Figure 11. Structural representations of ligand binding modes compared to experimental structures.

Incorrect loop placement and incorrect ligand orientation often prevent Rosetta from converging on the experimental ligand binding mode. Ligand binding modes from the experimental structures are shown in gray and the top ranked model via clustering by ligand RMSD is shown in yellow for A) A2Ar, B) KOR and C) H1R. Cases where top ranked binding modes captured the experimental binding mode within 2.0 Å were D) DOR and E) M2R.