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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: 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.  ...  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

A. Marchler-Bauer
2004 Nucleic Acids Research  
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

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: 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 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

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  ...  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

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.  ...  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

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 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

Rajan Pandey, Asif Mohmmed, Christine Pierrot, Jamal Khalife, Pawan Malhotra, Dinesh Gupta
2014 BMC Genomics  
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

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

Identification of hidden relationships from the coupling of Hydrophobic Cluster Analysis and Domain Architecture information

Guilhem Faure, Isabelle Callebaut
2013 Computer applications in the biosciences : CABIOS  
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

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.  ...  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

F. Real, R. O. Vidal, M. F. Carazzolle, J. M. C. Mondego, G. G. L. Costa, R. H. Herai, M. Wurtele, L. M. de Carvalho, R. C. e Ferreira, R. A. Mortara, C. L. Barbieri, P. Mieczkowski (+4 others)
2013 DNA Research  
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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