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This video tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL If you have never used AutoDock Vina before, please study the Video Tutorial before attempting to use it.

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The text of the license can be found here. Some of these projects average over 50 years worth of computation per day.Īverage time per receptor-ligand pair on the test set.ĪutoDock Vina is released under a very permissive Apache license, with few restrictions on commercial or non-commercial use, or on the derivative works.

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Qualified projects can run AutoDock Vina calculations for free on the massively parallelĮxisting projects using AutoDock Vina there include those targeting Īdditionally, Vina can take advantage of multiple CPUs or CPU cores on your system to significantly shorten its running time. Like in AutoDock 4, some receptor side chains can be chosen to be treated as flexible during docking.ĪutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude. 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.The invariance of the covalent bond lengths is automatically verified in the output structures.Attention is paid to checking the syntactic correctness of the input and reporting errors to the user in a lucid manner.By design, the results should not have a statistical bias related to the conformation of the input structure.The summary automatically remains in sync with the possible usage scenarios. The usage summary can be printed with ' vina -help'. Calculating grid maps and assigning atom charges is not needed.

All that is required is the structures of the molecules being docked and the specification of the search space including the binding site. Vina's design philosophy is not to require the user to understand its implementation details, tweak obscure search parameters, cluster results or know advanced algebra (quaternions). 'AutoDock' refers to AutoDock 4, and 'Vina' to AutoDock Vina 1. Other files, such as the AutoDock and AutoGrid parameter files (GPF, DPF) and grid map files are not needed.īinding mode prediction accuracy on the test set. PDBQT files can be generated (interactively or in batch mode) and viewed using MGLTools.

It should be noted that all six of the otherĭocking programs, to which it was compared, are distributed commercially.įor its input and output, Vina uses the same PDBQT molecular structure file format used by AutoDock. 'a strong competitor against the other programs, and at the top of the pack in many cases'. Īdditionally and independently, AutoDock Vina has been tested against a virtual screening benchmark called the Directory of Useful Decoys by the Watowich group, and was found to be 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.

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