|
WPDB 2.2
Introduction
WPDB is a protein structure database search and display tool for use on Windows 3.1, Windows 95 and Windows NT platforms. WPDB is useful for detailed analysis of a single structure or comparative analysis of two or more structures. It comes with a variety of databases, including a 10-fold compressed version of the complete PDB downloadable via ftp.
Alternatively, you can build your own database from PDB files with the WPDB Loader (WPDBL).
The major enhancement in v2.2 is a much improved 3-D structure viewer.
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.
Availability
WPDB is developed and maintained by Ilya Shindyalov and Phil Bourne at the San Diego Supercomputer Center. WPDB is available through the WPDB homepage or via the ftp server. To be placed on the mailing list, send a 'subscribe wpdb' message to majordomo@sdsc.edu
Information provided by: Philip Bourne
Resources and further information
San Diego Supercomputer Center
http://www.sdsc.edu/
Computational Molecular Biology Project Area: Biological Data Representation and Query at SDSC
http://www.sdsc.edu/pb/
WPDB 2.2 homepage
http://www.sdsc.edu/pb/wpdb/wpdb.htm
Download WPDB software
ftp://ftp.sdsc.edu/pub/sdsc/biology/WPDB/
External sites are not endorsed by EMBL-EBI |
