CATH: increased structural coverage of functional space

J 2021

CATH: increased structural coverage of functional space

SILLITOE, Ian, Nicola BORDIN, Natalie DAWSON, Vaishali P. WAMAN, Paul ASHFORD et. al.

Basic information

Original name

CATH: increased structural coverage of functional space

Authors

SILLITOE, Ian, Nicola BORDIN, Natalie DAWSON, Vaishali P. WAMAN, Paul ASHFORD, Harry M. SCHOLES, Camilla S.M. PANG, Laurel WOODRIDGE, Clemens RAUER, Neeladri SEN, Mahnaz ABBASIAN, Sean LE CORNU, Su Datt LAM, Karel BERKA, Ivana HUTAŘOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution), Jon LEES and Christine A. ORENGO

Edition

Nucleic Acids Research, Oxford, Oxford University Press, 2021, 0305-1048

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 19.160

RIV identification code

RIV/00216224:14740/21:00120994

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1093/nar/gkaa1079

UT WoS

000608437800035

Keywords in English

protein structures; CATH

Abstract

V originále

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.

Links

EF16_013/0001777, research and development project

Name: ELIXIR-CZ: Budování kapacit

90131, large research infrastructures

Name: ELIXIR-CZ II

Citovat

SILLITOE, Ian, Nicola BORDIN, Natalie DAWSON, Vaishali P. WAMAN, Paul ASHFORD, Harry M. SCHOLES, Camilla S.M. PANG, Laurel WOODRIDGE, Clemens RAUER, Neeladri SEN, Mahnaz ABBASIAN, Sean LE CORNU, Su Datt LAM, Karel BERKA, Ivana HUTAŘOVÁ VAŘEKOVÁ, Radka SVOBODOVÁ, Jon LEES and Christine A. ORENGO. CATH: increased structural coverage of functional space. Nucleic Acids Research. Oxford: Oxford University Press, 2021, vol. 49, D1, p. "D266"-"D273", 8 pp. ISSN 0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkaa1079.

@article{1730557,
   author = {Sillitoe, Ian and Bordin, Nicola and Dawson, Natalie and Waman, Vaishali P. and Ashford, Paul and Scholes, Harry M. and Pang, Camilla S.M. and Woodridge, Laurel and Rauer, Clemens and Sen, Neeladri and Abbasian, Mahnaz and Le Cornu, Sean and Lam, Su Datt and Berka, Karel and Hutařová Vařeková, Ivana and Svobodová, Radka and Lees, Jon and Orengo, Christine A.},
   article_location = {Oxford},
   article_number = {D1},
   doi = {http://dx.doi.org/10.1093/nar/gkaa1079},
   keywords = {protein structures; CATH},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {CATH: increased structural coverage of functional space},
   url = {https://doi.org/10.1093/nar/gkaa1079},
   volume = {49},
   year = {2021}
}

TY  - JOUR
ID  - 1730557
AU  - Sillitoe, Ian - Bordin, Nicola - Dawson, Natalie - Waman, Vaishali P. - Ashford, Paul - Scholes, Harry M. - Pang, Camilla S.M. - Woodridge, Laurel - Rauer, Clemens - Sen, Neeladri - Abbasian, Mahnaz - Le Cornu, Sean - Lam, Su Datt - Berka, Karel - Hutařová Vařeková, Ivana - Svobodová, Radka - Lees, Jon - Orengo, Christine A.
PY  - 2021
TI  - CATH: increased structural coverage of functional space
JF  - Nucleic Acids Research
VL  - 49
IS  - D1
SP  - "D266"-"D273"
EP  - "D266"-"D273"
PB  - Oxford University Press
SN  - 03051048
KW  - protein structures
KW  - CATH
UR  - https://doi.org/10.1093/nar/gkaa1079
L2  - https://doi.org/10.1093/nar/gkaa1079
N2  - 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.
ER  -

SILLITOE, Ian, Nicola BORDIN, Natalie DAWSON, Vaishali P. WAMAN, Paul ASHFORD, Harry M. SCHOLES, Camilla S.M. PANG, Laurel WOODRIDGE, Clemens RAUER, Neeladri SEN, Mahnaz ABBASIAN, Sean LE CORNU, Su Datt LAM, Karel BERKA, Ivana HUTAŘOVÁ VAŘEKOVÁ, Radka SVOBODOVÁ, Jon LEES and Christine A. ORENGO. CATH: increased structural coverage of functional space. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2021, vol.~49, D1, p.~''D266''-''D273'', 8 pp. ISSN~0305-1048. Available from: https://dx.doi.org/10.1093/nar/gkaa1079.

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