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Related Experiment Videos

Recognizing the fold of a protein structure.

Andrew Harrison1, Frances Pearl, Ian Sillitoe

  • 1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK.

Bioinformatics (Oxford, England)
|September 27, 2003
PubMed
Summary

A new graph-theoretic program, GRATH, rapidly and accurately matches novel protein structures to known ones. This tool aids in identifying structural similarities and inferring functional properties for newly determined protein domains.

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Structural biology

Background:

  • Protein structure classification is crucial for understanding function.
  • Existing methods for structure comparison can be computationally intensive.
  • The CATH database provides a framework for classifying structural domains.

Purpose of the Study:

  • To develop a rapid and accurate graph-theoretic program (GRATH) for matching novel protein structures against a library of known structures.
  • To introduce a novel scoring scheme for ranking structural similarity matches.
  • To benchmark GRATH's performance and optimize parameters for reliable fold identification.

Main Methods:

  • GRATH employs a graph-theoretic approach to compare protein structures.
  • It utilizes a similarity measure detailing geometric information, secondary structures, and residue counts.

Related Experiment Videos

  • A novel scoring scheme ranks identified matches, and the algorithm was benchmarked on 1702 non-redundant CATH structures.

    • Main Results:

    • GRATH achieves 90% accuracy in identifying the correct fold with the top score.
    • 98% of the time, the correct fold is found within the ten most likely assignments.
    • The program is available as a server for public use.

    Conclusions:

    • GRATH offers a fast and accurate method for protein structure comparison and fold identification.
    • It serves as an effective front-end filter for more computationally expensive algorithms like SSAP.
    • The GRATH server is a valuable resource for structural genomics, aiding in the functional inference of newly determined protein structures.