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A rapid classification protocol for the CATH Domain Database to support structural genomics.

F M Pearl1, N Martin, J E Bray

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

Nucleic Acids Research
|January 11, 2000
PubMed
Summary
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New protocols enhance the speed and accuracy of classifying protein structures in the CATH database. These advancements support structural genomics by improving target identification and data integrity for large-scale genome analysis.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Genomics

Background:

  • The CATH domain database classifies protein structures to support structural genomics.
  • Rapid classification and identification of suitable targets are crucial for ongoing initiatives.
  • Existing methods required enhancement for speed and sensitivity in recognizing distant structural relatives.

Purpose of the Study:

  • To develop new protocols for faster and more sensitive classification of protein structures within the CATH database.
  • To improve the integrity and query efficiency of the CATH Protein Family Database (CATH-PFDB) for genome analysis.
  • To expand the Dictionary of Homologous Superfamilies for better assignment of new structural relatives.

Main Methods:

  • Development of fast algorithms for structure comparison (GRATH).

Related Experiment Videos

  • Incorporation of genomic sequence information for improved recognition of distant relatives (DomainFinder).
  • Installation of the CATH Protein Family Database in a relational ORACLE database for enhanced validation and querying.
  • Expansion of the Dictionary of Homologous Superfamilies with structural alignments and functional information.

    • Main Results:

    • New protocols increase the speed of classifying new protein structures.
    • Improved sensitivity in recognizing distant structural relatives through sequence information.
    • The CATH-PFDB, containing over 25,000 domains and 160,000 sequence relatives, is now in a relational ORACLE database.
    • Preliminary classification levels are provided for new structures, with nearly three-quarters of non-identical structures rapidly classified using profile-based sequence analysis (e.g., PSI-BLAST).

    Conclusions:

    • The developed protocols and database enhancements significantly improve the efficiency and scope of the CATH database.
    • These advancements are vital for supporting large-scale structural genomics and genome analysis.
    • The integration of sequence and structure information enhances the identification of homologous protein families.