A Practical Covariance-Based Method for Efficient Detection of Protein-Protein Attractive and Repulsive Interactions in Molecular Dynamics Simulations

Molecular dynamics simulations of large protein–protein complexes require scalable analysis. We present a correlation-based workflow that systematically identifies both attractive (stabilizing) interactions, such as salt bridges, hydrogen bonds, and hydrophobic contacts, as well as repulsive (destabilizing) interactions across extensive interfaces. By constructing an inter-protein covariance matrix, filtering residue pairs based on distance, and identifying interactions underlying these correlations, our method focuses computational resources on the most relevant regions of the interface while preserving a high level of detail.