However, the source code, the scoring funcion and the actual algorithms used are brand new, so it’s more correct to think of AutoDock Vina as a new “generation” rather than “version” of AutoDock. It also uses the same type of structure format (PDBQT) for maximum compatibility with auxiliary software. 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. What is the difference between AutoDock Vina and AutoDock 4?ĪutoDock 4 (and previous versions) and AutoDock Vina were both developed in the Molecular Graphics Lab at The Scripps Research Institute. 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. 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.
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