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Related Experiment Videos

MMDB: annotating protein sequences with Entrez's 3D-structure database.

Yanli Wang1, Kenneth J Addess, Jie Chen

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

Nucleic Acids Research
|December 1, 2006
PubMed
Summary
This summary is machine-generated.

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Discovering protein function is easier with the Molecular Modeling Database (MMDB). This tool links protein sequences to known 3D structures, aiding in the identification of functional sites.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • A significant portion of protein families now have known three-dimensional (3D) structures.
  • Identifying homologous proteins with known 3D structures aids in inferring biological function and functional sites.
  • The Molecular Modeling Database (MMDB) within Entrez offers access to 3D structure data for functional annotation.

Purpose of the Study:

  • To describe a novel annotation service, Entrez's 'Related Structure' links.
  • To automate the process of linking protein sequences to homologous structures with known 3D conformations.
  • To enhance functional annotation of proteins by leveraging existing structural data.

Main Methods:

  • Utilizing the BLAST algorithm to detect similar sequences with known 3D structures for all proteins in Entrez.

Related Experiment Videos

  • Recording sequence alignments between query sequences and their structural homologs.
  • Integrating sequence similarity searches with structural database information.

    • Main Results:

    • The 'Related Structure' service automatically identifies and summarizes proteins with known 3D structures that are similar to a query sequence.
    • The service provides 3D visualizations that map sequence residues onto corresponding structures in the MMDB.
    • This facilitates the prediction of functional sites, such as binding motifs and catalytic centers.

    Conclusions:

    • The 'Related Structure' service streamlines the process of functional annotation for proteins.
    • It effectively bridges the gap between sequence information and 3D structural data.
    • This tool enhances the utility of large-scale structural databases for biological research.