MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of 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.
MODELLER is available for download for most Unix/Linux systems, Windows, and Mac.
- MODELLER version 9.17 (July 2016)
After reading and accepting the license for the first time, you will be able to review it's contents anytime by looking at /software/modeller/9.17/license.txt
First prepare environment variable using
module load modeller-9.17
Now, there are two basic ways to run MODELLER. Both prepare environmental variables first, so that MODELLER is made available to your python file.
But they differ in the Python interpreter used:
- 1) mod9.17 somescript.py (uses built-int Python 2.3 interpreter)
- 2) modpy.sh somescript.py (simply runs somescript.py - it has to be executable)
In the second case, MODELLER should work well with both 2.7.6 and 3.4.1 versions of Python in MetaCentrum.
You can find documentation at the official website: https://salilab.org/modeller/documentation.html.