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CDD: NCBI's conserved domain database

Aron Marchler-Bauer, Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Farideh Chitsaz, Lewis Y. Geer, Renata C. Geer, Jane He, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu (+8 others)
2014 Nucleic Acids Research  
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  
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

Aron Marchler-Bauer, Chanjuan Zheng, Farideh Chitsaz, Myra K. Derbyshire, Lewis Y. Geer, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz, Christopher J. Lanczycki, Fu Lu, Shennan Lu (+6 others)
2012 Nucleic Acids Research  
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

A. Marchler-Bauer, J. B. Anderson, F. Chitsaz, M. K. Derbyshire, C. DeWeese-Scott, J. H. Fong, L. Y. Geer, R. C. Geer, N. R. Gonzales, M. Gwadz, S. He, D. I. Hurwitz (+16 others)
2009 Nucleic Acids Research  
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

Aron Marchler-Bauer, Yu Bo, Lianyi Han, Jane He, Christopher J. Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K. Derbyshire, Renata C. Geer, Noreen R. Gonzales, Marc Gwadz, David I. Hurwitz (+10 others)
2016 Nucleic Acids Research  
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

A. Marchler-Bauer
2004 Nucleic Acids Research  
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

A. Marchler-Bauer, J. B. Anderson, M. K. Derbyshire, C. DeWeese-Scott, N. R. Gonzales, M. Gwadz, L. Hao, S. He, D. I. Hurwitz, J. D. Jackson, Z. Ke, D. Krylov (+13 others)
2007 Nucleic Acids Research  
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

A. Marchler-Bauer
2003 Nucleic Acids Research  
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

A. Marchler-Bauer
2002 Nucleic Acids Research  
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

A. Marchler-Bauer, S. Lu, J. B. Anderson, F. Chitsaz, M. K. Derbyshire, C. DeWeese-Scott, J. H. Fong, L. Y. Geer, R. C. Geer, N. R. Gonzales, M. Gwadz, D. I. Hurwitz (+15 others)
2010 Nucleic Acids Research  
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

Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Jane He, Gabriele H. Marchler, Zhouxi Wang, Aron Marchler-Bauer
2015 Database: The Journal of Biological Databases and Curation  
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

M. K. Derbyshire, C. J. Lanczycki, S. H. Bryant, A. Marchler-Bauer
2012 Database: The Journal of Biological Databases and Curation  
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

A. Marchler-Bauer, S. H. Bryant
2004 Nucleic Acids Research  
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

B. W. Brandt, J. Heringa
2009 Nucleic Acids Research  
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

M. G. Kann, P. A. Thiessen, A. R. Panchenko, A. A. Schaffer, S. F. Altschul, S. H. Bryant
2004 Bioinformatics  
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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