See Features It should be noted that the predictive accuracy varies a lot depending on the target, so it makes sense to evaluate AutoDock Vina against your particular target first, if you have known actives, or a bound native ligand structure, before ordering compounds. While evaluating any docking engine in a retrospective virtual screen, it might make sense to select decoys of similar size, and perhaps other physical characteristics, to your known actives. AutoDock Vina inherits some of the ideas and approaches of AutoDock 4, such as treating docking as a stochastic global opimization of the scoring function, precalculating grid maps Vina does that internally , and some other implementation tricks, such as precalculating the interaction between every atom type pair at every distance. It also uses the same type of structure format PDBQT for maximum compatibility with auxiliary software. However, for any given target, either program may provide a better result, even though AutoDock Vina is more likely to do so.
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