Figure 5

Flowchart of the substrate-imprinted docking. Starting from one enzyme structure (Enz1) and one substrate in a reaction intermediate form (Sub1), the substrate is covalently docked into the structure in a first round of docking. The best pose from the first docking is used to construct an enzyme-substrate complex (Enz1-Sub1)), which is then energy minimized and provides an optimised enzyme-substrate complex ([Enz1-Sub1] _Opt ). The substrate is removed from this optimised complex, yielding a substrate-imprinted enzyme structure (Enz1 _{Opt, Sub1} ). This structure-imprinted structure is used in a second round of docking of the same substrate (Sub1). The resulting substrate poses are classified according to geometric filter criteria into productive and non-productive, and ranked by docking score.