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CDD: NCBI's conserved domain database.

Aron Marchler-Bauer1, Myra K Derbyshire2, Noreen R Gonzales2

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

Nucleic Acids Research
|November 22, 2014
PubMed
Summary

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This summary is machine-generated.

The Conserved Domain Database (CDD) provides protein domain annotations to researchers. Ongoing efforts focus on enhancing annotation coverage and consistency for improved protein analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • The Conserved Domain Database (CDD) is a vital public resource for protein annotation.
  • It identifies conserved domain footprints within protein sequences.
  • CDD has been serving the scientific community for 15 years.

Purpose of the Study:

  • To outline the ongoing efforts to improve the coverage and consistency of protein domain annotations within CDD.
  • To highlight the database's features, including live search and bulk retrieval options.
  • To emphasize the integration of external domain collections and in-house curation.

Main Methods:

  • Maintaining a live search system for real-time access to annotations.
  • Providing an archive of pre-computed domain annotations for sequences in the Entrez protein database.

Related Experiment Videos

  • Implementing import procedures for incorporating public domain collections and in-house curated models.
  • Generating alignment models based on sequence fragments and 3D structural data for precise domain boundary definition.

    • Main Results:

    • CDD offers comprehensive domain annotation for a vast number of proteins.
    • The database integrates diverse domain models from multiple sources.
    • In-house curation enhances the granularity and accuracy of common protein domain classifications.

    Conclusions:

    • CDD continues to be a critical resource for understanding protein function and structure.
    • Future work focuses on expanding annotation coverage and refining classification accuracy.
    • The database is accessible online for public use.