WPDB - The Protein Data Bank Through Microsoft Windows
Last Update Jan. 24, 1998 PEB
Current Version 2.2
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:
- Find structures based on text and sequences searches (mismatches allowed).
- Sequence alignment of one register sequence against multiple target
sequences according to the method of Needleman and Wunsch (JMB 48(3):
443-453, 1970).
- Structure superposition using Calpha positions according to the method
of Hendrickson (Acta Cryst. A35:158-163, 1979 .
- Secondary structure assignments according to the method of Kabsch and
Sander.
- 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.
- 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.
- 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).
- Geometry calculation (bond lengths, bond angles, dihedral angles, close
non-bonded contacts) including graphical representation and deviations
from small molecule distances.
Computing:
- 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.
- 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.
- Direct access to Raswin
the popular molecular display program.
- Synchronized printed documentation and context sensitive help created
using the DocToHelp package.
Typical Uses
- Analysis of protein-protein and protein-ligand interactions.
- Analysis of internal interactions in proteins to reveal different folds
(e.g. helix-helix hydrophobic stacking).
- Analysis of sequence-structure correlation's using sequence search
and static property profiles.
- As above with sequence homology and structure superposition.
- Analysis of thermal motion using dynamic property profiles.
- Locate structures based on string searches of combinations of PDB record
types and/or sequence patterns.
- Basic molecular rendering.
- Basic geometry checking.
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:
- wpdbbin.zip [.7MB] - the executables and documentation (a Microsoft
help file). Includes raswin the molecule display program called directly
from WPDB.
- wpdb100r.zip [2.1MB] - a small test database of 100 structures, including
PDB REMARK records.
- wpdb420r.zip [9.8MB] - 420 "unique structures," including
PDB REMARK records
- full_1.zip [68.9MB] and full_2.zip [16.6MB] the complete PDB in two
parts (both required).
- wpdbps.zip [.5MB] - program manual in color Postscript.
- 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:
- Select a group of PDB files using the file selector.
- Optionally select whether PDB REMARKS, different members of an NMR
ensemble etc. are to be included
- Build the database
Note:
- An "average structure" takes from 1-5 minutes to load depending
on type of processor.
- An existing database can be incremented.
[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..
- 32-bit only version
- CDROM distribution - this depends on an amendment to the PDB licensing
agreement for non-profit distribution.
- Extended query capability like that found in MOOSE
- Links to external databases via the Internet
- A more intuitive Windows look and feel.
