A number of groups have developed classifications of protein structure and some of these are available via the WWW. The different databases vary in completeness, ethos and ease of updating.
The Structural Classification of Proteins SCOP database describes a manual classification of protein structure. The classification is at the domain level for many proteins, but in general, a protein is only split into domains, when there is a clear indication that the individual domains may have existed as independent proteins. In 3Dee, proteins tend to have more domains than shown in scop. For example, by default we define the serine proteinases to have two domains. scop mentions that serine proteinases have two domains, but does not explicitly list the isolated domains, nor provide a mechanism to show the location of the domains.
The CATH database provides an automatically generated classification of protein structure. Since December 1997 the database also includes classifications at the domain level. CATH has extensive additional information on each protein structure, for example secondary structure diagrams, motif identification and so on.
A set of protein structural domain definitions from the Biomolecular Modelling Laboratory at the Imperial Cancer Research Fund (ICRF-BMM).
Other sources of structural classifications
There are a number of other databases that store classifications of protein structure and structural alignments.
FSSP is a complete comparison of all pairs of protein structures in the PDB using an automatic procedure. It is the basis for the Dali Domain Dictionary.
Entrez includes a complete comparison of all pairs of protein structures using an automatic procedure.
