Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination
Fig 3
Protein-ligand docking results.
(A) Scatter plot comparing results of 46 cases between baseline (REF2015) and Rosetta-ECO. Values are the Boltzmann-weighted discrimination score ± 1σ from an average of three independent runs. (B) Energy funnels, similar to Fig 2, for PDB ID 1X8X, tyrosyl t-RNA synthase bound to tyrosine (red data point in 3A) C. Explicitly-solvated, near-native docking pose in pink (RMSD = 0.43 Å; pink data point in 3B) with native ligand in transparent blue. (D) Explicitly-solvated decoy binding pose (RMSD = 6.57 Å; yellow data point in 3B). (E-H) A comparison of recovered waters (red) to high-resolution crystallographic waters (green spheres) from PDB ID: 1N2J (Panels E-G) and PDB ID: 1U4D (Panel H).