Conserved Domain Database

Abbreviation:CDD

General Information

The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, NCBI Protein Clusters, TIGRFAM). NCBI-curated models are organized hierarchically into families, sub- and super-families, and come with annotation of functional sites.

Homepage https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

Countries that developed this resource United States

Created in 2008

Taxonomic range

All

Knowledge Domains

Subjects

How to cite this record FAIRsharing.org: CDD; Conserved Domain Database; DOI: https://doi.org/10.25504/FAIRsharing.b9st5p; Last edited: March 25, 2019, 9:44 p.m.; Last accessed: Jul 18 2019 10:50 a.m.

This record is maintained by marchlerbauer ORCID

Record updated: March 22, 2019, 9:12 a.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.b9st5p' by 'The FAIRsharing Team' at 09:10, 22 Mar 2019 (approved):

	'organizations' has been modified:
		Before:
			National Center for Biotechnology Information (NCBI), Rockville, MD, USA|http://www.ncbi.nlm.nih.gov/|Maintains
		After:
			National Center for Biotechnology Information (NCBI), Rockville, MD, USA|http://www.ncbi.nlm.nih.gov/|Maintains
			National Library of Medicine (NLM)), Bethesda, MD, USA|http://www.nlm.gov|Funds
		Added:
			National Library of Medicine (NLM)), Bethesda, MD, USA|http://www.nlm.gov|Funds
		Removed:

	'supportLinks' has been modified:
		Before:
			email|info@ncbi.nlm.nih.gov
			help|https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml
		After:
			blog|https://www.ncbi.nlm.nih.gov/Structure/cdd/docs/cdd_news.html
			email|info@ncbi.nlm.nih.gov
			help|https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml
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			blog|https://www.ncbi.nlm.nih.gov/Structure/cdd/docs/cdd_news.html
		Removed:

	'tools' has been modified:
		Before:
			BATCH CD-Search||http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi
			CDART (Conserved Domain Architecture Retrieval Tool)||http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi
			CDTree (domain hierarchy editor)|3.1|http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml
			Cn3D (structure viewer and alignment editor)|4.3|http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
		After:
			CDTree (domain hierarchy editor)|3.1|http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml
			Cn3D (structure viewer and alignment editor)|4.3.1|http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
		Added:
			Cn3D (structure viewer and alignment editor)|4.3.1|http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml
		Removed:
			BATCH CD-Search||http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi
			CDART (Conserved Domain Architecture Retrieval Tool)||http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi
			Cn3D (structure viewer and alignment editor)|4.3|http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

	'onto_domains' has been modified:
		Before:
			Multiple sequence alignment
			Protein domain
			protein
			sequence_feature
			structure
		After:
			Annotation
			Multiple sequence alignment
			Protein domain
			Protein structure
			Sequence alignment
			functional domain
			literature curation
			protein
			sequence_feature
			structure
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			Annotation
			Protein structure
			Sequence alignment
			functional domain
			literature curation
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	'onto_disciplines' has been modified:
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			Life Sciences
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			Data Submission, Annotation and Curation
			Life Sciences
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			Data Submission, Annotation and Curation
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	'dataProcesses' has been modified:
		Before:
			search
			Download
		After:
			Search
			FTP Download
			BATCH CD-Search
			CDART (Conserved Domain Architecture Retrieval Tool)
		Added:
			Search
			FTP Download
			BATCH CD-Search
			CDART (Conserved Domain Architecture Retrieval Tool)
		Removed:
			search
			Download

	'publications' has been modified:
		Before:
			CDD: specific functional annotation with the Conserved Domain Database.|Marchler-Bauer A., Anderson JB., Chitsaz F., Derbyshire MK., DeWeese-Scott C., Fong JH., Geer LY., Geer RC., Gonzales NR., Gwadz M., He S., Hurwitz DI., Jackson JD., Ke Z., Lanczycki CJ., Liebert CA., Liu C., Lu F., Lu S., Marchler GH., Mullokandov M., Song JS., Tasneem A., Thanki N., Yamashita RA., Zhang D., Zhang N., Bryant SH., |Nucleic Acids Res.|2009
			CDD: conserved domains and protein three-dimensional structure|Marchler-Bauer A., Zheng C., Chitsaz F., Derbyshire MK., Geer LY., Geer RC., Gonzales NR., Gwadz M., Hurwitz DI., Lanczycki CJ., Lu F., Lu S., Marchler GH., Song JS., Thanki N., Yamashita RA., Zhang D., Bryant SH.|Nucleic Acids Res.|2013
			CDD: NCBI's conserved domain database.|Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH|Nucleic Acids Research|2015
		After:
			CDD: specific functional annotation with the Conserved Domain Database.|Marchler-Bauer A., Anderson JB., Chitsaz F., Derbyshire MK., DeWeese-Scott C., Fong JH., Geer LY., Geer RC., Gonzales NR., Gwadz M., He S., Hurwitz DI., Jackson JD., Ke Z., Lanczycki CJ., Liebert CA., Liu C., Lu F., Lu S., Marchler GH., Mullokandov M., Song JS., Tasneem A., Thanki N., Yamashita RA., Zhang D., Zhang N., Bryant SH., |Nucleic Acids Res.|2009
			CDD: conserved domains and protein three-dimensional structure|Marchler-Bauer A., Zheng C., Chitsaz F., Derbyshire MK., Geer LY., Geer RC., Gonzales NR., Gwadz M., Hurwitz DI., Lanczycki CJ., Lu F., Lu S., Marchler GH., Song JS., Thanki N., Yamashita RA., Zhang D., Bryant SH.|Nucleic Acids Res.|2013
			CDD: NCBI's conserved domain database.|Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH|Nucleic Acids Research|2015
			CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.|Marchler-Bauer A,Bo Y,Han L,He J,Lanczycki CJ,Lu S,Chitsaz F,Derbyshire MK,Geer RC,Gonzales NR,Gwadz M,Hurwitz DI,Lu F,Marchler GH,Song JS,Thanki N,Wang Z,Yamashita RA,Zhang D,Zheng C,Geer LY,Bryant SH|Nucleic Acids Res|2016
		Added:
			CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.|Marchler-Bauer A,Bo Y,Han L,He J,Lanczycki CJ,Lu S,Chitsaz F,Derbyshire MK,Geer RC,Gonzales NR,Gwadz M,Hurwitz DI,Lu F,Marchler GH,Song JS,Thanki N,Wang Z,Yamashita RA,Zhang D,Zheng C,Geer LY,Bryant SH|Nucleic Acids Res|2016
		Removed:

	'homepage' has been modified:
		Before: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
		After: https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

Edits to 'https://fairsharing.org/FAIRsharing.b9st5p' by 'The FAIRsharing Team' at 14:52, 15 Dec 2016 (approved):

	'name' has been modified:
		Before: Conserved Domain Database (CDD)
		After: Conserved Domain Database

Edits to 'https://fairsharing.org/FAIRsharing.b9st5p' by 'The FAIRsharing Team' at 08:57, 10 Dec 2016 (approved):

	'year' has been modified:
		Before: None
		After: 2008

Edits to 'https://fairsharing.org/FAIRsharing.b9st5p' by 'The FAIRsharing Team' at 08:55, 10 Dec 2016 (approved):

	'contactName' has been modified:
		Before:
			NCBI Help Desk
		After:
			Aron Marchler-Bauer
		Added:
		Removed:

Support

General

blog	News
support email	info@ncbi.nlm.nih.gov
help	https://www.ncbi.nlm.nih.gov/Structure/c ...

Additional Information

Contact	Aron Marchler-Bauer ORCID
Identifiers.org	MIR:00000119

Tools

CDTree (domain hierarchy editor)	http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml	3.1
Cn3D (structure viewer and alignment editor)	http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml	4.3.1

Access / Retrieve Data

Conditions of Use

Applies to: Data use

Attribution required
Open Data Commons (ODC) Public Domain Dedication and Licence (PDDL) 1.0

Data Access

Search	https://www.ncbi.nlm.nih.gov/Structure/cdd/docs/cdd_search.html
FTP Download	ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd
BATCH CD-Search	http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi
CDART (Conserved Domain Architecture Retrieval Tool)	http://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi

Publications

CDD: specific functional annotation with the Conserved Domain Database.

Marchler-Bauer A., Anderson JB., Chitsaz F., Derbyshire MK., DeWeese-Scott C., Fong JH., Geer LY., Geer RC., Gonzales NR., Gwadz M., He S., Hurwitz DI., Jackson JD., Ke Z., Lanczycki CJ., Liebert CA., Liu C., Lu F., Lu S., Marchler GH., Mullokandov M., Song JS., Tasneem A., Thanki N., Yamashita RA., Zhang D., Zhang N., Bryant SH.,
Nucleic Acids Res. 2009

View Paper (PubMed) View Publication

CDD: conserved domains and protein three-dimensional structure

Marchler-Bauer A., Zheng C., Chitsaz F., Derbyshire MK., Geer LY., Geer RC., Gonzales NR., Gwadz M., Hurwitz DI., Lanczycki CJ., Lu F., Lu S., Marchler GH., Song JS., Thanki N., Yamashita RA., Zhang D., Bryant SH.
Nucleic Acids Res. 2013

View Paper (PubMed) View Publication

CDD: NCBI's conserved domain database.

Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Bryant SH
Nucleic Acids Research 2015

View Paper (PubMed) View Publication

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.

Marchler-Bauer A,Bo Y,Han L,He J,Lanczycki CJ,Lu S,Chitsaz F,Derbyshire MK,Geer RC,Gonzales NR,Gwadz M,Hurwitz DI,Lu F,Marchler GH,Song JS,Thanki N,Wang Z,Yamashita RA,Zhang D,Zheng C,Geer LY,Bryant SH
Nucleic Acids Res 2016

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

FASTA Sequence 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

This record is maintained by marchlerbauer ORCID

Funds

National Library of Medicine (NLM)), Bethesda, MD, USA (Government body)

Maintains

National Center for Biotechnology Information (NCBI), Rockville, MD, USA (Research institute)

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