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index [2017/10/12 14:56]
sayoni added cath(daily snapshot) and cath-plus to cath releases
index [2017/10/16 15:36] (current)
sayoni
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 three-dimensional space is used for assignment; at the [[glossary:topology|Topology/fold]] (T) level, three-dimensional space is used for assignment; at the [[glossary:topology|Topology/fold]] (T) level,
 information on how the secondary structure elements are connected and arranged information on how the secondary structure elements are connected and arranged
-is used; assignments are made to the [[glossary:homologous_superfamily|Homologous superfamily]] (H) level if there +is used; assignments are made to the [[glossary:homologous_superfamily|Homologous superfamily]] (H) level if there is good evidence that the domains are related by evolution, i.e. they are 
-is good evidence that the domains are related by evolution, i.e. they are +homologous. To browse the classification hierarchy, see [[http://cathdb.info/browse/tree|CATH hierarchy]].
-homologous.+
  
 Additional sequence data for domains with no experimentally determined Additional sequence data for domains with no experimentally determined
-structures are provided by our sister resource, [[http://gene3d.biochem.ucl.ac.uk/Gene3D|Gene3D]], which are used to +structures are provided by our sister resource, [[http://gene3d.biochem.ucl.ac.uk/Gene3D|Gene3D]], which are used to populate the homologous superfamilies. Protein sequences from UniProtKB and
-populate the homologous superfamilies. Protein sequences from UniProtKB and+
 Ensembl are scanned against CATH HMMs to predict domain sequence boundaries and Ensembl are scanned against CATH HMMs to predict domain sequence boundaries and
 make homologous superfamily assignments. make homologous superfamily assignments.
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 We aim to provide full releases of CATH (CATH-Plus) every 12 months. CATH-Plus adds a significant amount of data on top of the core classification information available in CATH. The CATH-Plus release process includes a number of manual annotation checks in addition to adding a huge amount of information combining protein structure, sequence and function. As a result, there is a greater depth of information available in CATH-Plus, though it may be missing information on the most recent structures. We aim to provide full releases of CATH (CATH-Plus) every 12 months. CATH-Plus adds a significant amount of data on top of the core classification information available in CATH. The CATH-Plus release process includes a number of manual annotation checks in addition to adding a huge amount of information combining protein structure, sequence and function. As a result, there is a greater depth of information available in CATH-Plus, though it may be missing information on the most recent structures.
  
-See [[release_notes|release notes]] for information on the statistics for specific releases.+CATH-Plus data includes:
  
-The latest release of CATH-Plus (v4.1was released in July 2016 and  +=== FunFams (Functional Families===
-consists of:+
  
-  * 308,999    structural protein domain entries +The homologous superfamilies in CATH-Gene3D can often be functionally and structurally diverse even though they share a conserved structural core. Therefore, the superfamilies have been sub-classified into functional families (FunFams) using a subclassification protocol purely based on sequence patterns. Relatives within these FunFams are likely to share highly similar structures and functions. The FunFams are useful in function prediction and in providing information on the evolution of function. 
-  * 53,479,436 non-structural protein domain entries + 
-  * 2,737       homologous superfamily entries +=== Structural clusters === 
-  * 92,882      functional family entries+ 
 +The structures within a homologous superfamily have been clustered at < 9 Å RMSD to form structural clustersalso known as structurally-similar groups (SSGs). These structural clusters are useful for understanding the structural diversity of a superfamily. 
 + 
 +=== Structural superpositions === 
 + 
 +The conserved structural core in the homologous superfamilies can be observed from the structural superpositions generated from its representative domains by [[cath_tools#cath_tools|CATH Tools]]. It is an effective way of observing the structural conservation and diversity across the superfamily. 
 + 
 +See [[release_notes|release notes]] for information on the statistics for specific releases.
  
 CATH and CATH-Plus data for all releases can be downloaded from [[data:index|Data Downloads]]. CATH and CATH-Plus data for all releases can be downloaded from [[data:index|Data Downloads]].
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