WPDB - The Protein Data Bank Through Microsoft Windows


Last Update Jan. 24, 1998 PEB

Current Version 2.2


NEW CDROM Available with over 6000 structures. Send email to pdbadmin@sdsc.edu requesting a copy.

Contents


What is WPDB?

The PDB through Microsoft Windows, or WPDB for short, is a Microsoft Windows 3.1 Windows95 and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above.


Features

The features supported by WPDB are divided into 2 categories, those that have scientific merit and those considered to be computationally interesting.

Scientific:

  1. Find structures based on text and sequences searches (mismatches allowed).
  2. Sequence alignment of one register sequence against multiple target sequences according to the method of Needleman and Wunsch (JMB 48(3): 443-453, 1970).
  3. Structure superposition using Calpha positions according to the method of Hendrickson (Acta Cryst. A35:158-163, 1979 .
  4. Secondary structure assignments according to the method of Kabsch and Sander.
  5. Amino acid property profile analysis, both static and dynamic: static according to the values compiled by Bogardt et al.; dynamic, mean exposure according to Lee and Richards (JMB 55:379-400, 1971) and experimental B factors. Profiles for a single polypeptide chain or difference profiles for two aligned polypeptide chains may be examined.
  6. Contact map analysis at different cut-off distances and with different atom groups in contact. Single structures or superimposed structures (difference contact maps) can be examined.
  7. Typical 3-D viewing and rendering, including options to display or highlight substructures, CPK representation, stereo, and simple surfaces (colored based on distance from user).
  8. Geometry calculation (bond lengths, bond angles, dihedral angles, close non-bonded contacts) including graphical representation and deviations from small molecule distances.

Computing:

  1. Data compression -- about a 20-fold reduction in storage over the PDB ASCII file distribution, but with: (i) bibliographic information limited to AUTHOR and JRNL records; (ii) optionally the first or all members of an ensemble of NMR or model structures included; (iii) only the first alternative conformation as defined in the PDB file for parts of a crystal structure with partial occupancies; (iv) atomic coordinates rounded to 2 and not 3 decimal places; (v) no PDB REMARK records.
  2. Interoperable display objects -- when a feature is selected in one display object (e.g. a contact map), all other visible display objects (e.g. 3-D viewer) and those invoked subsequently, are also updated to illustrate that feature.
  3. Direct access to Raswin the popular molecular display program.
  4. Synchronized printed documentation and context sensitive help created using the DocToHelp package.


Typical Uses


How to Get WPDB

WPDB is available via anonymous ftp from ftp.sdsc.edu in the directory /pub/sdsc/biology/WPDB. The distribution is organized into 6 parts:

  1. wpdbbin.zip [.7MB] - the executables and documentation (a Microsoft help file). Includes raswin the molecule display program called directly from WPDB.
  2. wpdb100r.zip [2.1MB] - a small test database of 100 structures, including PDB REMARK records.
  3. wpdb420r.zip [9.8MB] - 420 "unique structures," including PDB REMARK records
  4. full_1.zip [68.9MB] and full_2.zip [16.6MB] the complete PDB in two parts (both required).
  5. wpdbps.zip [.5MB] - program manual in color Postscript.
  6. install - installation script (DOS)

Only one of 2-4 is required. All files are compressed using pkzip. The program pkunzip.exe (runs under DOS) is available in the distribution directory if needed.

The loader (WPDBL) for building your own WPDB database is available here also.

[Download]


Building Your Own Databases with WPDBL

The software to build your own databases is called WPDBL and is available in the same location as WPDB. The basic steps in building a database are:

  1. Select a group of PDB files using the file selector.
  2. Optionally select whether PDB REMARKS, different members of an NMR ensemble etc. are to be included
  3. Build the database

Note:

[Download] | [Example]


References and Citing WPDB

Those using WPDB should cite:
I.N.Shindyalov and P.E.Bourne J. App. Cryst. 1995, 28(6) 847-852. WPDB A PC-based Tool for Analyzing Protein Structure. [Postscript]

Further details of the data model used by WPDB can be found in I.N.Shindyalov and P.E. Bourne CABIOS 1997, Submitted. Protein Data Representation and Query Using Optimized Data Decomposition.


Contact Information and Mailing List

Need help?

Contact the authors: Ilya Shindyalov and Phil Bourne

Join the mailing list: send mail to majordomo@sdsc.edu with the body of the message containing subscribe wpdb


Future Directions

Some of the enhancements that we are working on for v3.0 are as follows..