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Related Experiment Videos

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.

Daniel W A Buchan1, Adrian J Shepherd, David Lee

  • 1Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom.

Genome Research
|March 5, 2002
PubMed
Summary

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Gene3D is a new web resource providing structural domain assignments for genes and genomes. It enhances understanding of gene function and structure across diverse organisms.

Area of Science:

  • Genomics
  • Structural Biology
  • Bioinformatics

Background:

  • Structural domain assignment is crucial for understanding gene function.
  • Existing methods for genome-wide structural annotation are limited.
  • Integrating structural and functional data aids biological interpretation.

Purpose of the Study:

  • To introduce Gene3D, a novel web-based resource for precalculated structural assignments to gene sequences and genomes.
  • To link structural domains from the CATH database to functional annotations in DHS and PDBsum.
  • To provide structural annotations for a significant number of complete genomes.

Main Methods:

  • Utilizing the CATH domain database for structural assignments.
  • Employing PSI-BLAST (profile-based method) for matching structural domains to gene sequences.

Related Experiment Videos

  • Implementing the DRange protocol to resolve conflicting homologous superfamily matches.

    • Main Results:

    • Gene3D offers precalculated structural annotations for 36 complete genomes (2 eukaryotes, 6 archaea, 28 bacteria).
    • Approximately 30-40% of genes within a genome can be structurally annotated using Gene3D.
    • The resource links structural domains to curated functional and structural annotations.

    Conclusions:

    • Gene3D provides a valuable, scalable resource for exploring structural genomics.
    • The integration of structural and functional data facilitates deeper biological insights.
    • This resource supports comparative genomics and functional studies across various species.