To understand the distinct behavior of the two scoring functions concerning BEDROC and EF1%, we investigated the performance of the two scoring functions on a per-molecule basis. We found that there was indeed a strong correlation between the Gnina scores derived from DiffDock-L and Vina poses (Figure ). However, we noted many compounds, particularly decoys, to which the Vina scoring function assigned substantially higher scores for Vina poses than DiffDock-L poses (see Figure for examples and Figure for a complete set of figures). While the exact reason for this behavior is difficult to pinpoint, the VS process seems to benefit from independent pose generation and scoring processes (the Vina pose sampling algorithm utilizes the Vina scoring function for navigating the sampling process towards the scoring function minima).