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CDD/SPARCLE: the conserved domain database in 2020.

Shennan Lu1, Jiyao Wang1, Farideh Chitsaz1

  • 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.

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The Conserved Domain Database (CDD) provides hierarchical classifications and conserved site information for protein domains, aiding hypothesis-driven research. It offers archived annotations and live search services for diverse biological queries.

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Structural Biology

Background:

  • The Conserved Domain Database (CDD) is a publicly available resource developed by the National Library of Medicine (NLM).
  • CDD has been operational for 20 years, providing valuable data for biomolecular research.
  • Ongoing curation efforts are essential for maintaining and expanding the database.

Purpose of the Study:

  • To highlight the continued development and services of the Conserved Domain Database (CDD).
  • To emphasize CDD's role in classifying protein domain families and identifying conserved sites.
  • To showcase CDD's utility in supporting hypothesis-driven biomolecular research.

Main Methods:

  • Hierarchical classification of protein domain families.
  • Recording of conserved sites linked to molecular function.
  • Development of curated domain architectures for protein family characterization.
  • Provision of live search services for single and multiple sequence queries.
  • Availability of domain architecture definitions via SPARCLE (Subfamily Protein Architecture Labeling Engine).

Main Results:

  • CDD provides a comprehensive archive of pre-computed domain annotations.
  • Live search services facilitate queries for single proteins, nucleotides, and larger sequence sets.
  • Significant corpus of curated domain architectures has been established.
  • These architectures support the naming of bacterial proteins in RefSeq.
  • SPARCLE engine makes architecture definitions accessible.

Conclusions:

  • The Conserved Domain Database (CDD) remains a vital and evolving resource for the scientific community.
  • CDD's curated classifications and search capabilities empower biomolecular research.
  • Continued development ensures CDD's relevance in characterizing protein families and supporting data annotation.