WPDB V1.0 Available

Wed Aug 31 11:56:06 EST 1994

             WPDB - PC-based Macromolecular Structure Interrogation
                             Version 1.0 Available

WPDB (the Protein Data Bank through Microsoft Windows) is a macromolecular
structure query and analysis tool designed to complement rendering tools
such as Raswin and Kinemage. 

Typical uses
        o Analysis of protein-protein and protein-ligand interactions
          using the three-level zooming feature of the contact map 
          viewer and the residue selection feature of the 3D-viewer.
        o Analysis of internal interactions in proteins to reveal
          different folds (e.g. helix-helix hydrophobic stacking,
          4-helix bundle) using contact map, hydrophobicity profile
          and secondary structure selection feature in 3D-view.
        o Analysis of sequence-structure correlations using sequence
          search and static property profiles.
        o Analysis of thermal motion using dynamic property profiles.
        o Locate structures based on string searches of combinations
          of PDB record types and/or sequence patterns.

To take a peek

How to get it?
        1. Anonymous ftp to cuhhca.hhmi.columbia.edu (
        2. Change directory to /pub/programs/WPDB/doc.
        3. Get the file install.
        4. Follow instructions in the install file.

Note: Two compressed databases are available:
        (i) random selection of 100 structures; 
       (ii) "unique" structures (320) as defined by Hobohm and Sander.

The README file in /pub/programs/WPDB/doc describes how to get the software 
to build your own database.

Please send questions/comments/criticisms to wpdb at cuhhca.hhmi.columbia.edu

Some features

        o 20-fold compression of PDB files (minus REMARK records).
        o Real-time query based on text string searches of PDB record
          types and sequence.
        o Clickable contact map with three levels of zooming for analyzing
          intra- and inter-molecular interactions: level 1 - molecules,
          level 2 - fragments, level 3 - atoms.
        o Clickable profile with two levels of zooming to examine static 
          properties (volume, polarity, isoelectric point, hydrophobicity,
          mean exposure) and isotropic temperature factor.
        o 3D rendering tool with special capabilities for easy selection
          of substructures and fragments by specifying chains,
          secondary structure, residues (by location or name).
        o Interoperability between display tools (3-D renderer, contact
          maps and profile), i.e. selection made in one object will
          be propagated to other visible display objects. For example
          selecting a close contact in a contact map will be highlighted
          in the structure.
        o Secondary structure analysis according to Kabsch and Sander.
        o Comprehensive manual and Windows-based help.
        o A hook to the more advanced display features of Raswin.

Hardware/software requirements
Intel 486/33 processor or above with a color monitor, 4MB RAM or better,
and Windows.
WPDB was designed, written and produced by Ilya Shindyalov and Phil Bourne.


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