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MMDB: Entrez's 3D structure database

A Marchler-Bauer1, K J Addess, C Chappey

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

Nucleic Acids Research
|December 10, 1998
PubMed
Summary
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Discovering protein structure-function relationships is easier with public databases. Entrez

Area of Science:

  • * Structural Biology
  • * Bioinformatics
  • * Molecular Biology

Background:

  • * Public databases now contain 3D structures for nearly half of all protein families.
  • * Knowledge of homologous protein structures can reveal unexpected structure-function relationships.
  • * Accessibility of this data is crucial for molecular biologists.

Purpose of the Study:

  • * To present Entrez's 3D-structure database as a tool for molecular biologists.
  • * To demonstrate how sequence and structure analysis can infer protein function.
  • * To illustrate the utility of these tools using the PTEN gene product as an example.

Main Methods:

  • * Utilizing Entrez's 3D-structure database.
  • * Employing a search engine based on sequence and structure 'neighboring'.

Related Experiment Videos

  • * Using an integrated visualization system for sequence and structure alignments.

    • Main Results:

    • * Identified homologous proteins with known 3D structures.
    • * Enabled detailed comparison of aligned sequences and structures.
    • * Facilitated the identification of conserved features for functional inference.

    Conclusions:

    • * Entrez's tools enhance the investigation of newly discovered protein structures and functions.
    • * Comparative analysis of sequence and structure aids in understanding protein families.
    • * The PTEN gene product serves as a practical example of these analytical capabilities.