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Related Experiment Videos

MMDB: Entrez's 3D-structure database.

Yanli Wang1, John B Anderson, Jie Chen

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Nucleic Acids Research
|December 26, 2001
PubMed
Summary
This summary is machine-generated.

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Entrez's 3D-structure database enhances access to protein structural information. New features link biopolymer chains to organism taxonomy and similar 3D structures for molecular biologists.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Molecular Biology

Background:

  • Increasing availability of three-dimensional (3D) protein structures.
  • Need for accessible functional annotation derived from known structures.
  • Prevalence of protein homologs with known structures in sequence databases.

Purpose of the Study:

  • To enhance accessibility of 3D structure information and functional annotation for molecular biologists.
  • To introduce novel features within Entrez's Molecular Modeling Database (MMDB).

Main Methods:

  • Utilizing Entrez's search engine with features like sequence and structure neighbors.
  • Implementing links between databases (e.g., MEDLINE to 3D structures).
  • Providing sequence and structure visualization tools for inferring 3D structure.

Related Experiment Videos

Main Results:

  • Focus on two previously undescribed MMDB features: taxonomic links for biopolymer chains and structure neighbor links for chains/domains.
  • Enabling navigation from individual biopolymer chains to organism taxonomy.
  • Facilitating identification of structurally similar chains and domains.

Conclusions:

  • Entrez's MMDB provides powerful tools for exploring protein structural data.
  • New features enhance the ability to connect protein structures with biological context and similarity.
  • Improved access to structural information aids molecular biology research.