Gene3D

General Information

Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.

Homepage http://gene3d.biochem.ucl.ac.uk

Countries that developed this resource United Kingdom

Created in 2003

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: Gene3D; Gene3D; DOI: https://doi.org/10.25504/FAIRsharing.fyqk5z; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Aug 25 2019 8:45 p.m.

Publication for citation Gene3D: Extensive prediction of globular domains in proteins. Lewis TE,Sillitoe I,Dawson N,Lam SD,Clarke T,Lee D,Orengo C,Lees J; Nucleic Acids Res ; 2017; 10.1093/nar/gkx1069;

Record updated: Nov. 21, 2018, 10:01 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 10:01, 21 Nov 2018 (approved):

	'domains' has been modified:
		Before:
			Annotation
			Gene
			Genome
			Hidden Markov model (HMM)
			Life Science
			Protein interactions
			Protein structure
		After:
			Amino acid sequence
			Annotation
			Gene
			Genome
			Hidden Markov model (HMM)
			Life Science
			Protein domain
			Protein interactions
			Protein structure
		Added:
			Amino acid sequence
			Protein domain
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 17:25, 13 Aug 2018 (approved):

	'dataProcesses' has been modified:
		Before:
			Protein Search
			automated curation
			Family Search
			download
			search
			CATH Search Sequence scanning
		After:
			Protein Search
			automated curation
			Family Search
			download
			search
			CATH Search Sequence scanning
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. 
		Added:
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. 
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 17:14, 13 Aug 2018 (approved):

	'description' has been modified:
		Before: Precalculated structural assignments for whole genomes.
		After: Gene3D takes CATH domain families (from PDB structures) and assigns them to the millions protein sequences (using Hidden Markov models generated from HMMER) with no PDB structures.

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 00:56, 02 Aug 2018 (approved):

	'organizations' has been modified:
		Before:
			University College London|http://www.ucl.ac.uk/smb|Maintains
			European Commission|http://ec.europa.eu/|Funds
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
			National Institutes of Health|https://www.nih.gov|Funds
			Research Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower St, London. WC1E 6BT, UK.|http://www.ucl.ac.uk/smb|Maintains
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
		After:
			European Commission|http://ec.europa.eu/|Funds
			U.S. National Library of Medicine|https://www.nlm.nih.gov/|Funds
			National Institutes of Health|https://www.nih.gov|Funds
			The Wellcome Trust, UK|https://wellcome.ac.uk|Funds
			Wellcome Trust, UK|http://www.wellcome.ac.uk|Funds
			University College London|http://www.ucl.ac.uk/smb|Maintains
			Research Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower St, London. WC1E 6BT, UK.|http://www.ucl.ac.uk/smb|Maintains
			The Wellcome Trust|https://wellcome.ac.uk/|Funds
			National Institutes of Health|http://www.nih.gov|Funds
		Added:
			The Wellcome Trust|https://wellcome.ac.uk/|Funds
			National Institutes of Health|http://www.nih.gov|Funds
		Removed:

	'related_databases' has been modified:
		Before:
			ProtoNet
			Statistical Torsional Angles Potentials of NMR Refinement Database
			Plant Transcription Factor Database
			CATH Protein Structure Classification
		After:
			IntAct molecular interaction database
			Pfam Protein Families
			ProtoNet
			Statistical Torsional Angles Potentials of NMR Refinement Database
			Plant Transcription Factor Database
			DrugBank
			Integrated resource of protein families, domains and functional sites
			Ensembl
			UniProt Knowledgebase
			CATH Protein Structure Classification
		Added:
			IntAct molecular interaction database
			Pfam Protein Families
			DrugBank
			Integrated resource of protein families, domains and functional sites
			Ensembl
			UniProt Knowledgebase
		Removed:

	'dataProcesses' has been modified:
		Before:
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. We currently store only the current versions domain assignments.
			download
			three times a year releanse (dependent on the yearly releases of CATH)
			automated curation
			search
		After:
			Family Search
			download
			Protein Search
			automated curation
			search
			CATH Search Sequence scanning
		Added:
			Family Search
			Protein Search
			CATH Search Sequence scanning
		Removed:
			Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated. We currently store only the current versions domain assignments.
			three times a year releanse (dependent on the yearly releases of CATH)

	'miriam_id' has been modified:
		Before: None
		After: 

	'publications' has been modified:
		Before:
			The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.|Yeats C., Lees J., Carter P., Sillitoe I., Orengo C., |Nucleic Acids Res.|2011
			Gene3D: merging structure and function for a Thousand genomes.|Lees J., Yeats C., Redfern O., Clegg A., Orengo C., |Nucleic Acids Res.|2010
		After:
			The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.|Yeats C., Lees J., Carter P., Sillitoe I., Orengo C., |Nucleic Acids Res.|2011
			Gene3D: merging structure and function for a Thousand genomes.|Lees J., Yeats C., Redfern O., Clegg A., Orengo C., |Nucleic Acids Res.|2010
			Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.|Das S,Lee D,Sillitoe I,Dawson NL,Lees JG,Orengo CA|Bioinformatics|2015
			Gene3D: Extensive prediction of globular domains in proteins.|Lewis TE,Sillitoe I,Dawson N,Lam SD,Clarke T,Lee D,Orengo C,Lees J|Nucleic Acids Res|2017
		Added:
			Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.|Das S,Lee D,Sillitoe I,Dawson NL,Lees JG,Orengo CA|Bioinformatics|2015
			Gene3D: Extensive prediction of globular domains in proteins.|Lewis TE,Sillitoe I,Dawson N,Lam SD,Clarke T,Lee D,Orengo C,Lees J|Nucleic Acids Res|2017
		Removed:

	'tools' has been modified:
		Before:
			Genome comparison||http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
		After:
			Genome comparison||http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
			MODELLER||https://salilab.org/modeller/
		Added:
			MODELLER||https://salilab.org/modeller/
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.fyqk5z' by 'The FAIRsharing Team' at 15:09, 06 Sep 2016 (approved):

	'description' has been modified:
		Before: Precalculated structural assignments for whole genomes
		After: Precalculated structural assignments for whole genomes.

Support

General

support email	Gene3D.Contact@gmail.com
help	http://gene3d.biochem.ucl.ac.uk/examples

Additional Information

Contact

Corin Yeats

TeSS training resources

Cath gene3d

Tools

Genome comparison	http://gene3d.biochem.ucl.ac.uk/compare?mode=genomes
MODELLER	https://salilab.org/modeller/

Access / Retrieve Data

Conditions of Use

Data Versioning

Version numbers are updated on a CATH release. Point updates are made when sequence sets are updated.

No link recorded

Data Release

Protein Search

http://gene3d.biochem.ucl.ac.uk/searchForm?mode=protein

Data Curation

automated curation

No link recorded

Data Access

Family Search	http://gene3d.biochem.ucl.ac.uk/searchForm?mode=family
download	http://download.cathdb.info/gene3d/CURRENT_RELEASE/
search	No link recorded
CATH Search Sequence scanning	http://www.cathdb.info/search/by_sequence

Publications

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.

Yeats C., Lees J., Carter P., Sillitoe I., Orengo C.,
Nucleic Acids Res. 2011

View Paper (PubMed) View Publication

Gene3D: merging structure and function for a Thousand genomes.

Lees J., Yeats C., Redfern O., Clegg A., Orengo C.,
Nucleic Acids Res. 2010

View Paper (PubMed) View Publication

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.

Das S,Lee D,Sillitoe I,Dawson NL,Lees JG,Orengo CA
Bioinformatics 2015

View Paper (PubMed) View Publication

Gene3D: Extensive prediction of globular domains in proteins.

Lewis TE,Sillitoe I,Dawson N,Lam SD,Clarke T,Lee D,Orengo C,Lees J
Nucleic Acids Res 2017

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

Gene Ontology

Models and Formats

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

This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

U.S. National Library of Medicine (Government body)
European Commission (Government body)
Wellcome Trust, UK (Charitable foundation)
The Wellcome Trust, UK (Charitable foundation)
National Institutes of Health (NIH), Bethesda, MD, USA (Government body)
The Wellcome Trust, UK (Charitable foundation)

Maintains

Grant Number(s)

081989/Z/07/Z (The Wellcome Trust, UK)
DE-AC02-065CH11357 (National Institutes of Health (NIH), Bethesda, MD, USA)
HHSN272200700058C (National Institutes of Health (NIH), Bethesda, MD, USA)
LSHG-CT-2003-503265 (European Commission)
LSHG-CT-2004-512092 (European Commission)
LSHG-CT-2005-518254 (European Commission)
LSHG-CT-2005-518254 (European Commission)

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