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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. ...
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: 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. ...
cores of domain families as well as annotate conserved features. ...
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: a Conserved Domain Database for protein classification
2004
Nucleic Acids Research
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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. ...
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. ...
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: 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: 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 . ...
This allows users to search for domain types by name, for example, or to view the domain architecture of any protein in Entrez's sequence database. ...
ACKNOWLEDGEMENTS We thank the NIH Intramural Research Program for support. We thank the authors of Pfam, SMART and LOAD, for creating invaluable resources and for helping with access to data. ...
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. ...
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 ...
analysis of imported alignments. ...
doi:10.1093/nar/30.1.281
pmid:11752315
pmcid:PMC99109
fatcat:bbra2ceqbrhannorscvbnga4ra
Predicting Gene Ontology Functions from ProDom and CDD Protein Domains
2002
Genome Research
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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
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. ...
linked to the generic function of the domain family, and (2) a conservative procedure is used to qualify a match for mapping sites. ...
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
2014
Progress in Biophysics and Molecular Biology
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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
2014
Computer applications in the biosciences : CABIOS
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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 conserved domains (CDs) in the CDD database are organized into families of CDs related by common evolutionary ancestry. ...
doi:10.1093/bioinformatics/btu605
pmid:25212755
pmcid:PMC4271147
fatcat:2wwumnmptjeqxp4brys6mb2kxi
Genome wide in silico analysis of Plasmodium falciparum phosphatome
2014
BMC Genomics
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The phylogenetic trees for each of the known phosphatase super families reveal a considerable phylogenetic closeness amongst apicomplexan organisms and a considerable phylogenetic distance with other eukaryotic ...
These Plasmodium phosphatase proteins were classified into 13 super families based on NCBI CDD search. ...
Acknowledgements The authors thank Department of Biotechnology (DBT, India) grants for ...
doi:10.1186/1471-2164-15-1024
pmid:25425018
pmcid:PMC4256932
fatcat:uqt65xtftvetja5d6g2at4mtfm
A Study of Functional Genomics for Unknown Proteins in Chlamydomonas reinhardtii
2013
International Journal of Computer Applications
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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
Identification of hidden relationships from the coupling of Hydrophobic Cluster Analysis and Domain Architecture information
2013
Computer applications in the biosciences : CABIOS
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It can also be used in a reverse way for refining domain profiles, by starting from known protein domain families and identifying highly divergent members, hitherto considered as orphan. ...
Results: We present here an original novel approach, called TREMOLO-HCA, for the analysis of orphan domain sequences and inspired from our experience in the use of Hydrophobic Cluster Analysis (HCA). ...
Jean-Paul Mornon for insightful developments associated with Hydrophobic Cluster Analysis, his enthusiastic suggestions and comments. We also thank Dr. ...
doi:10.1093/bioinformatics/btt271
pmid:23677940
fatcat:3kvuaj6tmnernhwrqtvutg7vri
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes
2011
Database: The Journal of Biological Databases and Curation
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Acknowledgements We thank Naigong Zhang for providing the data mapping conserved domains onto proteins. ...
We also thank the Information Engineering Branch of NCBI for much of the software used in the paper. Conflict of interest. None declared. ...
For our analysis, we used domain models in a manually curated subset of NCBI's Conserved Domain Database (CDD). ...
doi:10.1093/database/bar019
pmid:21571812
pmcid:PMC3096321
fatcat:f55fpbp2jra3tfiqpcypi5xcke
The Genome Sequence of Leishmania (Leishmania) amazonensis: Functional Annotation and Extended Analysis of Gene Models
2013
DNA Research
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Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. ...
The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment. ...
(OrthoMCL); and (iii) screening for information about conserved protein domains deposited in CDD and PFAM databases. ...
doi:10.1093/dnares/dst031
pmid:23857904
pmcid:PMC3859324
fatcat:gwx5enpj2rdmrilwachfwmg3xi
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