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PROCOGNATE

General Information

This record was deprecated on Jan. 10, 2019 for the following reason(s): This resource is no longer maintained as its homepage is no longer available.

PROCOGNATE is a database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers.

Homepage http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html

Countries that developed this resource Austria , Belgium , Croatia , Czech Republic , Denmark , Finland , France , Germany , Greece , Hungary , Iceland , Israel , Italy , Lithuania , Luxembourg , Malta , Montenegro , Netherlands , Norway , Portugal , Republic of Ireland , Slovakia , Spain , Sweden , Switzerland , United Kingdom

Created in 2006

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: PROCOGNATE; PROCOGNATE; DOI: https://doi.org/10.25504/FAIRsharing.ct66a3; Last edited: Feb. 10, 2020, 3 p.m.; Last accessed: Jul 31 2021 10:33 p.m.

Publication for citation PROCOGNATE: a cognate ligand domain mapping for enzymes. Bashton M,Nobeli I,Thornton JM; Nucleic Acids Res ; 2007; 10.1093/nar/gkm611;

Record updated: Feb. 10, 2020, 3 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.ct66a3' by 'The FAIRsharing Team' at 15:00, 10 Feb 2020 (approved):

	'miriam_id' has been modified:
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	'countries' has been modified:
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			European Union
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			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
			United Kingdom
		Added:
			Austria
			Belgium
			Croatia
			Czech Republic
			Denmark
			Finland
			France
			Germany
			Greece
			Hungary
			Iceland
			Israel
			Italy
			Lithuania
			Luxembourg
			Malta
			Montenegro
			Netherlands
			Norway
			Portugal
			Republic of Ireland
			Slovakia
			Spain
			Sweden
			Switzerland
			United Kingdom
		Removed:
			European Union

Edits to 'https://fairsharing.org/FAIRsharing.ct66a3' by 'The FAIRsharing Team' at 13:37, 10 Jan 2019 (approved):

	'status' has been modified:
		Before: RDY
		After: DEP

	'miriam_id' has been modified:
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		After: None

	'description' has been modified:
		Before: PROCOGNATE is a database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers. 
		After: PROCOGNATE is a database of cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers.

Edits to 'https://fairsharing.org/FAIRsharing.ct66a3' by 'The FAIRsharing Team' at 13:34, 10 Jan 2019 (approved):

	'organizations' has been modified:
		Before:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains
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			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Added:
			European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK|https://www.ebi.ac.uk/|Maintains
		Removed:
			Swiss Institute of Bioinformatics (SIB), Switzerland|https://www.sib.swiss|Maintains

	'miriam_id' has been modified:
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	'onto_domains' has been modified:
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			Enzymes
			protein
			small molecule
			structure
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			Enzymes
			enzyme
			protein
			small molecule
			structure
		Added:
			enzyme
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.ct66a3' by 'The FAIRsharing Team' at 09:55, 29 Sep 2016 (approved):

	'contactName' has been modified:
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		After:
			Matthew Bashton
			Domain list has changed: 
			Previous values:
			Enzyme|material|http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#nlx_mol_20090405
			Life Science|domain|
			Protein|material|http://purl.org/obo/owl/GO#GO_0003675
			Small molecule|material|
			New values: 
			Enzyme|material|http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#nlx_mol_20090405
			Life Science|domain|
			Protein|material|http://purl.org/obo/owl/GO#GO_0003675
			Small molecule|material|
			Structure data|information content entity|http://purl.org/obo/owl/PATO#PATO_0000141
			Publication List has changed: 
			Previous values:
			PROCOGNATE: a cognate ligand domain mapping for enzymes.
			New values: 
			PROCOGNATE: a cognate ligand domain mapping for enzymes.
			Cognate ligand domain mapping for enzymes.
			Tools have changed: 
			Previous values:
			search
			New values: 
			Data processes have changed: 
			Previous values:
			Download
			New values: 
			Download
			search
		Added:
		Removed:

Support

General

help	http://www.ebi.ac.uk/thornton-srv/databa ...

Additional Information

Contact

Matthew Bashton

Tools

No tools defined

Access / Retrieve Data

Conditions of Use

Data Access

Download	http://www.ebi.ac.uk/thornton-srv/databases/procognate/download.html
search	http://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html

Publications

PROCOGNATE: a cognate ligand domain mapping for enzymes.

Bashton M,Nobeli I,Thornton JM
Nucleic Acids Res 2007

View Paper (PubMed) View Publication

Cognate ligand domain mapping for enzymes.

Bashton M,Nobeli I,Thornton JM
J Mol Biol 2006

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Protein Data Bank Format

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

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Maintains

European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK (Research institute) Lead

PROCOGNATE

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