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Database Commons - CSA

CSA

Citations: 614

z-index 38.59

Short name CSA
Full name Catalytic Site Atlas
Description The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure.
URL http://www.ebi.ac.uk/thornton-srv/databases/CSA/
Year founded 2003
Last update & version NA    v2.0
Availability Free to all users
University/Institution hosted European Bioinformatics Institute
Address Hinxton,Cambridge CB10 1SD,UK
City Cambridge
Province/State
Country/Region United Kingdom
Contact name Nicholas Furnham
Contact email nickf@ebi.ac.uk
Data type(s)
Major organism(s)
Keyword(s)
  • catalytic residue
  • enzyme active site
Publication(s)
  • The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. [PMID: 24319146]

    Nicholas Furnham, Gemma L Holliday, Tjaart A P de Beer, Julius O B Jacobsen, William R Pearson, Janet M Thornton
    Nucleic acids research 2014:42(Database issue)
    42 Citations (Google Scholar as of 2016-01-25)

    Abstract: Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The original version of the Catalytic Site Atlas (CSA) (http://www.ebi.ac.uk/thornton-srv/databases/CSA) published in 2004, which catalogs the residues involved in enzyme catalysis in experimentally determined protein structures, had only 177 curated entries and employed a simplistic approach to expanding these annotations to homologous enzyme structures. Here we present a new version of the CSA (CSA 2.0), which greatly expands the number of both curated (968) and automatically annotated catalytic sites in enzyme structures, utilizing a new method for annotation transfer. The curated entries are used, along with the variation in residue type from the sequence comparison, to generate 3D templates of the catalytic sites, which in turn can be used to find catalytic sites in new structures. To ease the transfer of CSA annotations to other resources a new ontology has been developed: the Enzyme Mechanism Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface.

  • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. [PMID: 14681376]

    Craig T Porter, Gail J Bartlett, Janet M Thornton
    Nucleic acids research 2004:32(Database issue)
    572 Citations (Google Scholar as of 2016-01-25)

    Abstract: The Catalytic Site Atlas (CSA) provides catalytic residue annotation for enzymes in the Protein Data Bank. It is available online at http://www.ebi.ac.uk/thornton-srv/databases/CSA. The database consists of two types of annotated site: an original hand-annotated set containing information extracted from the primary literature, using defined criteria to assign catalytic residues, and an additional homologous set, containing annotations inferred by PSI-BLAST and sequence alignment to one of the original set. The CSA can be queried via Swiss-Prot identifier and EC number, as well as by PDB code. CSA Version 1.0 contains 177 original hand- annotated entries and 2608 homologous entries, and covers approximately 30% of all EC numbers found in PDB. The CSA will be updated on a monthly basis to include homologous sites found in new PDBs, and new hand-annotated enzymes as and when their annotation is completed.

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Accessibility

Rate of accessibility:
HTTP status codeDate requested
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200 OK2018-04-24
200 OK2018-04-20
200 OK2018-04-17
200 OK2018-04-13
200 OK2018-04-10
200 OK2018-04-06
200 OK2018-04-03
200 OK2018-02-27
200 OK2018-02-23
200 OK2018-02-20
200 OK2018-02-16
-1 Failed2018-02-13
200 OK2018-02-09
200 OK2018-02-06
200 OK2018-02-02
200 OK2018-01-30
200 OK2018-01-26
200 OK2018-01-23
200 OK2018-01-19
-1 Failed2018-01-16
-1 Failed2018-01-12
-1 Failed2018-01-09
-1 Failed2018-01-05
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-1 Failed2017-12-29
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-1 Failed2017-10-06
-1 Failed2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
200 OK2016-12-30
200 OK2016-12-27
200 OK2016-12-23
200 OK2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
200 OK2016-11-18
200 OK2016-11-15
200 OK2016-11-11
200 OK2016-11-08
200 OK2016-11-04
200 OK2016-11-01
200 OK2016-10-28
200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
403 Failed2016-09-09
403 Failed2016-09-06
500 Failed2016-09-02
500 Failed2016-08-30
200 OK2016-08-26
200 OK2016-08-23
200 OK2016-08-19
200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
200 OK2016-05-24
200 OK2016-05-20
200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
200 OK2016-03-23
200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

Protein Structure
catalytic residue enzyme active site

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Mengwei Li [2016-03-31]
    • Mengwei Li [2016-02-21]
    • Mengwei Li [2015-12-06]
    • Mengwei Li [2015-06-29]
    • Mengwei Li [2015-06-27]
Stats