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Supported Applications


  • Description

    used for homology or comparative modeling of protein three-dimensional structures. From a sequence alignment with known related structures, MODELLER automatically calculates a model containing all non-hydrogen atoms using comparative protein structure modeling by satisfaction of spatial restraints. It can also perform de novo modeling of loops in protein structures and optimize various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

  • Usage

    To list all executables provided by MODELLER, run: $ sbgrid-list modeller Copy to clipboard
  • Usage Notes

    MODELLER is run from the command line using typically using the sbgrid-provided python for modeller. Typical usage is python.modeller There are some tutorials to get you started available at

    A graphical interface to MODELLER is commercially available from Accelrys, as part of Discovery Studio Modeling 1.1.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install modeller Copy to clipboard Available operating systems: Linux 64, OS X INTEL
  • Primary Citation*

    B. Webb and A. Sali. 2016. Comparative Protein Structure Modeling Using MODELLER. Current protocols in bioinformatics. 54: 5.6.1-5.6.37.

    • *Full citation information available through