CDD: a Conserved Domain Database for protein classification
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which...
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| Veröffentlicht in: | Nucleic acids research 2005-01, Vol.33 (suppl-1), p.D192-D196 |
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| container_title | Nucleic acids research |
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| creator | Marchler-Bauer, Aron Anderson, John B. Cherukuri, Praveen F. DeWeese-Scott, Carol Geer, Lewis Y. Gwadz, Marc He, Siqian Hurwitz, David I. Jackson, John D. Ke, Zhaoxi Lanczycki, Christopher J. Liebert, Cynthia A. Liu, Chunlei Lu, Fu Marchler, Gabriele H. Mullokandov, Mikhail Shoemaker, Benjamin A. Simonyan, Vahan Song, James S. Thiessen, Paul A. Yamashita, Roxanne A. Yin, Jodie J. Zhang, Dachuan Bryant, Stephen H. |
| description | The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system. |
| doi_str_mv | 10.1093/nar/gki069 |
| format | Article |
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CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.</description><identifier>ISSN: 0305-1048</identifier><identifier>ISSN: 1362-4962</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gki069</identifier><identifier>PMID: 15608175</identifier><identifier>CODEN: NARHAD</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Amino Acid Sequence ; Conserved Sequence ; Databases, Protein ; Phylogeny ; Protein Structure, Tertiary ; Proteins - classification ; Sequence Alignment ; Sequence Analysis, Protein ; User-Computer Interface</subject><ispartof>Nucleic acids research, 2005-01, Vol.33 (suppl-1), p.D192-D196</ispartof><rights>Copyright Oxford Publishing Limited(England) Jan 1 2005</rights><rights>Copyright © 2005 Oxford University Press 2005</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c471t-8f733d705fb030d1e914eecabc13f26f540e1b4e05a5f895afb7170b9d739f933</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC540023/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC540023/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15608175$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Marchler-Bauer, Aron</creatorcontrib><creatorcontrib>Anderson, John B.</creatorcontrib><creatorcontrib>Cherukuri, Praveen F.</creatorcontrib><creatorcontrib>DeWeese-Scott, Carol</creatorcontrib><creatorcontrib>Geer, Lewis Y.</creatorcontrib><creatorcontrib>Gwadz, Marc</creatorcontrib><creatorcontrib>He, Siqian</creatorcontrib><creatorcontrib>Hurwitz, David I.</creatorcontrib><creatorcontrib>Jackson, John D.</creatorcontrib><creatorcontrib>Ke, Zhaoxi</creatorcontrib><creatorcontrib>Lanczycki, Christopher J.</creatorcontrib><creatorcontrib>Liebert, Cynthia A.</creatorcontrib><creatorcontrib>Liu, Chunlei</creatorcontrib><creatorcontrib>Lu, Fu</creatorcontrib><creatorcontrib>Marchler, Gabriele H.</creatorcontrib><creatorcontrib>Mullokandov, Mikhail</creatorcontrib><creatorcontrib>Shoemaker, Benjamin A.</creatorcontrib><creatorcontrib>Simonyan, Vahan</creatorcontrib><creatorcontrib>Song, James S.</creatorcontrib><creatorcontrib>Thiessen, Paul A.</creatorcontrib><creatorcontrib>Yamashita, Roxanne A.</creatorcontrib><creatorcontrib>Yin, Jodie J.</creatorcontrib><creatorcontrib>Zhang, Dachuan</creatorcontrib><creatorcontrib>Bryant, Stephen H.</creatorcontrib><title>CDD: a Conserved Domain Database for protein classification</title><title>Nucleic acids research</title><addtitle>Nucl. Acids Res</addtitle><description>The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.</description><subject>Amino Acid Sequence</subject><subject>Conserved Sequence</subject><subject>Databases, Protein</subject><subject>Phylogeny</subject><subject>Protein Structure, Tertiary</subject><subject>Proteins - classification</subject><subject>Sequence Alignment</subject><subject>Sequence Analysis, Protein</subject><subject>User-Computer Interface</subject><issn>0305-1048</issn><issn>1362-4962</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1v1DAQhi0Eokvhwg9AEQcOSKEzsR3HIA50AxRRiQOf6sWaJHZxm423draCf49XuyofF04jzTzv6J15GXuI8AxB86OJ4tH5pYda32IL5HVVCl1Xt9kCOMgSQTQH7F5KFwAoUIq77ABlDQ0quWAvlm37vKBiGaZk47UdijasyE9FSzN1lGzhQizWMcw2N_uRUvLO9zT7MN1ndxyNyT7Y10P2-c3rT8uT8vTD23fLV6dlLxTOZeMU54MC6bpsaECrUVjbU9cjd1XtpACLnbAgSbpGS3KdQgWdHhTXTnN-yF7u9q433coOvZ3mSKNZR7-i-NME8ubvyeS_m_NwbfJmqLb6J3t9DFcbm2az8qm340iTDZtkasWr7En_F0TV8EbjFnz8D3gRNnHKTzAVQF1prVSGnu6gPoaUonU3jhHMNjiTgzO74DL86M8bf6P7pDJQ7gCfZvvjZk7xcutfSXPy7cx8Ofso3rdfwRzzX05Wo3w</recordid><startdate>20050101</startdate><enddate>20050101</enddate><creator>Marchler-Bauer, Aron</creator><creator>Anderson, John B.</creator><creator>Cherukuri, Praveen F.</creator><creator>DeWeese-Scott, Carol</creator><creator>Geer, Lewis Y.</creator><creator>Gwadz, Marc</creator><creator>He, Siqian</creator><creator>Hurwitz, David I.</creator><creator>Jackson, John D.</creator><creator>Ke, Zhaoxi</creator><creator>Lanczycki, Christopher J.</creator><creator>Liebert, Cynthia A.</creator><creator>Liu, Chunlei</creator><creator>Lu, Fu</creator><creator>Marchler, Gabriele H.</creator><creator>Mullokandov, Mikhail</creator><creator>Shoemaker, Benjamin A.</creator><creator>Simonyan, Vahan</creator><creator>Song, James S.</creator><creator>Thiessen, Paul A.</creator><creator>Yamashita, Roxanne A.</creator><creator>Yin, Jodie J.</creator><creator>Zhang, Dachuan</creator><creator>Bryant, Stephen H.</creator><general>Oxford University Press</general><general>Oxford Publishing Limited (England)</general><scope>BSCLL</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20050101</creationdate><title>CDD: a Conserved Domain Database for protein classification</title><author>Marchler-Bauer, Aron ; 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Acids Res</addtitle><date>2005-01-01</date><risdate>2005</risdate><volume>33</volume><issue>suppl-1</issue><spage>D192</spage><epage>D196</epage><pages>D192-D196</pages><issn>0305-1048</issn><issn>1362-4962</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=cdd. CD-Search, which is available at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi, is a fast, interactive tool to identify conserved domains in new protein sequences. CD-Search results for protein sequences in Entrez are pre-computed to provide links between proteins and domain models, and computational annotation visible upon request. Protein–protein queries submitted to NCBI's BLAST search service at http://www.ncbi.nlm.nih.gov/BLAST are scanned for the presence of conserved domains by default. While CDD started out as essentially a mirror of publicly available domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and in some cases replace these models with domain hierarchies curated at the NCBI. Here, we report on the progress of the curation effort and associated improvements in the functionality of the CDD information retrieval system.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>15608175</pmid><doi>10.1093/nar/gki069</doi><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 0305-1048 |
| ispartof | Nucleic acids research, 2005-01, Vol.33 (suppl-1), p.D192-D196 |
| issn | 0305-1048 1362-4962 1362-4962 |
| language | eng |
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| source | Oxford Journals Open Access Collection; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Amino Acid Sequence Conserved Sequence Databases, Protein Phylogeny Protein Structure, Tertiary Proteins - classification Sequence Alignment Sequence Analysis, Protein User-Computer Interface |
| title | CDD: a Conserved Domain Database for protein classification |
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