README files and scripts to run M3 framework
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Integrative Structure Determination files:

To use this software you need a special version of HADDOCK. See for that the README file under the HADDOCK2.3-nmol directory.

The additional scripts to perform analysis and model selection in the HADDOCK2.3-nmol framework are located under analysis_scripts. See the README file in that directory.

Starting structures, restraints files, and final models for each benchmark case are given under the respective folder in cases/. Each case also contains an example new.html and instructions about specific HADDOCK parameter settings.

Finally, statistics within this framework are calculated using Matlab, although in principle any other statistics toolkit/programming language can be used instead.

If you use this software in your work, please cite us:

Karaca, E., Rodrigues, J.P.G.L.M., Graziadei, A., Bonvin, A.M.J.J., and Carlomagno, T. (2017). M3: an integrative framework for structure determination of molecular machines. Nat Meth 14, 897–902 doi:10.1038/nmeth.4392