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CDD: NCBI's conserved domain database
2014
Nucleic Acids Research
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NCBI's CDD, the Conserved Domain Database, enters its 15 th year as a public resource for the annotation of proteins with the location of conserved domain footprints. ...
We maintain a live search system as well as an archive of pre-computed domain annotation for sequences tracked in NCBI's Entrez protein database, which can be retrieved for single sequences or in bulk. ...
We are grateful to the authors of Pfam, SMART, COGs, TIGRFAMs and NCBI's Protein Clusters database for providing access to their resources and data, and the users of CDD for their acknowledgements and ...
doi:10.1093/nar/gku1221
pmid:25414356
pmcid:PMC4383992
fatcat:fmwggydorjhetcwv6griivaci4
CDD/SPARCLE: the conserved domain database in 2020
2019
Nucleic Acids Research
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As NLM's Conserved Domain Database (CDD) enters its 20th year of operations as a publicly available resource, CDD curation staff continues to develop hierarchical classifications of widely distributed ...
CDD staff has continued to characterize protein families via conserved domain architectures and has built up a significant corpus of curated domain architectures in support of naming bacterial proteins ...
We are indebted to the authors of Pfam, SMART, COGs, TIGR-FAMs, NCBIfam and NCBI's Protein Clusters database for providing access to their resources and data, and the users of CDD for their acknowledgements ...
doi:10.1093/nar/gkz991
pmid:31777944
pmcid:PMC6943070
fatcat:uk6lpxuw7bfubpmruh4ociv2oa
CDD: conserved domains and protein three-dimensional structure
2012
Nucleic Acids Research
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CDD, the Conserved Domain Database, is part of NCBI's Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/ Structure/cdd/cdd.shtml. ...
CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. ...
We are grateful to the authors of Pfam, SMART, COGs, TIGRFAMs and NCBI's Protein Clusters database for providing such vital resources. ...
doi:10.1093/nar/gks1243
pmid:23197659
pmcid:PMC3531192
fatcat:kyfhbmseffcrjpuj7ie33t7trq
CDD: specific functional annotation with the Conserved Domain Database
2009
Nucleic Acids Research
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NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. ...
CDD provides annotation of domain footprints and conserved functional sites on protein sequences. ...
ACKNOWLEDGEMENTS We thank the authors of Pfam, SMART, COGs and NCBI's Protein Clusters database; and Paul Thiessen and the NCBI Information Engineering Branch for continuing assistance with software development ...
doi:10.1093/nar/gkn845
pmid:18984618
pmcid:PMC2686570
fatcat:2f6k3dlptnbpxidor4mcmk42hi
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures
2016
Nucleic Acids Research
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NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints ...
An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. ...
We are grateful to the authors of Pfam, SMART, COGs, TIGRFAMs and NCBI's Protein Clusters database for providing access to their resources and data, and the users of CDD for their acknowledgements and ...
doi:10.1093/nar/gkw1129
pmid:27899674
pmcid:PMC5210587
fatcat:uwnork4w2bfhrovmauui7o5ejm
CDD: a Conserved Domain Database for protein classification
2004
Nucleic Acids Research
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The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. ...
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. ...
Building the domain family hierarchies and recording conserved features are major goals of NCBI's curation effort. ...
doi:10.1093/nar/gki069
pmid:15608175
pmcid:PMC540023
fatcat:yk7toda26vee7jutivsxy5mete
CDD: a conserved domain database for interactive domain family analysis
2007
Nucleic Acids Research
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The conserved domain database (CDD) is part of NCBI's Entrez database system and serves as a primary resource for the annotation of conserved domain footprints on protein sequences in Entrez. ...
Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. ...
A protein sequence found in NCBI's Entrez database was inspected for the presence of conserved domains. ...
doi:10.1093/nar/gkl951
pmid:17135202
pmcid:PMC1751546
fatcat:de5sprwh4radjiev6azt2i4sry
CDD: a curated Entrez database of conserved domain alignments
2003
Nucleic Acids Research
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The Conserved Domain Database (CDD) is now indexed as a separate database within the Entrez system and linked to other Entrez databases such as MEDLINE 1 . ...
Users may also employ the CD-Search service to identify conserved domains in new sequences, at http://www.ncbi.nlm.nih.gov/ Structure/cdd/wrpsb.cgi. ...
USING CDD TO FIND DOMAINS IN ENTREZ Users of NCBI's services are likely to encounter CDD in two ways. ...
doi:10.1093/nar/gkg087
pmid:12520028
pmcid:PMC165534
fatcat:qexucece6reudeilu2swyzjg3i
CDD: a database of conserved domain alignments with links to domain three-dimensional structure
2002
Nucleic Acids Research
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The Conserved Domain Database (CDD) is a compilation of multiple sequence alignments representing protein domains conserved in molecular evolution. ...
CD-Search is run by default for protein-protein queries submitted to NCBI's BLAST service at http://www.ncbi.nlm.nih.gov/BLAST. ...
Alignments from Pfam and SMART have been imported into the Conserved Domain Database (CDD), to serve a variety of purposes. ...
doi:10.1093/nar/30.1.281
pmid:11752315
pmcid:PMC99109
fatcat:bbra2ceqbrhannorscvbnga4ra
CDD: a Conserved Domain Database for the functional annotation of proteins
2010
Nucleic Acids Research
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NCBI's Conserved Domain Database (CDD) is a resource for the annotation of protein sequences with the location of conserved domain footprints, and functional sites inferred from these footprints. ...
CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/ structure/function relationships. ...
ACKNOWLEDGEMENTS The authors thank the authors of Pfam, SMART, COG, TIGRFAM and NCBI's Protein Clusters database, and ...
doi:10.1093/nar/gkq1189
pmid:21109532
pmcid:PMC3013737
fatcat:qmwp2djqczc2xo72zqm6u7grzy
Improving the consistency of domain annotation within the Conserved Domain Database
2015
Database: The Journal of Biological Databases and Curation
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Improving the consistency of domain annotation within the conserved domain database (CDD). ...
, including tandem repeats of domain hits reported at a more conservative threshold. ...
Acknowledgements We thank the Conserved Domain Curators past and present for compiling the domain annotations analyzed in this work, Farideh ...
doi:10.1093/database/bav012
pmid:25767294
pmcid:PMC4356950
fatcat:uyjohnfrnjfrzjyj55me6gs5pa
Annotation of functional sites with the Conserved Domain Database
2012
Database: The Journal of Biological Databases and Curation
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Acknowledgements We thank the Conserved Domain Curators for compiling the site annotations analyzed in this work, Farideh Chitsaz, Noreen Gonzales, Marc Gwadz, Fu Lu, Gabriele Marchler, James Song, Narmada ...
Thanki, Roxanne Yamashita, Chanjuan Zheng, as well as the CDD alumni Anastasia Conflict of interest. ...
Introduction The Conserved Domain Database (CDD) (1) is a manually curated protein annotation resource developed and maintained by the National Center for Biotechnology Information (NCBI). ...
doi:10.1093/database/bar058
pmid:22434827
pmcid:PMC3308149
fatcat:xwt5xq6kwrgedmsbf7ujgsp32e
CD-Search: protein domain annotations on the fly
2004
Nucleic Acids Research
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We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. ...
CD-Search can be accessed at http:// www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. ...
We thank the architects of the Pfam, SMART and COGs collections and the curators of the CDD for their invaluable contributions. We also thank the NIH Intramural Research Program for support. ...
doi:10.1093/nar/gkh454
pmid:15215404
pmcid:PMC441592
fatcat:kqqxv7qtwbfx7cwdz2ktmbkvhe
webPRC: the Profile Comparer for alignment-based searching of public domain databases
2009
Nucleic Acids Research
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We have developed webPRC server, which makes it straightforward to search for distant homologues or similar alignments in a number of domain databases. ...
For this purpose, PRC is used by, for example, the CATH and Pfamdomain databases. ...
CDD/KOG: NCBI's Conserved Domain Database [CDD (19) ] and KOG (20) HMMs have been built from the seed alignments downloaded via the CDD site (http:// www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml). ...
doi:10.1093/nar/gkp279
pmid:19420063
pmcid:PMC2703954
fatcat:6onhwiiourci7iqgc4f52no24m
A structure-based method for protein sequence alignment
2004
Bioinformatics
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of domain alignments from NCBI's Conserved Domain Database. ...
PSSMs can capture information about conserved patterns within families, which can be used to increase the sensitivity of searches for related sequences. ...
Domain Database (CDD) (Marchler-Bauer et al., 2003) . ...
doi:10.1093/bioinformatics/bti233
pmid:15613392
fatcat:brrkpsrrb5barjenm5tzj6dxdy
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