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 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
Usage Notes

MODELLER is run from the command line using typically using the sbgrid-provided python for modeller. Typical usage is python.modeller 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.
Installation
Use the following command to install this title with the CLI client: $ sbgrid-cli install modeller 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

Keywords

Computational Chemistry, Multiple Structure Alignment, Protein Structure Analysis, Proteomics
Default Versions

Linux 64: 10.5 (352.5 MB)
OS X INTEL: 10.5 (307.5 MB)
Other Versions
- OS X INTEL:
  10.3 (308.7 MB) , 10.4 (778.3 MB) , 9.24 (410.4 MB)
Developers

Andrej Sali, Ben Webb