Table 2.

EF5% obtained with Flexi-pharma and Pharmagist for the benchmark systems in the training set. To obtain the EFs with Flexi-pharma, 6 MD trajectories of 10ns (starting from two crystal structures), 100 frames per trajectory, and a grid-percentage threshold of 0.7% were used. For Pharmagist [62, 63] we used two sets of training ligands. The first set uses three ligands that are not included in the compound library as templates. The second uses ligands that are contained in the compound libraries (see “Methods” section)

	CDK2	ER	COX	GAR
Flexi-pharma	3.1	2.9	2.3	2.6
Pharmagist set 1	1.6	0.2	1.4	1.2
Pharmagist set 2	2.6	3.4	3.0	19.3