 | |
| Content | |
|---|---|
| Description | Protein Structure Classification |
| Contact | |
| Research center | University College London |
| Laboratory | Institute of Structural and Molecular Biology |
| Primary citation | Dawson et al. (2016)[1] |
| Release date | 1997 |
| Access | |
| Website | cathdb |
| Download URL | cathdb |
| Miscellaneous | |
| Data release frequency | CATH-B is released daily. Official releases are approximately annual. |
| Version | 4.3 |
TheCATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships ofprotein domains. It was created in the mid-1990s by ProfessorChristine Orengo and colleagues includingJanet Thornton andDavid Jones,[2] and continues to be developed by the Orengo group atUniversity College London. CATH shares many broad features with theSCOP resource, however there are also many areas in which the detailed classification differs greatly.[3][4][5][6]
Experimentally determined protein three-dimensional structures are obtained from theProtein Data Bank and split into their consecutivepolypeptide chains, where applicable. Protein domains are identified within these chains using a mixture of automatic methods and manual curation.[7]
The domains are then classified within the CATH structural hierarchy: at the Class (C) level, domains are assigned according to theirsecondary structure content, i.e. allalpha, allbeta, a mixture of alpha and beta, or little secondary structure; at the Architecture (A) level, information on the secondary structure arrangement in three-dimensional space is used for assignment; at the Topology/fold (T) level, information on how the secondary structure elements are connected and arranged is used; assignments are made to theHomologous superfamily (H) level if there is good evidence that the domains are related by evolution[2] i.e. they are homologous.
| # | Level | Description |
|---|---|---|
| 1 | Class | the overall secondary-structure content of the domain. (Equivalent to theSCOPClass) |
| 2 | Architecture | high structural similarity but no evidence ofhomology. |
| 3 | Topology/fold | a large-scale grouping of topologies which share particular structural features (Equivalent to the 'fold' level in SCOP) |
| 4 | Homologous superfamily | indicative of a demonstrable evolutionary relationship. (Equivalent to SCOPsuperfamily) |
Additional sequence data for domains with no experimentally determined structures are provided by CATH's sister resource, Gene3D, which are used to populate the homologous superfamilies. Protein sequences from UniProtKB and Ensembl are scanned against CATH HMMs to predict domain sequence boundaries and make homologous superfamily assignments.
The CATH team releases new data both as daily snapshots, and official releases approximately annually. The latest release of CATH-Gene3D (v4.3) was released in December 2020 and consists of:[8]
CATH is anopen source software project, with developers developing and maintaining a number of open-source tools,[9] which are available publicly onGitHub.[10]