psntools - a Python package for protein structure network analysis

Abstract

The application of network theory to investigate protein structures and conformational ensembles through Protein Structure Networks (PSNs) has proven particularly insightful to study protein dynamics, the potentially disruptive effects of disease-related mutations, and allosteric mechanisms. Here, we present psntools, a novel Python package for downstream analysis of PSNs. psntools is completely PSN-agnostic, in contrast with several available tools in the community. psntools relies only on a few Python dependencies, most notably MDAnalysis and NetworkX, works without external software, and can be incorporated into Python-based analysis pipelines. We also present an example of the usage of psntools on a case of study of biological interest, which helped produce novel insights on the structural details of the interaction between BCL-xL and the BH3 motif of BECLIN-1. The psntools package and the data associated with the case study are available at https://github.com/ELELAB/psntools.