Fig. 9
From: EDock: blind protein–ligand docking by replica-exchange monte carlo simulation
The docking results under different van der Waals potential and binding pocket distance restraint weights for 1mkaA_BS02_DAC. The I-TASSER model (cyan) has an extra steric bump inside the binding cavity, compared to the native receptor structure (pink) in the background. The upper-right inset shows the docking poses by EDock (yellow), AutoDock Vina (magenta), and DOCK6 (blue) with an RMSD of 3.82Å, 8.03Å, and 6.74 Å from the native ligand pose (red), respectively. The lower-right compares the models by EDock with the composite weights (yellow), and two uniform weights of \(w_{3} = 1\) (green, RMSD = 9.26 Å) and 0 (orange, RMSD 8.85 Å), respectively