CATH database

Source: Wikipedia, the free encyclopedia.
CATH
Research center
University College London
LaboratoryInstitute of Structural and Molecular Biology
Primary citationDawson et al. (2016) [1]
Release date1997
Access
Websitecathdb.info
Download URLcathdb.info/download
Miscellaneous
Data release
frequency		CATH-B is released daily. Official releases are approximately annual.
Version4.3
Schematic representation of the three top levels of the CATH classification scheme.[2]

The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of

SCOP resource, however there are also many areas in which the detailed classification differs greatly.[3][4][5][6]

Hierarchical organization

Experimentally determined protein three-dimensional structures are obtained from the

polypeptide chains, where applicable. Protein domains are identified within these chains using a mixture of automatic methods and manual curation.[citation needed
]

The domains are then classified within the CATH structural hierarchy: at the Class (C) level, domains are assigned according to their secondary structure content, i.e. all alpha, all beta, 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 the Homologous superfamily (H) level if there is good evidence that the domains are related by evolution[2] i.e. they are homologous.

The four main levels of the CATH hierarchy:
# Level Description
1 Class the overall secondary-structure content of the domain. (Equivalent to the SCOP Class)
2 Architecture high structural similarity but no evidence of homology.
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 SCOP superfamily)

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.

Releases

The CATH team aim to provide official releases of the CATH classification every 12 months. This release process is important because it allows for the provision of internal validation, extra annotations and analysis. However, it can mean that there is a time delay between new structures appearing in the PDB and the latest official CATH release,[citation needed]

In order to address this issue: CATH-B provides a limited amount of information to the very latest domain annotations (e.g., domain boundaries and superfamily classifications).

The latest release of CATH-Gene3D (v4.3) was released in December 2020 and consists of:

  • 500,238 structural protein domain entries [1]
  • 151 mln non-structural protein domain entries [1]
  • 5,481 homologous superfamily entries [1]
  • 212,872 functional family entries [1]

Open-source software

CATH is an

open source software project, with developers developing and maintaining a number of open-source tools.[7] CATH maintains a todo list on GitHub to allow external users to create and keep track of issues relating to the CATH protein structure classification.[citation needed
]

References

  1. ^
    PMID 27899584
    .
  2. ^
    PMID 9309224
    .
  3. ^ "CATH: Protein Structure Classification Database at UCL". Cathdb.info. Retrieved 9 March 2017.
  4. ^ "CATH". Cathdb.info. Retrieved 9 March 2017.
  5. ^ "CATH Database (@CATHDatabase)". Twitter. Retrieved 9 March 2017.
  6. PMID 12520050
    .
  7. ^ "Tools". cathdb.info. Retrieved 18 December 2016.

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