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===== What is CATH? =====

The CATH 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, and 
continues to be developed by the Orengo group at University College London.

===== How is CATH-Gene3D created? =====

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 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, i.e. they are
homologous.

Additional sequence data for domains with no experimentally determined
structures are provided by our 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.

===== CATH Releases =====

We aim to provide official releases of the CATH classification every 12 months.
This release process is important because is allows us to provide 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 (v4.1) was released in July 2016 and 
consists of:

  * 308,999    structural protein domain entries
  * 53,479,436 non-structural protein domain entries
  * 2,737       homologous superfamily entries
  * 92,882      functional family entries

===== Open Source Software =====

CATH is proud to be a member of the open source software community. Our developers use and contribute towards the development and maintenance of a number of open source tools. For a full list of the open source software used in the making of this resource (both in the pipeline and our web pages), please visit the [[CATH tools]] page.

===== Contact us =====

If you have any comments/suggestions/criticisms, please let us know:

http://www.cathdb.info/support/contact

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