InSty: A ProDy Module for Evaluating Protein Interactions and Stability

Abstract

ProDy is a widely used application programming interface for analyzing the collective dynamics of proteins and their complexes, offering enhanced capabilities to address the growing needs of the computational biology community to bridge structure and function. Here, we introduce InSty, a new module integrated into ProDy to identify and quantify intra- and intermolecular interactions critical to protein stability and structural dynamics. InSty analyzes the non-covalent interactions using conformational ensemble data from both experiments and computational predictions, assesses their time evolution and persistence during molecular dynamics simulations as well as their conservation across homologs. It provides insights into the significance of these interactions in achieving function and/or supporting stability. InSty outputs lend themselves to statistical evaluation, visualization, and automated ensemble analysis for interpreting the significance of the interactions in the context of protein dynamics, sequence evolution, and allostery. Consolidation of InSty with various ProDy modules enables its efficient usage as a versatile tool that supports mutagenesis studies and identifies critical spots for functional interactions. The InSty module is available as part of the ProDy package at https://github.com/prody/ProDy.

Keywords: PDB; ProDy; elastic network models; molecular dynamics; non-covalent interactions.