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ModBase: Database of Comparative Protein Structure Models

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MODBASE is no longer under active development, and contains theoretically calculated models, not experimentally determined structures. The models may contain significant errors.


ModBase Search

ModBase is a database of comparative protein structure models, calculated by our modeling pipeline ModPipe.


Search type Display type

To include the academic (comprehensive) dataset, go to Current Datasets!
All available datasets are selected

Search by properties
Organism    or

Select property options
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Model Details Example

Database ID: Q12321

This page makes all models and model details for one sequence available.

Example details
  • The current model is shown prominently
  • Additional models are accessible through their thumbnails.
  • Use the Perform action pull-down menu for
    • Coordinates
    • Alignments
    • Various ModBase representations
    • links to UCSF Chimera

Overview Example

Dengue Virus

Models for several sequences are displayed on the Sequence Overview page.

Example dataset
  • A coverage sketch illustrates sequence section(s) covered by a model
  • The sketch also links to the Model Details page.
Users of ModBase are requested to cite this article in their publications:
MODBASE, a database of annotated comparative protein structure models and associated resources. Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges, Andrej Sali Nucleic Acids Research 42, D336-46, 2014.
MODBASE is maintained by Ben Webb in the group of Andrej Sali, Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biomedical Research, Mission Bay Campus, Byers Hall, University of California San Francisco, San Francisco, CA 94143. Please address all inquiries to .