MDInteractions: A Python package for the distance-based analysis of intra- and inter-protein interactions

Intra-protein and inter-protein amino acids contacts are fundamental to protein folding, signal transduction, and pathogenesis. Despite the growing use of molecular dynamics (MD) simulations to model these contacts, there are few flexible and accessible tools for analysing the patterns of amino acid contacts that are revealed by MD simulations. Here we present such a tool, MDInteractions, designed to identify and analyse intra- and inter-protein amino acid contacts using post-convergence MD simulation trajectories. We demonstrate the utility of MDInteractions through a case study involving an analysis of intra- and inter-protein interactions between HIV-1 envelope protein promoters, to provide complementary support for current models of these interactions previously derived through experimental functional and structural analyses of HIV-1 envelope. MDInteractions is available for installation via pip or GitHub at https://github.com/afowdar/MDInteractions. Scientific contribution The MDInteractions package enables users to track atomic-resolution contact-based intra- and inter-protein interactions across MD simulation trajectories. Users have the flexibility to specify parameters to describe these interactions, such as interactive distance thresholds between individual atoms within one group when studying intra-protein interactions and between two groups when studying inter-protein interactions.