AutoDock Vina evaluates a receptor’s entire binding pocket at once to find a docking site (lowest-energy binding) for a ligand of interest. The deepest part of the pocket (the actual binding site
for auxin shown at the bottom of (1) naturally has a low energy requirement, and this is where, in the case of tryptophan (2), the software suggests a docking site. But by forcing the software to move in incremental steps—starting at the mouth of the pocket and moving inward—TomoDock finds an interaction of tryptophan with residues farther up the pocket (3) that prevents deeper entry. In the case of auxin, however, TomoDock finds the same binding site as that found using AutoDock Vina (step-wise progress of TomoDock shown in (1).
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