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

Figure 2. RMSD and rank comparisons between standard and protein-centric water docking of HIV-1 PR/PI.

Figure 2

Left panel: RMSD of top scoring Rosetta model. 69 models fall below the diagonal (improved RMSDs) while 30 lie above it. Red dashed lines represent the 2 Å RMSD metric for successful docking. Predictions in the lower-right quadrant turn from failures to successes up on water docking. Upper-left quadrant contains predictions that succeeded without water docking and fail with water docking. Right panel: rank of the lowest scoring Rosetta model with RMSD under 2 Å. Where multiple HIV-1 cross-docking predictions achieved the same rank with and without water docking, these points are replaced with text indicating the number of overlapping points.