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CATH: increased structural coverage of functional space
I. Sillitoe, N. Bordin, N. Dawson, VP. Waman, P. Ashford, HM. Scholes, CSM. Pang, L. Woodridge, C. Rauer, N. Sen, M. Abbasian, S. Le Cornu, SD. Lam, K. Berka, IH. Varekova, R. Svobodova, J. Lees, CA. Orengo
Language English Country Great Britain
Document type Journal Article, Research Support, Non-U.S. Gov't
Grant support
104960/Z/14/Z
Wellcome Trust - United Kingdom
203780/Z/16/A
Wellcome Trust - United Kingdom
NLK
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from 1974
PubMed
33237325
DOI
10.1093/nar/gkaa1079
Knihovny.cz E-resources
- MeSH
- Molecular Sequence Annotation MeSH
- COVID-19 epidemiology prevention & control virology MeSH
- Databases, Protein statistics & numerical data MeSH
- Epidemics MeSH
- Internet MeSH
- Humans MeSH
- Protein Domains * MeSH
- Proteins chemistry genetics metabolism MeSH
- SARS-CoV-2 genetics metabolism physiology MeSH
- Amino Acid Sequence MeSH
- Sequence Analysis, Protein methods MeSH
- Sequence Homology, Amino Acid MeSH
- Viral Proteins chemistry genetics metabolism MeSH
- Computational Biology methods statistics & numerical data MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
CATH (https://www.cathdb.info) identifies domains in protein structures from wwPDB and classifies these into evolutionary superfamilies, thereby providing structural and functional annotations. There are two levels: CATH-B, a daily snapshot of the latest domain structures and superfamily assignments, and CATH+, with additional derived data, such as predicted sequence domains, and functionally coherent sequence subsets (Functional Families or FunFams). The latest CATH+ release, version 4.3, significantly increases coverage of structural and sequence data, with an addition of 65,351 fully-classified domains structures (+15%), providing 500 238 structural domains, and 151 million predicted sequence domains (+59%) assigned to 5481 superfamilies. The FunFam generation pipeline has been re-engineered to cope with the increased influx of data. Three times more sequences are captured in FunFams, with a concomitant increase in functional purity, information content and structural coverage. FunFam expansion increases the structural annotations provided for experimental GO terms (+59%). We also present CATH-FunVar web-pages displaying variations in protein sequences and their proximity to known or predicted functional sites. We present two case studies (1) putative cancer drivers and (2) SARS-CoV-2 proteins. Finally, we have improved links to and from CATH including SCOP, InterPro, Aquaria and 2DProt.
References provided by Crossref.org
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