Table 1.

Influence of the flexibility of the ligand on the success rate observed with EADock DSS, the docking engine of SwissDock, in a redocking assay carried out on 251 protein–ligand complexes

Max no. of rotatable bonds of the ligand	FDA-approved drugs (%)	SR0 (%)	SR5 (%)
5	63	84	93
10	93	77	86
15	99	69	83
20	100	66	81

As can be expected, the success rate decreases as the ligand flexibility increases. Interestingly, 93% of FDA-approved drugs have 10 or less rotatable bonds. For 86% of such ligands in our data set, EADock is able to propose a binding mode within 2 Å root mean square deviation to the experimental BM within among the five most favorable predictions. See text for details.