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MODBASE, a database of annotated comparative protein structure models.

R Sánchez1, U Pieper, N Mirković

  • 1Laboratories of Molecular Biophysics, The Pels Family Center for Biochemistry, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Nucleic Acids Research
|December 11, 1999
PubMed
Summary

MODBASE is a queryable database offering annotated comparative protein structure models derived from automated pipelines. It provides 3D models for thousands of proteins across multiple species, aiding structural biology research.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Genomics

Background:

  • Protein structure modeling is crucial for understanding biological function.
  • Automated pipelines facilitate large-scale protein structure prediction.
  • Databases integrating predicted structures with quality assessments are valuable research tools.

Purpose of the Study:

  • To introduce MODBASE, a queryable database of annotated comparative protein structure models.
  • To provide access to 3D models for a significant number of proteins from complete genomes and key species.
  • To offer fold assignments, alignments, and quality assessments for the protein models.

Main Methods:

  • Protein models generated using the automated MODPIPE pipeline.
  • MODPIPE utilizes PSI-BLAST for sequence analysis and MODELLER for structure modeling.

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  • Database construction involves integrating 3D models, fold assignments, alignments, and quality metrics.

    • Main Results:

    • MODBASE contains 3D models for approximately 17,000 proteins from 10 complete genomes.
    • Includes models for Caenorhabditis elegans, Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana, and Homo sapiens.
    • Provides fold assignments, alignments, and detailed model quality assessments.

    Conclusions:

    • MODBASE serves as a valuable resource for researchers needing access to predicted protein structures.
    • The database facilitates comparative analysis and structural genomics studies.
    • Accessibility via a web interface enhances its utility for the scientific community.