Implementation

3Dee was first created on the 24th November 1994. Since then, the update techniques have been used to update the database 12 times. Seven of these updates were full updates which bring the database in line with the version of the PDB available, when an update is started; five updates were domain definition updates, where some of the domain definitions in the database are changed without updating the version of the PDB used by 3Dee. The first release of 3Dee comprised 2,646 PDB files containing 4,205 distinct chains and 6,074 domains. The November 1999 release contains 7,995 PDB files, 12,458 chains and 18,896 domains, so in terms of domains more than three times the original size. A non-redundant set of 1,715 domain sequences has been produced which are classified further according to their structural similarity into a conservative 1199 domain structure families. A detailed analysis of the data stored in 3Dee is presented by Siddiqui et al. (2000). Pages for each PDB chain available in 3Dee are accessible via a search engine on the World Wide Web (WWW). On these chain pages, the default domain definition and links to alternative domain definition(s) are provided. If the RasMol interface is installed, it is possible to view the structural domain(s) defined. From a chain page, one can enter the classification for the default domain definition which offers information about the domain sequence family and links to the 3Dee and SCOP-like structural classification trees. The structural hierarchy of domains can also be accessed directly. Structural superpositions of domains in the hierarchy can be viewed for clusters formed at a similarity score above 3.0. To improve the speed of this operation, the structural superposition software has to be installed on a local computer. Only the transformation matrix is downloaded and matrix operations are carried out on local PDB files. The latest version of 3Dee, a guide to using the database and its history, can be accessed on the WWW at the URL http://barton.ebi.ac.uk/servers/3Dee.html. In addition to the information accessible on the WWW, 3Dee stores non-redundant set(s) of domain sequences and structures, secondary structure definitions calculated with different methods, combined secondary structure definitions for PDB entries and consensus secondary structure definitions for the structurally aligned domain sequence families.