AutoDock Vina AutoDock Vina is a new open-source program for drug discovery, molecular docking and virtual screening, offering multi-core capability, high performance and enhanced accuracy and ease of use.[1] AutoDock Vina has been designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The Scripps Research Institute. 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

O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461

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.[*] Additionally 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 "a strong competitor against the other programs, and at the top of the pack in many cases". It should be noted that all six of the other docking programs, to which it was compared, are distributed commercially. AutoDock Tools Compatibility For its input and output, Vina uses the same PDBQT molecular structure file format used by AutoDock. PDBQT files can be generated (interactively or in batch mode) and viewed using MGLTools. Other files, such as the AutoDock and AutoGrid parameter files (GPF, DPF) and grid map files are not needed.

Binding mode prediction accuracy on the test set. "AutoDock" refers to AutoDock 4, and "Vina" to AutoDock Vina 1.

Ease of Use

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). 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.

Speed AutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude.[*] Multiple CPUs/Cores Vina can take advantage of multiple CPUs or CPU cores on your system to significantly shorten its running time. Reproducibility Given the same binary version of the program, the same input, options and random seed, the results should be reproducible with any value of "cpu".

Average time per receptor-ligand pair on the test set. "AutoDock" refers to AutoDock 4, and "Vina" to AutoDock Vina 1.

License

Video Tutorial

This video tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL

Questions?