Since the correlation between predicted and experimental affinities was better for the subset of ligands modeled in the structure 2WF3 than in 4EWO (Table ), we recalculated the docking and MM-GBSA scores for the ligands modeled in 4EWO using the 2WF3 structure instead. Then, the correlation coefficients on the entire set were computed using the updated scores (Table ). The performance of MM-GBSA improved, displaying a Kendall τ equal to 0.30 ± 0.05, while the performance of docking remained constant (Kendall τ equal to 0.21 ± 0.06). This shows that MM-GBSA is potentially better than docking, in agreement with the more accurate physical description, but the results are sensitive to modeling choices, such as protein conformation and protonation state, making it difficult to achieve optimal predictive performance in a prospective context.