A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary v.3

The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank. The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to (1) supersecondary structural motifs (attractors in fold space), (2) the topology of globular domains (fold types), (3) remote homologues (functional families), and (4) homologues with sequence identity above 25 % (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10531 PDB entries comprising 17101 chains, which were partitioned into 5 attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99582 unique homologous sequences in the HSSP database, which increases the number of effectively known structures severalfold. The resulting database contains the description of protein domain architecture, the definition of structural neighbours around each known structure, the definition of structurally conserved cores, and a comprehensive library of explicit multiple alignments of distantly related protein families.