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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.


Warning.gif WARNING: If you want to be able to use MODELLER in MetaCentrum, you have to read and accept it's license agreement. Please note that academic license of MODELLER prohibits some behaviour, such as commercial computations.

Read and accept MODELLER's license agreement here!

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


Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/

to your script before loading a module. Then, you can list all versions of modeller and load default version of modeller as

module avail modeller/ # list available modules
module load modeller   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail modeller

and choose explicit version you want to use.

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 (uses built-int Python 2.3 interpreter)
  • 2) (simply runs - 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 more information about various ways to run MODELLER on the official website.


You can find documentation at the official website:

Official website