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MMDB: 3D structure data in Entrez.

Y Wang1, K J Addess, L Geer

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

Nucleic Acids Research
|December 11, 1999
PubMed
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Entrez's 3D structure database provides access to protein structures, aiding in inferring function. It links sequence data to known structures and offers visualization tools for molecular biologists.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Approximately 50% of protein families now have known three-dimensional (3D) structures.
  • Identifying homologous proteins with known structures is crucial for inferring structure-function relationships.

Purpose of the Study:

  • To enhance accessibility and utility of 3D protein structure information for molecular biologists.
  • To integrate sequence and structure data for improved biological insights.

Main Methods:

  • Utilizing Entrez's search engine with features for database linking (e.g., Medline to 3D structures).
  • Employing sequence and structure neighbor identification to link similar sequences to known 3D structures.
  • Implementing combined molecular-graphic and alignment displays for 3D structure visualization and inference.

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Main Results:

  • Entrez's 3D structure database facilitates the connection between sequence data and known protein structures.
  • The system enables users to find and visualize 3D structures related to their sequences of interest.
  • Database links and visualization tools support the inference of structure-function properties.

Conclusions:

  • Entrez's Molecular Modeling DataBase (MMDB) effectively serves as a resource for molecular biologists.
  • The integrated approach of linking sequence, structure, and literature enhances biological research.
  • Improved access to 3D structural information aids in understanding protein function.