RED-E-Function-Based Equilibrium Parameter Finder:\nFinding the Best Restraint Parameters in Absolute Binding Free Energy\nCalculations

Free energy perturbation (FEP)-based\nabsolute binding free energy\n(ABFE) calculations have emerged as a powerful tool for the accurate\nprediction of ligand–protein binding affinities in drug discovery.\nThe restraint addition is crucial in FEP-ABFE calculations; however,\ndue to the non-orthogonal couplings between the restrained degrees\nof freedom, it typically requires numerous λ windows to ensure\nthe phase-space overlap during restraint addition. This study introduces\nthe RED-E-function-based equilibrium parameter finder (REPF), a novel\nmethod that relies on harmonic restraints to optimize the equilibrium\nvalues in restraints, enhancing phase-space overlap and improving\nthe convergence of the restraint addition. REPF was applied to 44\nprotein–ligand complexes across 5 targets and compared to restraint\nschemes reported in the literature. We found that REPF-optimized restraints\nachieve an accuracy comparable to that of the 12λ approach while\nusing only 2λ simulations, resulting in a significant reduction\nin computational costs. Extensive tests confirmed the improved convergence\nbehavior and reduced energy fluctuations of REPF-optimized restraints.