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MODBASE, a database of annotated comparative protein structure models, and associated resources.

Ursula Pieper1, Narayanan Eswar, Hannes Braberg

  • 1Department of Biopharmaceutical Sciences, and California Institute for Quantitative Biomedical Research, Mission Bay Genentech Hall, 600 16th Street, Suite N472D, University of California San Francisco, San Francisco, CA 94143-2240, USA.

Nucleic Acids Research
|December 19, 2003
PubMed
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MODBASE is a comprehensive protein structure model database, utilizing automated pipelines for accurate predictions. It provides valuable insights into protein function and interactions, aiding structural genomics research.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Chemistry

Background:

  • Protein structure modeling is crucial for understanding protein function and biological processes.
  • Existing databases offer valuable protein sequence and structure data, but comprehensive model repositories are needed.
  • Automated comparative modeling pipelines enhance the scale and efficiency of structure prediction.

Purpose of the Study:

  • To present MODBASE, a relational database of annotated comparative protein structure models.
  • To describe the MODPIPE automated modeling pipeline and its reliance on the MODELLER package.
  • To highlight MODBASE's utility for querying, visualization, and supporting structural genomics initiatives.

Main Methods:

  • Comparative modeling using the MODPIPE pipeline, incorporating fold assignment, sequence-structure alignment, and model assessment.

Related Experiment Videos

  • Database management using MySQL for efficient querying and CHIMERA for visualization.
  • Regular updates incorporating new sequence and structure data, and software improvements.

    • Main Results:

    • MODBASE contains over 126,000 models for domains across nearly 660,000 protein sequences from Swiss-Prot/TrEMBL.
    • Includes models based on significant alignments and those predicted to have correct folds despite insignificant alignments.
    • Supports structural genomics by characterizing sequences, predicting binding sites, and modeling interactions.

    Conclusions:

    • MODBASE serves as a valuable resource for exploring protein structures and functions.
    • The database facilitates target selection and structure-based annotation in structural biology.
    • Associated resources like DBALI, MODWEB, MODLOOP, and SNPWEB extend its utility for various modeling and analysis tasks.