WPDB 2.0

Philip Bourne bourne at SDSC.EDU
Wed Nov 8 22:02:03 EST 1995

             WPDB - PC-based Macromolecular Structure Interrogation
                        For Research and Education
                                Version 2.0 
      Shindyalov and Bourne, J. Appl. Cryst.,  Vol. 28 Part 6, pp. 847-852

The San Diego Supercomputer Center (SDSC) is pleased to announce the
availability of WPDB v2.0. WPDB is a Microsoft Windows based application
for exploring the 3D structure of biological macromolecules as found in
the Protein Data Bank (PDB). Version 2.0 supports comparative analysis on
multiple structures with emphasis on sequence alignment and structure

WPDB comprises a set of tools to locate and analyze structures of interest 
from a compressed version of all or parts of the PDB (10-20 fold depending 
on kinds of information to be retained). The tools includes fast but simple
3d-renderer, a contact map analyzer, profile tool and alignment 

The following databases are available:

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

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

Typical uses of WPDB are:

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

Examples of these uses are given in the Web pages. The software and databases 
may be downloaded through the Web pages or via anonymous ftp from
rosebud.sdsc.edu in the directory /pub/SDSC/biology/WPDB.

WPDB was developed by Ilya N. Shindyalov (shindyal at sdsc.edu)
and Philip E. Bourne (bourne at sdsc.edu). The WPDB manual is available 
on line. Printed copies may be requested by sending mail to consult at sdsc.edu.

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