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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.  ...  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.  ...  ACKNOWLEDGEMENTS We thank the authors of Pfam, SMART and COG, for creating invaluable resources and for helping with access to data. We also thank the NIH Intramural Research Program for support.  ... 
doi:10.1093/nar/gki069 pmid:15608175 pmcid:PMC540023 fatcat:yk7toda26vee7jutivsxy5mete

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: 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 incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and wellcharacterized  ...  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/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: 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 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.  ...  More importantly, CDD and CDTree used in concert, serve as a powerful tool in protein classification, as they allow users to analyze protein sequences in the context of domain family hierarchies.  ...  Funding to pay the Open Access publication charges for this article was provided by Intramural Research Program of the National Library of Medicine at National Institutes of Health/DHHS.  ... 
doi:10.1093/nar/gkl951 pmid:17135202 pmcid:PMC1751546 fatcat:de5sprwh4radjiev6azt2i4sry

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.  ...  Protein query sequences may be compared against databases of position-specific score matrices derived from alignments in CDD, using a service named CD-Search, which can be found at http://www.ncbi.nlm.nih.gov  ...  Aravind for providing sequence alignment data, Tom Madden and Sergei Shavirin for making RPS-BLAST available, Richard Copley for providing access to SMART data, and Naomi Ariel for help with the initial  ... 
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.  ...  Pre-computed domain annotation is available for proteins in the Entrez/Protein dataset, and a novel interface, Batch CD-Search, allows the computation and download of annotation for large sets of protein  ...  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

Predicting Gene Ontology Functions from ProDom and CDD Protein Domains

J. Schug
2002 Genome Research  
The Conserved Domain Database (CDD) is comprised of a mirror of two major domain databases, the Simple Modular Architecture Research Tool (SMART) (Schultz et al. 2000) and Pfam (Bateman et al. 2000)  ...  A heuristic algorithm for associating Gene Ontology (GO) defined molecular functions to protein domains as listed in the ProDom and CDD databases is described.  ... 
doi:10.1101/gr.222902 pmid:11932249 pmcid:PMC187511 fatcat:6mh26zvp7zft5cq66uvuty3tdu

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

Coverage of protein domain families with structural protein–protein interactions: Current progress and future trends

Alexander Goncearenco, Benjamin A. Shoemaker, Dachuan Zhang, Alexey Sarychev, Anna R. Panchenko
2014 Progress in Biophysics and Molecular Biology  
potential targets for structural studies with a focus on protein interactions.  ...  We analyze the coverage of protein domain families (defined according to CDD and Pfam databases) by structures, structural proteinprotein complexes and unique protein binding sites.  ...  Acknowledgments We thank Thomas Madej and Christopher Lanczycki for help with the MMDB database.  ... 
doi:10.1016/j.pbiomolbio.2014.05.005 pmid:24931138 pmcid:PMC4250425 fatcat:g2d6sd6jtbbltblrelyrzcijem

cddApp: a Cytoscape app for accessing the NCBI conserved domain database

John H. Morris, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer, Thomas E. Ferrin
2014 Computer applications in the biosciences : CABIOS  
conserved domain database (CDD).  ...  Motivation: cddApp is a Cytoscape extension that supports the annotation of protein networks with information about domains and specific functional sites from the National Center for Biotechnology Information's  ...  The National Center for Bioinformatics Information's (NCBI) conserved domain database (CDD) (Marchler-Bauer et al., 2011) is a repository of manually curated and computationally derived protein domain  ... 
doi:10.1093/bioinformatics/btu605 pmid:25212755 pmcid:PMC4271147 fatcat:2wwumnmptjeqxp4brys6mb2kxi

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).  ...  Abstract When annotating protein sequences with the footprints of evolutionarily conserved domains, conservative score or E-value thresholds need to be applied for RPS-BLAST hits, to avoid many false positives  ...  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

A Study of Functional Genomics for Unknown Proteins in Chlamydomonas reinhardtii

Manisha D.Giripunje, Abhay B. Fulke, Pravin U. Meshram
2013 International Journal of Computer Applications  
The web tools like CDD-BLAST, INTERPROSCAN and PFAM were used for the prediction of functions in the proteins by searching protein databases for the presence of conserved domains.  ...  Chlamydomonas reinhardtii is a unicellular green alga, which has been used as a reference organism for identifying proteins.  ...  First, Conserved Domain Database CDD-BLAST tool search was executed for Chlamydomonas reinhardtii (http://www.ncbi.nlm.nih.gov/BLAST/) that presented as an annotation of protein domains [12, 13 and 14  ... 
doi:10.5120/14045-1710 fatcat:2fzxtrl3nvcxnldiihv7pc32le
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