To investigate the effect of using docked or crystallographic ligand binding modes on binding affinity prediction, we performed a five-fold cross-validation on the PDBbind Training Set. We tested three strategies for predicting the binding affinity of a ligand using its docked poses: (i) predicting the binding affinity using the pose ranked highest by Smina; (ii) predicting the binding affinity for each docked pose and taking the highest; and (iii) predicting the binding affinity for each docked pose and taking the arithmetic mean.