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SBGridTV

Supported Applications

MODELLER

  • 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, 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 Notes

    MODELLER is run from the command line using typically using the included modpy.sh script with the sbgrid-provided python. Typical usage is modpy.sh python my_modller_pythonscript.py. There are some tutorials to get you started available at http://salilab.org/modeller/tutorial/.

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

  • Primary Citation*

    A. Sali and T. Blundell. 1993. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 234(3): 779-815.


    • *Full citation information available through

  • Keywords

    Computational Chemistry

  • Default Versions

    Linux 64:  9.18
    OS X INTEL:  9.16

  • Other Available Versions

      Linux 32:

      9.9, 9.12, 9.11, 9.10
    • Linux 64:

      9.16, 9.15, 9.14
    • OS X INTEL:

      9.15, 9.14
    • powermac:

      9v9, 9v8, 9v7, 9v4, 8v1
  • Developers

    Andrej Sali, Ben Webb.

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