Table 2.

Performance of AutoDock4 and HADDOCK in reproducing the experimental structures of the complexes between ADK and the four ligands investigated in this work. For each compound, two cluster sets (gEDES and MD_std) were employed in ensemble-docking calculations. The Autodock results refer to clusters of docking poses obtained from a cluster analysis performed on all generated complexes (see Methods) while for HADDOCK they refer to the single structures from a single run starting from the ensemble of MD conformations. The sampling performance is calculated as the percentage of poses within 2.5 Å from the native (for HADDOCK calculated at the rigid-body stage out of 50000 poses). The pose ranking refers to the first native-like conformation obtained using the highest score within each cluster. The next row reports the heavy atoms RMSD of the ligand and for the binding site calculated for the first native-like conformation following ranking. F_nat indicates the fraction of native contacts recovered within a shell of 5 Å from the ligand in the experimental structures. The overall best poses are highlighted in bold and shown in Figure 4.

		AP5		AMP		ADP		GCP
		MDstd	gEDES	MDstd	gEDES	MDstd	gEDES	MDstd	gEDES
Autodock	Sampl. perf. [%]	0.6	1.8	-	0.9	1.9	2.7	1.2	1.8
	Pose rank	19	2	-	7	10	1	16	1
	RMSDlig/BS [Å]	2.3/4.9	2.2/2.2	-	2.1/3.1	2.3/3.8	0.9/1.1	2.5/1.7	2.3/2.0
	Fnat	0.58	0.79	-	0.74	0.57	0.86	0.75	0.80
HADDOCK	Sampl. perf. [%]	2.8	0.57	-	0.004	0.06	0.1	1.01	1.4
	Pose rank	61	1	643	193	23	1	390	11
	RMSDlig/BS [Å]	2.2/7.9	1.6/2.1	2.4/8.5	1.7/2.7	2.3/4.2	0.6/1.4	2.0/3.5	1.7/2.0
	Best RMSDlig [Å] / rank	1.8/68	0.9/16	2.4/643	1.7/193	2.2/81	0.5/7	1.9/644	0.8/74
	Fnat	0.38	0.82	0.33	0.67	0.54	0.88	0.43	0.86