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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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Detalles Bibliográficos
Autores principales: 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.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540023/
https://www.ncbi.nlm.nih.gov/pubmed/15608175
http://dx.doi.org/10.1093/nar/gki069
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author 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.
author_facet 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.
author_sort Marchler-Bauer, Aron
collection PubMed
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.
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spelling pubmed-5400232005-01-04 CDD: a Conserved Domain Database for protein classification 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. Nucleic Acids Res Articles 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. Oxford University Press 2005-01-01 2004-12-17 /pmc/articles/PMC540023/ /pubmed/15608175 http://dx.doi.org/10.1093/nar/gki069 Text en Copyright © 2005 Oxford University Press
spellingShingle Articles
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.
CDD: a Conserved Domain Database for protein classification
title CDD: a Conserved Domain Database for protein classification
title_full CDD: a Conserved Domain Database for protein classification
title_fullStr CDD: a Conserved Domain Database for protein classification
title_full_unstemmed CDD: a Conserved Domain Database for protein classification
title_short CDD: a Conserved Domain Database for protein classification
title_sort cdd: a conserved domain database for protein classification
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540023/
https://www.ncbi.nlm.nih.gov/pubmed/15608175
http://dx.doi.org/10.1093/nar/gki069
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