Filters








4,941 Hits in 6.8 sec

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  
CDD provides annotation of domain footprints and conserved functional sites on protein sequences.  ...  Starting with the latest version of CDD, v2.14, information from redundant and homologous domain models is summarized at a superfamily level, and domain annotation on proteins is flagged as either 'specific  ...  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: 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.  ...  Going forward, we strive to improve the coverage and consistency of domain annotation provided by CDD.  ...  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  
protein domain families, and to record conserved sites associated with molecular function, so that they can be mapped onto user queries in support of hypothesis-driven biomolecular 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  ...  ACKNOWLEDGEMENTS We thank the NCBI Information Engineering Branch and the NCBI RefSeq team for continuing support and assistance with software and database development.  ... 
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 provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints.  ...  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.  ...  ACKNOWLEDGEMENTS We thank Paul Thiessen, Lianyi Han and the NCBI Information Engineering Branch for assistance with software development.  ... 
doi:10.1093/nar/gks1243 pmid:23197659 pmcid:PMC3531192 fatcat:kyfhbmseffcrjpuj7ie33t7trq

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.  ...  with domain hierarchies curated at the NCBI.  ...  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: 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 .  ...  This alignment model allows NCBI curators to annotate 'columns' corresponding to functional sites conserved among family members.  ...  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 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.  ...  Domain annotation for proteins in Entrez has been pre-computed and is readily available in the form of 'Conserved Domain' links.  ...  group, the NCBI IEB and the NCBI C++ toolkit developers.  ... 
doi:10.1093/nar/gkl951 pmid:17135202 pmcid:PMC1751546 fatcat:de5sprwh4radjiev6azt2i4sry

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 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.  ...  By default, domain footprints are annotated with the corresponding superfamily designation, on top of which specific annotation may indicate high-confidence assignment of family membership.  ...  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

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.  ...  It has been populated with alignment data from the public collections Pfam and SMART, as well as with contributions from colleagues at NCBI.  ...  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

Predicting Gene Ontology Functions from ProDom and CDD Protein Domains

J. Schug
2002 Genome Research  
This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.  ...  The publication costs of this article were defrayed in part by payment of page charges.  ...  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)  ... 
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.  ...  33% of the SwissProt sequences with specific CDD domain annotation, CDD provides the only site annotation.  ... 
doi:10.1093/database/bar058 pmid:22434827 pmcid:PMC3308149 fatcat:xwt5xq6kwrgedmsbf7ujgsp32e

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 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

Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes

V. Sridhara, A. Marchler-Bauer, S. H. Bryant, L. Y. Geer
2011 Database: The Journal of Biological Databases and Curation  
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.  ...  One advantage of using NCBI curated domain models is that they often classify protein domains into functionally specific sub-families which may not be the case with other domain databases that focus on  ... 
doi:10.1093/database/bar019 pmid:21571812 pmcid:PMC3096321 fatcat:f55fpbp2jra3tfiqpcypi5xcke

InterPro in 2017—beyond protein family and domain annotations

Robert D. Finn, Teresa K. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, Alan J. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft (+35 others)
2016 Nucleic Acids Research  
Here, we report recent developments with InterPro and its associated software, in-cluding the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and  ...  These developments enrich the annotations provided by In-terPro, increase the overall number of residues annotated and allow more specific functional inferences.  ...  As a result, two new databases have been added to the resource: the Conserved Domains Database (CDD) and Structure-Function Linkage Database (SFLD).  ... 
doi:10.1093/nar/gkw1107 pmid:27899635 pmcid:PMC5210578 fatcat:wa7z5pgpuffnrh5bf5ycimw7kq
« Previous Showing results 1 — 15 out of 4,941 results