Some of these projects average over 50 years worth of computation per day.Īverage time per receptor-ligand pair on the test set.
Existing projects using AutoDock Vina there include those targeting AIDS, Malaria, Leishmaniasis and Schistosomiasis.
#Pymol tutorial and answers for free#
Qualified projects can run AutoDock Vina calculations for free on the massively parallel World Community Grid. Īdditionally, Vina can take advantage of multiple CPUs or CPU cores on your system to significantly shorten its running time. SpeedAutoDock Vina tends to be faster than AutoDock 4 by orders of magnitude. Like in AutoDock 4, some receptor side chains can be chosen to be treated as flexible during docking.
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 other docking 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. 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 “a strong competitor against the other programs, and at the top of the pack in many cases”.
Features AccuracyAutoDock 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.