Figure 10. Clustering captures binding modes with lower RMSD and increased contact coverage.

Binding modes for each receptor were clustered by ligand heavy-atom RMSD with a cutoff of 2.0 Å. When compared to smaller cluster sizes, the large cluster sizes were more likely to capture A) lower average ligand RMSD to the experimental binding mode and B) a higher percentage of correct ligand contacts. Contact coverage was calculated using SimiCon [42].