Source-code version


The source-code version of MMMx runs under Matlab 2019b or later and requires the Matlab Oprimization, Global Optimization, Parallel Computing, and Statistics and Machine Learning toolboxes. Please use the executable version if you do not have a license for this software.

For certain functionality, MMMx relies on third-party software, such as SCWRL4, ATSAS, MUSCLE, MSMS, DSSP, HYDROPRO, or YASARA. Except for YASARA structure, which we use for structure refinement, this software is freely available for academic purposes, but may require registration and a license agreement.


The latest stable version of the MMMx package is available as a ZIP file at The newest development version of the source code is available at GitHub. Unpack the ZIP file.

Matlab path

The main MMMx directory and all its subdirectories must be on the Matlab path. Likewise, the directories of all required third-party software, often including subdirectories, must be on the Matlab path.

Getting started

Type MMMx help or MMMx docs to access the documentation.

Type MMMx distributions.mcx to run a first example. Examples exist for all modules.

Type just MMMx to open a file browser. You can select any MMMx control file (.mcx) to run a modeling pipeline.

For programmatic access from within Matlab, refer to the programmer’s documentation.