PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles

• DOI: 10.1021/acs.jcim.3c00574
• Publication Date: 2023-07-12T18:45:11Z
• Authors: Valentina Sora; Matteo Tiberti; Ludovica Beltrame; Deniz Dogan; Shahriyar Mahdi R...; Joshua Rubin; Elena Papaleo
• Keywords: Protein Conformation; Reproducibility of Results; Proteins; Software

Due to the complex nature of noncovalent interactions and their long-range effects, analyzing protein conformations using network theory can be enlightening. Protein Structure Networks (PSNs) provide a convenient formalism study structures in relation essential properties such as key residues for structural stability, allosteric communication, effects modifications protein. PSNs defined according very different principles, available tools have limitations input formats, supported models, version control. Other outstanding problems are related definition cutoffs assessment stability properties. The science community could benefit from common framework carry out these analyses make them easier reproduce, reuse, evaluate. We here two open-source software packages, PyInteraph2 PyInKnife2, implement analyze reproducible documented manner. interfaces with multiple formats ensembles incorporates models possibility integrating into macronetwork performing various downstream analyses, including hubs, connected components, several other centrality measures, visualizes networks or further analyzes thanks compatibility Cytoscape.PyInKnife2 that supports implemented PyInteraph2. It employs jackknife resampling approach estimate convergence streamline selection distance cutoffs. foresee modular structure code control system will promote transition community-driven effort, boost reproducibility, establish protocols PSN field. As developers, we guarantee introduction new functionalities maintenance, assistance, training contributors.