A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
CDD: a Conserved Domain Database for protein classification
2004
Nucleic Acids Research
Preserved Fulltext
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
2014
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2012
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2009
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2007
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2002
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2010
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2002
Genome Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2014
Progress in Biophysics and Molecular Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2015
Database: The Journal of Biological Databases and Curation
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2013
International Journal of Computer Applications
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 3,076 results