Data and code for the comparison the local partitioning of atomic contacts in the Amino Acid Networks of protein variants. The presented method and results are described in:

• Lorenza Pacini, Claire Lesieur, A computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures, Bioinformatics, Volume 38, Issue 3, 1 February 2022, Pages 703–709, https://doi.org/10.1093/bioinformatics/btab736

Python 3.x is required and jupyter is needed to run the case_studies notebook. The calculations are built upon Rodrigo Dorantes-Gilardi's module biographs. The modules required for the calculation and the plotting of the results are listed in requirements.txt and can be installed using

pip install -r requirements.txt

You need to have LaTex installed on your system in order to produce the plots with Matplotlib. On Ubuntu, you can install LaTex and the necessary extensions by running

sudo apt-get install dvipng texlive-latex-base texlive-latex-extra texlive-fonts-recommended

and if you still get an error, try installing cm-super:

sudo apt-get install cm-super

For other operating systems, or if you encounter problems, please follow the instructions in Matplotlib's tutorial.

Lorenza Pacini - lorpac

If you use this code in your work, please cite:

• Lorenza Pacini, Claire Lesieur, A computational methodology to diagnose sequence-variant dynamic perturbations by comparing atomic protein structures, Bioinformatics, Volume 38, Issue 3, 1 February 2022, Pages 703–709, https://doi.org/10.1093/bioinformatics/btab736

The Building network source code is available under the CeCILL licence. Please see LICENCE.txt for details.