WPDB V1.0 Available

WPDB Account wpdb at cuhhca.hhmi.columbia.EDU
Tue Sep 6 20:21:39 EST 1994


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             WPDB - PC-based Macromolecular Structure Interrogation
                             Version 1.0 Available
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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
--------------
           http://cuhhca.hhmi.columbia.edu/wpdb.html

How to get it?
-------------
        1. Anonymous ftp to cuhhca.hhmi.columbia.edu (128.59.98.1).
        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 above two databases and the software and documentation to access them 
are free. WPDBL (WPDB Loader) for building your own databases is available 
for US$59.00 (single user non-profit) from ViSoft Inc. 21 Oak Rise, 
Irvington NY, 10533. Fax: (914) 591-9617.

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,
who are affliated with ViSoft Inc. as part of a technology transfer 
agreement.



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