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

Ursula Pieper1, Benjamin M Webb, Guang Qiang Dong

  • 1Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, Byers Hall at Mission Bay, Office 503B, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA, Graduate Group in Biophysics, University of California at San Francisco, CA 94158, USA, Structural Bioinformatics Unit, Structural Biology and Chemistry department, Institut Pasteur, 25 rue du Docteur Roux, 75015 Paris, France, Université Paris Diderot-Paris 7, école doctorale iViv, Paris Rive Gauche, 5 rue Thomas Mann, 75013 Paris, France, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA, Life Sciences Division, Department of Molecular Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Nucleic Acids Research
|November 26, 2013
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Summary

ModBase is a comprehensive protein structure model database, offering millions of reliable models computed via automated pipelines. It provides on-demand modeling and integrates new tools for protein dynamics and ligand interactions.

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • ModBase is a database of annotated comparative protein structure models.
  • It utilizes the ModPipe automated modeling pipeline, primarily relying on Modeller for various modeling stages.

Purpose of the Study:

  • To update on the current state and capabilities of the ModBase database.
  • To introduce recently developed associated resources and highlight key applications.

Main Methods:

  • Automated comparative protein modeling using ModPipe and Modeller.
  • Development of specialized servers for protein dynamics, SAXS profile analysis, docking, and ligand scoring.
  • Integration with external resources like the Protein Model Portal.

Main Results:

  • ModBase now contains nearly 30 million reliable models for 4.7 million unique protein sequences.
  • New associated servers (AllosMod, AllosMod-FoXS, FoXSDock, SAXS Merge, Pose & Rank) have been developed.
  • Applications include structural coverage of the human alpha-helical transmembrane proteome and HIV-1 protease specificity determination.

Conclusions:

  • ModBase continues to expand its collection of protein structure models.
  • Associated tools enhance the analysis of protein dynamics, interactions, and structural ensembles.
  • The database and its resources support diverse research applications in structural biology and beyond.