subset of structures of interest that can then be manually augmented as needed. Structures can then be displayed in a variety of ways - 3D visualization, Calpha contact maps, sequence-based property profiles, and plots showing stereochemical quality. Limited comparative structure analysis is possible, specifically, sequence alignment (Needleman and Wunsch) followed by least-squares based superposition of aligned structures and difference contact maps.
WPDB is free and available via anonymous ftp from ftp://ftp.sdsc.edu/pub/sdsc/biology/WPDB/ and on CD-ROM. Our goal is to update the FTP site quarterly and the CD-ROM once per year to include new structures. A new CD-ROM with 10,000 structures will be available soon. CD-ROMs can be obtained by sending e-mail to firstname.lastname@example.org including a full mailing address. Please note that this is a separate distribution from the PDB CD-ROM (see the article in this issue of Newsletter), which contains the PDB data files in a standard compressed text (ASCII) format.
WPDB is now part of the RCSB-PDB and will slowly be integrated. A long-term goal as specified in the RCSB's grant application (http://www.rcsb.org/pdb/docs/grant/toc.html) is to convert WPDB to a Java-based application which will make it available on all major computing platforms. At that time, the interface will be redesigned based on the feedback we have received in the past.
WPDB was developed by Ilya Shindyalov and Phil Bourne with funding from the National Science Foundation and the San Diego Supercomputer Center.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.