PyInteraph is a software suite designed to identify intramolecular interactions from protein ensembles and join them in a graph representation, which can be used to identify pathways of structural communication. It includes Python and C libraries and front-end scripts as well as a PyMOL plugin, Interaction Plotter, which is designed to plot the interactions on the protein three-dimensional structure.
The package can be found here, together with a comprehensive tutorial and test data set. The test data set also includes instructions on the format of the configuration files and instructions on how to install and use the Interaction Plotter plugin. It also includes a bash file with several use tests and useful comments on the various flags available to the user.
Installation instructions and requirements are found in the INSTALL file.
When using PyInteraph for publication, please cite:
Matteo Tiberti, Gaetano Invernizzi, Matteo Lambrughi, Yuval Inbar, Gideon Schreiber, and Elena Papaleo PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins J. Chem. Inf. Model., 2014, 54 (5), 1537–1551