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Related Experiment Videos

Model building by comparison at CASP3: using expert knowledge and computer automation.

P A Bates1, M J Sternberg

  • 1Biomolecular Modeling Laboratory, Imperial Cancer Research Fund, London, United Kingdom. p.bates@icrf.icnet.uk

Proteins
|October 20, 1999
PubMed
Summary
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This study presents protein structure prediction models for CASP3, finding that multi-parent models are more accurate than single-parent ones. A new loop-modeling algorithm using fragment searches and mean-field calculations is also introduced.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • The Critical Assessment of Techniques for Protein Structure Prediction (CASP) is a community-wide experiment to assess protein structure prediction methods.
  • Comparative modeling relies on the availability of known protein structures (templates) with significant sequence similarity to the target protein.

Purpose of the Study:

  • To construct and evaluate protein models for the CASP3 comparative modeling category.
  • To investigate the impact of template selection (single vs. multiple parents) on model accuracy.
  • To introduce a novel algorithm for protein loop modeling.

Main Methods:

  • Development of ten comparative models for CASP3 targets with sequence identities ranging from 12% to 64%.

Related Experiment Videos

  • Hybrid modeling protocol combining automated algorithms with human intervention for critical steps like sequence alignment and parameter selection.
  • Construction of models using either single-parent or multiple-parent templates.
  • Implementation of a novel loop-modeling algorithm involving fragment database searches, fragment libraries, and mean-field calculations.

    • Main Results:

    • Models constructed from multiple-parent templates demonstrated higher accuracy compared to those built from single-parent templates.
    • Seven targets were modeled using single-parent templates, while three utilized multiple parents.
    • The study discusses the rationale behind the observed ratio of single-parent modeling.

    Conclusions:

    • Multi-parent template approaches enhance the accuracy of protein structure prediction in comparative modeling.
    • The novel loop-modeling algorithm shows promise for improving predictions in regions with conformational flexibility.
    • The findings contribute to the ongoing development of more reliable protein structure prediction techniques.