The estimation of the correct binding mode and affinity of a ligand into
a target protein using computational methods is challenging. However,
docking can introduce poses from which the correct binding mode could be
identified using other methods. Here, we analyzed the reliability of
binding energy estimation using the molecular mechanics‐generalized Born
surface area (MMGBSA) method without and with energy minimization to
identify the likely ligand binding modes within docking results. MMGBSA
workflow (a) outperformed docking in recognizing the correct binding
modes of androgen receptor ligands and (b) improved the correlation
coefficient of computational and experimental results of rescored
docking poses to phosphodiesterase 4B. Combined with stability and
atomic distance analysis, MMGBSA helped to (c) identify the binding
modes and sites of metabolism of cytochrome P450 2A6 substrates. The
standard deviation of estimated binding energy within one simulation was
lowered by minimization in all three example cases. Minimization
improved the identification of the correct binding modes of androgen
receptor ligands. Although only three case studies are shown, the
results are analogous and indicate that these behaviors could be
generalized. Such identified binding modes could be further used, for
example, with free energy perturbation methods to understand binding
energetics more accurately.