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CDD: a Conserved Domain Database for protein classification.

Aron Marchler-Bauer1, John B Anderson, Praveen F Cherukuri

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38 A, Room 8N805, 8600 Rockville Pike, Bethesda, MD 20894, USA. bauer@ncbi.nlm.nih.gov

Nucleic Acids Research
|December 21, 2004
PubMed
Summary

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This summary is machine-generated.

The National Center for Biotechnology Information

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • The Conserved Domain Database (CDD) is a key component of NCBI's Entrez system for protein classification.
  • CDD integrates with other Entrez databases like Proteins, Taxonomy, and PubMed.
  • It provides access to conserved domain information for protein sequences.

Purpose of the Study:

  • To report on the progress of NCBI's curation efforts for the Conserved Domain Database (CDD).
  • To highlight improvements in the functionality of the CDD information retrieval system.
  • To detail the ongoing effort to update and curate domain models within CDD.

Main Methods:

  • Utilizing the CD-Search tool for rapid identification of conserved domains in protein sequences.

Related Experiment Videos

  • Leveraging pre-computed CD-Search results within Entrez for enhanced protein-domain links and annotations.
  • Integrating conserved domain scanning into default protein-protein queries via NCBI's BLAST service.

    • Main Results:

    • CDD has evolved from mirroring external domain collections to incorporating NCBI-curated domain hierarchies.
    • Improvements in curation have led to enhanced functionality within the CDD information retrieval system.
    • CD-Search provides interactive identification of conserved domains and links them to protein sequences.

    Conclusions:

    • NCBI's ongoing curation efforts are enhancing the accuracy and utility of the Conserved Domain Database.
    • The CDD and its associated tools like CD-Search offer valuable resources for protein sequence analysis and annotation.
    • Continued development of CDD improves the integration and accessibility of conserved domain information within the broader Entrez system.