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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.

MODELLER is available for download for most Unix/Linux systems, Windows, and Mac.


Available versions:

  • MODELLER version 9.17 (July 2016)


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


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 (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:

Program administrator

Official website