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Gene3D: modelling protein structure, function and evolution.

Corin Yeats1, Michael Maibaum, Russell Marsden

  • 1Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK. yeats@biochem.ucl.ac.uk

Nucleic Acids Research
|December 31, 2005
PubMed
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The Gene3D database offers integrated structural, functional, and evolutionary protein data for over 240 species. This release enhances protein annotation and prediction capabilities with new data sources and improved web portal functionality.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Gene3D database integrates structural, functional, and evolutionary information for proteins.
  • It focuses on annotating protein sequences lacking existing structural representatives, including complete proteomes from numerous species.
  • Protein sequences are clustered into whole-chain families to facilitate functional prediction.

Purpose of the Study:

  • To present Gene3D release 4, a comprehensive database and web portal for protein analysis.
  • To provide enhanced structural annotation for a wide range of protein sequences.
  • To improve functional prediction and evolutionary insights through integrated data.

Main Methods:

  • Utilizing Hidden Markov Model (HMM) models based on the CATH (atorvastatin) domain families for structural annotation.

Related Experiment Videos

  • Clustering protein sequences into whole-chain families.
  • Integrating data from UniProt, Pfam, COGs, KEGG, GO, MINT, and BIND.

    • Main Results:

    • Inclusion of over 100 new genomes and the UniProt sequence database.
    • Incorporation of domain data from Pfam, metabolic pathway and functional data from COGs, KEGG, and GO.
    • Addition of protein-protein interaction data from MINT and BIND.
    • Rebuilt website with enhanced querying capabilities and clearer data presentation.
    • Availability of all data for download in XML format for user-driven analysis.

    Conclusions:

    • Gene3D release 4 provides a significantly expanded and more functional resource for exploring the protein world.
    • The integrated data and improved web portal facilitate sophisticated analysis of protein structure, function, and evolution.
    • The database supports researchers in complex investigations by enabling data download and local analysis.