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It was designed and implemented by Dr. The image on the left illustrates the results of flexible docking green superimposed on the crystal structures of a indinavir, b atorvastatin, c imatinib, and d oseltamivir bound to their respective targets.
Publication If you used AutoDock Vina in your work, please cite: Features Accuracy AutoDock Vina significantly improves the average accuracy of the binding mode predictions compared to AutoDock 4, judging by our tests on the training set used in AutoDock 4 development.
It should be noted that all six of the other docking programs, to which it was compared, are distributed commercially. Binding mode prediction accuracy on the test set. All that is required is the structures of the molecules being docked and the specification of the search space including the binding site.
Calculating grid maps and assigning atom charges is not needed. The usage summary can be printed with "vina --help". The summary automatically remains in sync with the possible usage scenarios.
Implementation Quality By design, the results should not have a statistical bias related to the conformation of the input structure. Attention is paid to checking the syntactic correctness of the input and reporting errors to the user in a lucid manner. The invariance of the covalent bond lengths is automatically verified in the output structures.
Vina avoids imposing artificial restrictions, such as the number of atoms in the input, the number of torsions, the size of the search space, the exhaustiveness of the search, etc. Flexible Side Chains Like in AutoDock 4, some receptor side chains can be chosen to be treated as flexible during docking.
Some of these projects average over 50 years worth of computation per day. Average time per receptor-ligand pair on the test set. License AutoDock Vina is released under a very permissive Apache license, with few restrictions on commercial or non-commercial use, or on the derivative works.
The text of the license can be found here. Video Tutorial.
Molecular docking with AutoDock Vina
Docking results are shown automatically in ViewDock. See also: AddH , Dock Prep The web service is a public shared resource, and this interface only allows docking a single ligand with very limited sampling. For a more intensive sampling of space, as needed for most research applications, or access to other options such as ligand database search, we recommend downloading the AutoDock Vina program and using it directly. Other limitations are given below.
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.
Note: Having rotatable bonds makes the search slower but may result in more realistic docking. You can activate or deactivate these rotatable bonds by clicking on the cylinders using the delegate editor. They will change colors when you switch their state. Green means the bond can rotate, and red means the bond cannot rotate. For the sake of the tutorial, we will deactivate some rotatable bonds. Select the delegate editor then click on a rotatable bond 2. Setting up the search grid The next step is to set the search grid.