Technical report: 3Dee as an example of a derived database
Asim S. Siddiqui$^{ 1}$, Uwe Dengler$^{ 2}$ and Geoffrey J. Barton$^{ 1,2}$
$^1$ University of Oxford, Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, United Kingdom
$^2$ EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom

Abstract:

Motivation: The domain is an important intermediate in the protein structural hierarchy. However, domains are not defined systematically in the Protein Data Bank (PDB) and sequence and structural relationships between domains are not recorded.
Results: The 3Dee database, a repository of protein structural domains, stores alternative domain definitions for the same protein, organises the domains into sequence and structural hierarchies, contains non-redundant set(s) of sequences and structures, multiple structure alignments for all domain families, secondary structure and fold name definitions, and allows previous versions of the database to be regenerated. 3Dee solves the problem of maintaining a complex derived database when the primary database is growing rapidly. Although developed specifically for protein structural domains, the techniques described are general to other derived molecular biology databases. In particular solutions to the problems of adding new data without regenerating the complete database and minimising human input during a database update are presented.
Availability: 3Dee is accessible on the World Wide Web at the URL http://barton.ebi.ac.uk/servers/3Dee.html.
Contact: Geoff Barton; http://barton.ebi.ac.uk