Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
Fig 2
Protein-protein docking results.
(A) Scatter plot comparing results of 53 cases between REF2015 and Rosetta-ECO. Values are the average Boltzmann-weighted discrimination score ± 1σ from three independent runs. (B) Energy funnels for PDB ID 1E6E, adrenodoxin reductase bound to adrenodoxin (red data point in 2A), plotting computed ΔGbind vs. RMSD from the native binding conformation for three different scoring methods. Discrimination scores for each distribution are noted in bottom right of each plot. (C) Explicitly solvated near-native docking pose (RMSD = 0.14 Å; pink data point in 2B) with the reductase in grey and adrenodoxin in rainbow (N- to C-terminus colored blue to red). (D) Coordination of some predicted interface waters.