The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of
protein domains. It was created in the mid-1990s by Professor
Christine Orengo and colleagues including
Janet Thornton and
David Jones,
and continues to be developed by the Orengo group at
University College London. CATH shares many broad features with the
SCOP resource, however there are also many areas in which the detailed classification differs greatly.
Hierarchical organization
Experimentally-determined protein three-dimensional structures are obtained from the
Protein Data Bank and split into their consecutive
polypeptide chains, where applicable. Protein domains are identified within these chains using a mixture of automatic methods and manual curation.
The domains are then classified within the CATH structural hierarchy: at the Class (C) level, domains are assigned according to their
secondary structure
Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...
content, i.e. all
alpha
Alpha (uppercase , lowercase ; grc, ἄλφα, ''álpha'', or ell, άλφα, álfa) is the first letter of the Greek alphabet. In the system of Greek numerals, it has a value of one. Alpha is derived from the Phoenician letter aleph , whic ...
, all
beta
Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiod ...
, 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
[ i.e. they are homologous.
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,
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 [
* 151 mln non-structural protein domain entries ][
* 5,481 homologous superfamily entries ][
* 212,872 functional family entries ][
]
Open source software
CATH is an open source software project, with developers developing and maintaining a number of open source tools.
References
{{Use dmy dates, date=April 2017
Protein structure
Protein folds
Biological databases
Protein classification
Protein superfamilies