There is an excellent recap of the latest literature on ligand efficiency at our friends' place. I read the Bembenek paper, several times, and something inherently bother me about it.
This is what bothers me. An empirically derived weighting function. To me, ligand efficiency makes sense from a physical standpoint. It's a value that measure how well every atom contributes overall to the binding. It makes sense to me that bigger molecules are worse at using their atoms.
This scaling function makes no physical sense to me. Somebody please explain to me (and admittedly I maybe totally miss the point), but please explain why Fit Quality is a better measure than LE from a physical standpoint of the origin of the measures.