BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.

We present BindFlow, a Python-based software for automated absolute binding free energy (ABFE) calculations at the free energy perturbation (FEP) or at the molecular mechanics Poisson-Boltzmann/generalized Born surface area [MM(PB/GB)SA] level of theory. BindFlow is free, open-source, user-friendly, and easily customizable, runs on workstations or distributed computing platforms, and provides extensive documentation and tutorials. BindFlow uses GROMACS as a molecular dynamics engine and provides built-in support for the small-molecule force fields GAFF, OpenFF, and Espaloma, as well as support for user-provided custom force fields. We test BindFlow by computing affinities for 139 receptor-ligand pairs, involving eight different targets, including six soluble proteins, one membrane protein, and one nonprotein host-guest system. We find that the agreement of BindFlow predictions with experiments is overall similar to gold standards in the field. Interestingly, we find that MM(PB/GB)SA achieves correlations that, for some systems and force fields, approach those obtained with FEP while requiring only a fraction of the computational cost. This study establishes BindFlow as a validated and accessible tool for ABFE calculations.