Refinement of Docked Protein-Protein Complexes Using Repulsive Scaling Replica Exchange Simulations

Accurate prediction and evaluation of protein-protein complex structures is of major importance to understand the cellular interactome. Predicted complex structures based on deep learning approaches or traditional docking methods require often structural refinement and rescoring for realistic evaluation. Standard molecular dynamics (MD) simulations are time-consuming and often do not structurally improve docking solutions. Better refinement can be achieved with our recently developed replica-exchange-based scheme employing different levels of repulsive biasing between proteins in each replica simulation (RS-REMD). The bias acts specifically on the intermolecular interactions based on an increase in effective pairwise van der Waals radii without changing interactions within each protein or with the solvent. It allows for an improvement of the predicted protein-protein complex structure and simultaneous realistic free energy scoring of protein-protein complexes. The setup of RS-REMD simulations is described in detail including the application on two examples (all necessary scripts and input files can be obtained from https://gitlab.com/TillCyrill/mmib ).