Fig. 4

An example of the case with a large difference between the energetical maximum identified by CaverDock and the geometrical bottleneck identified by CAVER. A Energy profile from CaverDock (solid) and the geometric profile from CAVER (dotted). The tunnel region with the energy maximum is highlighted with the red line, and the region with a geometric bottleneck is highlighted with the green line. B Visualisation of the tunnel with highlights corresponding to the energy profile. C Visualisation of the cognate ligand β-d-glucose conformations extracted from the trajectory from tunnel 1 of the structure of glucose dehydrogenase (PDB ID 2VWG). The binding pose based on the energy maximum (red) and geometric tunnel bottleneck (green)