Table 1 Commonly-used evaluation metrics for protein binding site prediction

DCA

Distance from site Centre to ligand Atom: the distance in Å from the predicted binding site centre to any ligand heavy atom from the experimentally-determined complex

DCC

Distance from site Centre to ligand Centre: the distance in Å from the predicted binding site centre to the centre of the ligand from the experimentally-determined complex

DVO

Discretized Volume Overlap: intersection over union of the volume of the predicted binding site and the volume of the ligand from the experimentally-determined complex

Atom IoU

Atom Intersection over Union: for use in methods where protein atoms are individually labelled as ligand-binding or non-ligand-binding, intersection over union of the predicted ligand-binding atoms and the experimentally-observed ligand-binding atoms is calculated