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

Ursula Pieper1, Narayanan Eswar, Fred P Davis

  • 1Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, Office 503B, University of California at San Francisco 1700 4th Street, San Francisco, CA 94158, USA.

Nucleic Acids Research
|December 31, 2005
PubMed
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MODBASE provides a large, updated database of protein structure models generated by automated pipelines. This resource aids in understanding protein function and facilitates further structural biology research.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein modeling

Background:

  • Comparative protein modeling is crucial for understanding protein function when experimental structures are unavailable.
  • Automated pipelines streamline the generation of large-scale protein structure models.

Purpose of the Study:

  • To present MODBASE, a comprehensive database of annotated comparative protein structure models.
  • To highlight the capabilities of the MODPIPE pipeline and the MODWEB server for model generation.
  • To introduce integrated resources for protein structure analysis.

Main Methods:

  • Utilizing MODPIPE, an automated pipeline leveraging MODELLER for fold assignment, alignment, and model building.
  • Employing statistical significance and fold assessment for model reliability.

Related Experiment Videos

  • Integrating multiple databases for alignments (DBAli), ligand sites, and interfaces (PIBASE).

    • Main Results:

    • MODBASE contains over 3 million reliable models for nearly 1.1 million protein sequences from UniProt.
    • Models are included based on statistically significant alignments or correct fold assessment.
    • The database is regularly updated with growing sequence and structure data.

    Conclusions:

    • MODBASE serves as a valuable, up-to-date resource for comparative protein structure modeling.
    • The integrated resources (DBAli, PIBASE, LS-SNP) enhance functional and structural analysis.
    • MODWEB provides a user-friendly interface for generating custom protein models.