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Related Experiment Videos

Exploring protein domain structure.

J C Ison1

  • 1Bioinformatics Applications Group, UK MRC Human Genome Mapping Project Resource Centre, Hinxton, Cambridge, UK. jison@hgmp.mrc.ac.uk

Briefings in Bioinformatics
|July 24, 2001
PubMed
Summary
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This review explores protein structure databases like SCOP and CATH, essential tools for understanding protein relationships and genome functions in bioinformatics research.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Genomics

Background:

  • The Protein Data Bank (PDB) houses over 10,000 protein structures, comprising more than 25,000 structural domains.
  • Understanding protein structural, functional, and evolutionary relationships is fundamental to bioinformatics and genome research.

Purpose of the Study:

  • To review the SCOP (Structural Classification of Proteins) and CATH (Class, Architecture, Topology, Homologous superfamily) databases.
  • To explain the hierarchical structure, usage, and annotation of these protein domain classification systems.
  • To introduce other tools for exploring protein structure relationships.

Main Methods:

  • Description of the SCOP database and its classification principles.
  • Description of the CATH database and its hierarchical classification system.

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  • Overview of annotation strategies and tools for exploring protein structure data.

    • Main Results:

    • SCOP and CATH provide comprehensive classifications for protein domains within the PDB.
    • These databases facilitate the investigation of structural, functional, and evolutionary relationships among proteins.
    • The hierarchical nature of SCOP and CATH aids in understanding protein domain organization.

    Conclusions:

    • SCOP and CATH are vital resources for bioinformatics research, enabling detailed analysis of protein structures.
    • These databases are crucial for functional genomics and understanding the human genome.
    • Exploration of protein structure relationships is enhanced by these classification systems and associated tools.