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Database Commons - CDD

CDD

Citations: 4407

z-index 171.38

Short name CDD
Full name Conserved Domain Database
Description CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.
URL http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Year founded 2008
Last update & version 2016-06-27    v3.15
Availability Free to all users
University/Institution hosted National Center for Biotechnology Information
Address Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA
City Bethesda
Province/State MD
Country/Region United States
Contact name Aron Marchler-Bauer
Contact email bauer@ncbi.nlm.nih.gov
Data type(s)
Major organism(s)
Keyword(s)
  • conserved domain
Publication(s)
  • CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. [PMID: 27899674]

    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, Fu Lu, Gabriele H Marchler, James S Song, Narmada Thanki, Zhouxi Wang, Roxanne A Yamashita, Dachuan Zhang, Chanjuan Zheng, Lewis Y Geer, Stephen H Bryant
    Nucleic acids research 2017:45(D1)
    0 Citations (Google Scholar as of 2017-02-13)

    Abstract: 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. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  • CDD: NCBI's conserved domain database. [PMID: 25414356]

    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, Gabriele H Marchler, James S Song, Narmada Thanki, Zhouxi Wang, Roxanne A Yamashita, Dachuan Zhang, Chanjuan Zheng, Stephen H Bryant
    Nucleic acids research 2015:43(Database issue)
    713 Citations (Google Scholar as of 2017-02-13)

    Abstract: 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 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 also maintain import procedures so that CDD contains domain models and domain definitions provided by several collections available in the public domain, as well as those produced by an in-house curation effort. The curation effort aims at increasing coverage and providing finer-grained classifications of common protein domains, for which a wealth of functional and structural data has become available. CDD curation generates alignment models of representative sequence fragments, which are in agreement with domain boundaries as observed in protein 3D structure, and which model the structurally conserved cores of domain families as well as annotate conserved features. CDD can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by US Government employees and is in the public domain in the US.

  • CDD: conserved domains and protein three-dimensional structure. [PMID: 23197659]

    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, Gabriele H Marchler, James S Song, Narmada Thanki, Roxanne A Yamashita, Dachuan Zhang, Stephen H Bryant
    Nucleic acids research 2013:41(Database issue)
    620 Citations (Google Scholar as of 2017-02-13)

    Abstract: 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. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches. 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 well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.

  • CDD: a Conserved Domain Database for the functional annotation of proteins. [PMID: 21109532]

    Aron Marchler-Bauer, Shennan Lu, John B Anderson, Farideh Chitsaz, Myra K Derbyshire, Carol DeWeese-Scott, Jessica H Fong, Lewis Y Geer, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, John D Jackson, Zhaoxi Ke, Christopher J Lanczycki, Fu Lu, Gabriele H Marchler, Mikhail Mullokandov, Marina V Omelchenko, Cynthia L Robertson, James S Song, Narmada Thanki, Roxanne A Yamashita, Dachuan Zhang, Naigong Zhang, Chanjuan Zheng, Stephen H Bryant
    Nucleic acids research 2011:39(Database issue)
    2021 Citations (Google Scholar as of 2017-02-13)

    Abstract: 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. CDD includes manually curated domain models that make use of protein 3D structure to refine domain models and provide insights into sequence/structure/function relationships. Manually curated models are organized hierarchically if they describe domain families that are clearly related by common descent. As CDD also imports domain family models from a variety of external sources, it is a partially redundant collection. To simplify protein annotation, redundant models and models describing homologous families are clustered into superfamilies. 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. 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 queries. CDD can be accessed via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

  • CDD: specific functional annotation with the Conserved Domain Database. [PMID: 18984618]

    Aron Marchler-Bauer, John B Anderson, Farideh Chitsaz, Myra K Derbyshire, Carol DeWeese-Scott, Jessica H Fong, Lewis Y Geer, Renata C Geer, Noreen R Gonzales, Marc Gwadz, Siqian He, David I Hurwitz, John D Jackson, Zhaoxi Ke, Christopher J Lanczycki, Cynthia A Liebert, Chunlei Liu, Fu Lu, Shennan Lu, Gabriele H Marchler, Mikhail Mullokandov, James S Song, Asba Tasneem, Narmada Thanki, Roxanne A Yamashita, Dachuan Zhang, Naigong Zhang, Stephen H Bryant
    Nucleic acids research 2009:37(Database issue)
    1053 Citations (Google Scholar as of 2017-02-13)

    Abstract: 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. The collection can be accessed at http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml, and is also part of NCBI's Entrez query and retrieval system, cross-linked to numerous other resources. CDD provides annotation of domain footprints and conserved functional sites on protein sequences. Precalculated domain annotation can be retrieved for protein sequences tracked in NCBI's Entrez system, and CDD's collection of models can be queried with novel protein sequences via the CD-Search service at http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi. 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' (identifying molecular function with high confidence) or as 'non-specific' (identifying superfamily membership only).

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Tags

Protein Structure
conserved domain

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lina Ma [2017-06-21]
    • Shixiang Sun [2017-02-13]
    • Mengwei Li [2016-04-12]
    • Mengwei Li [2016-03-31]
    • Mengwei Li [2015-12-01]
    • Mengwei Li [2015-06-29]
    • Mengwei Li [2015-06-27]
Stats