Protein-Protein Docking with Dynamic Residue Protonation States
Figure 6
Hydrogen bonding recovery correlates with docking performance.
Docking plots generated using RosettaDock and pHDock for (A) tumor susceptibility gene 101 protein–Ubiquitin complex (1S1Q; pH 4.6), (B) PPARgamma+RXRalpha–GW409544+co-activator peptide complex (1K74; pH 7.5), and (C) CDK2 kinase–cell cycle-regulatory protein CksHs1 complex (1BUH; pH 7.5). Grey, orange, red, and blue points represent incorrect, acceptable-, medium-, and high-quality models, respectively. Discrimination scores are shown in the bottom right corner of the plots. The right panel shows structures of the top pHDock (blue) and RosettaDock (green) models superimposed on the native complex (red). The number of native hydrogen bonds among the total interface hydrogen bonds observed in the bound crystal complex, and the top-scoring pHDock
and RosettaDock
models are also listed.