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Tools for comparative protein structure modeling and analysis.

Narayanan Eswar1, Bino John, Nebojsa Mirkovic

  • 1Department of Biopharmaceutical Sciences and California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94143-2240, USA.

Nucleic Acids Research
|June 26, 2003
PubMed
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This study introduces a suite of bioinformatics tools for protein structure modeling and analysis. These resources facilitate comparative modeling, loop modeling, and prediction of mutation impacts, aiding protein structure research.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Comparative protein modeling is crucial for understanding protein function and evolution.
  • Accurate protein structure prediction aids in drug discovery and protein engineering.

Purpose of the Study:

  • To present a comprehensive suite of integrated resources for protein structure modeling and analysis.
  • To provide tools for automated comparative modeling, loop modeling, and functional impact prediction of mutations.

Main Methods:

  • MODELLER: comparative modeling by satisfaction of spatial restraints.
  • MODWEB: automated comparative modeling using PSI-BLAST, IMPALA, and MODELLER.
  • MODLOOP: automated loop modeling.
  • MOULDER: protocol for modeling based on distant structures.

Related Experiment Videos

  • MODBASE: database of annotated comparative models.
  • MODVIEW: integrated sequence and structure visualization.
  • SNPWEB: structure-based prediction of single amino acid substitution impacts.

    • Main Results:

    • Availability of MODELLER for spatial restraint satisfaction modeling.
    • MODWEB and MODLOOP offer automated comparative and loop modeling.
    • MOULDER extends modeling to distant structures.
    • MODBASE provides a large database of protein models.
    • MODVIEW enables integrated visualization.
    • SNPWEB predicts functional impact of amino acid substitutions.

    Conclusions:

    • The described resources offer a powerful and integrated platform for protein structure modeling and analysis.
    • These tools enhance the ability to predict protein structures and functional impacts, supporting various biological research areas.