Figure 2:

Example “funnel” plots depicting GlycanDock N₅ and 〈N₅〉 performance on bound target 4BJ0 at different initial ring-RMSD values. “Funnel” plots depict the relationship between interface score and ring-RMSD of a set of models (gray circles). While 〈N₅〉 must be calculated, N₅ can be determined directly by counting the number of near-native models (models below 2 Å ring-RMSD) within the top-5-scoring models (blue diamonds). (A) GlycanDock models predicted from 2.0 ± 0.1 Å initial ring-RMSD input structures demonstrate unambiguous (〈N₅〉 = 5.00) funneling toward the refined native crystal structure (maroon circles). (B) Models from 4.0 ± 0.1 Å initial ring-RMSD input structures demonstrate acceptable funneling (〈N₅〉 = 3.66) toward the refined native. (C) Models from 6.0 ± 0.1 Å initial ring-RMSD input structures demonstrate no funneling (〈N₅〉 = 0.30) toward the refined native. Accordingly, the funnel plots in panels A and B demonstrate docking success while the funnel plot in panel C demonstrates docking failure.