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MODBASE, a database of annotated comparative protein structure models.

Ursula Pieper1, Narayanan Eswar, Ashley C Stuart

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

Nucleic Acids Research
|December 26, 2001
PubMed
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MODBASE is a comprehensive protein structure model database, offering valuable insights into protein function and evolution. This resource aids researchers in understanding protein structures and their implications across various biological studies.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Comparative protein modeling is crucial for understanding protein function when experimental structures are unavailable.
  • Databases of protein models facilitate large-scale biological research and discovery.

Purpose of the Study:

  • To introduce MODBASE, a relational database of annotated comparative protein structure models.
  • To provide access to a large collection of protein models derived from automated pipelines.

Main Methods:

  • Utilized PSI-BLAST, IMPALA, and MODELLER within the MODPIPE automated modeling pipeline.
  • Employed MySQL for efficient database management and MODVIEW for structure visualization.
  • Organized models into distinct datasets for targeted research applications.

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Main Results:

  • Generated comparative protein structure models for a significant portion of the TrEMBL protein sequence database.
  • Included models based on significant sequence alignments and validated fold assessments.
  • Developed specialized datasets for genomics, structural genomics, and specific biological systems.

Conclusions:

  • MODBASE serves as a valuable, regularly updated resource for protein structure modeling.
  • The database supports diverse research areas, including functional genomics and structural annotation.
  • Automated modeling pipelines and robust database systems are key to creating large-scale structural biology resources.