Fig. 3

Pilot molecular dynamics simulations. Benzamidine ligand (sticks) started the MD simulations from three positions at different distances (as indicated in the legend) from the native binding site on the trypsin target (grey cartoon). Arrows in a point from starting (t = 0 ns) to final (t = 1000 ns) ligand positions. Only two of the three 1000 ns-long simulations with the closest starting position succeeded in finding the reference binding pose (*) known from the crystallographic structure (3ptb). b Time-dependence of root mean squared deviation (RMSD) of the ligand measured from its reference pose