PyInteraph is a software research tool for the analysis of structural communication protein ensembles. It has been designed to analyze MD and structural ensembles with attention to binary interactions between residues, such as hydrogen bonds, salt bridges, and hydrophobic interactions. Once the interactions have been calculated, it is able to use different classes of intra- and intermolecular interactions, combined or alone, to calculate comprehensive interaction graphs. These graphs can be thoroughly analyzed using included network analysis tools, which are able to point out the most important features of the network for the discovery of paths of structural communication in proteins. The tool works best together with the xPyder PyMOL plugin, which allows for further analysis and easily understandable representation of the calculated networks and graphs.
The PyInteraph package can be downloaded here as a compressed archive. The package includes the libinteract library, the frontend scripts, required configuration files and detailed installation instructions for Linux and OS X. A test and tutorial package which includes a short xtc trajectory file of the Ubc1 E2 enzyme (PDB ID 1FXT), the corresponding gro topology file and a reference pdb is also available. The tutorial also comprises a bash script with comments and description of the available options for the front-end scripts, as well as documentation files.
PyInteraph best works together with the xPyder PyMOL plugin. xPyder is designed to analyze and plot in an interactive environment protein networks expressed as matrices, such as the graph files produced by PyInteraph. More information can be found at the xPyder website