Database of unique protein 3D structural domains

A database of protein 3D structural domains was derived from the Brookhaven Protein Databank [Bernstein et al., 1977]. non-identical chains were clustered by sequence comparison [Barton, 1993][Smith \& Waterman, 1981] to leave sequence families. One representative of each family was chosen to have the highest resolution and lowest R-factor. The representative structures were then split into domains by eye. A sub-database of higher quality domains was created for analysis. This contained only those structures determined by X-ray crystallography, refined and of a resolution of Å or better. Secondary structures for all domains were defined by the programs DSSP (definition of secondary structure in proteins) [Kabsch \& Sander, 1983] or by DEFINE [Richards \& Kundrot, 1988] when only atoms were available. Axial coordinates were calculated for all secondary structures as described in [Richards \& Kundrot, 1988]. Extra axial coordinates were calculated at the N- and C- terminal ends to allow for possible differences in secondary structure length. The domain database is available via the WWW (http://barton.ebi.ac.uk/).