ProtACon

ProtACon is a project by Simone Chiarella and Renato Eliasy for the courses of Pattern Recognition and Complex Networks, MSc Physics, University of Bologna.

To install it, clone the repository in some folder. In this folder, launch:

pip install --editable ProtACon

Once you installed it, you can run the application from any path. You can launch different scripts by typing in the command line ProtACon followed by one of the following commands:

• on_set Compute the attention alignment with the contact between the residues of each peptide chain contained in a specified set. The attention alignment and the pairwise attention similarity of each peptide chain are finally averaged together.
• on_chain Do the same as on_set, but on a single protein, to specify using its unique identification code.
• net_viz Visualize a network showing the 3D structure of one protein, together with one specified property (pH, charge, contact), and the corresponding alignment with the attention given to each residue (still to implement).

From the configuration file config.txt, it is possible to set the folder names where to store the plots and the PDB files of the proteins, and also the cutoffs for the thresholding of the contact maps. From there, you can also specify the set of proteins that you want to process with the command on_set.