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. 2013 Jun 28;8(6):e67536. doi: 10.1371/journal.pone.0067536

Figure 8. Docking results for CSAR complex set1_181.

Figure 8

Top: experimental structure with ligand in blue, water as a red sphere, and polar contacts as black dashed lines. 22 polar contacts are predicted by PyMOL, 4 of which contact the water molecule. Middle: Top scoring model from docking without water. Native ligand and water in grey, Rosetta model in cyan. PyMOL predicts 16 polar contacts. Bottom: Lowest RMSD model from docking with loose waters. Rosetta model shown in green. No model within the top 100 by total energy score has RMSD <2.0 Å (hence rank is ‘n/a’). Shown is the lowest RMSD structure. PyMOL predicts 11 polar contacts (1 with water).