AutoDock web site. AutoDock Vina Video Tutorial! This video tutorial demonstrates molecular docking of imatinib using Vina with AutoDock Tools and PyMOL. Using AutoDock 4 and. Vina with. AutoDockTools: A Tutorial. Written by Ruth Huey, Garrett M. Morris and Stefano Forli. The Scripps Research. – AutoDock 4. Current version of AutoDock. Many parameters available to user. – AutoDock Vina. Rewritten by Oleg Trott, new approach to scoring.
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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. Ease of Use Vina’s design philosophy is not to require the user to understand its autoxock 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 tutroial 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 autodkck 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. Watching the video tutorial might be the best way to do that. What is the meaning or significance of the name “Vina”?
Why was it developed? Please see this mailing list post. How accurate is AutoDock Vina?
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 internallyand some other implementation tricks, such as precalculating the turorial between every atom type pair at every distance.
It also uses the same type of structure format PDBQT for maximum compatibility with auxiliary software. However, the source code, the scoring funcion and the actual algorithms used are brand new, so it’s more correct to think of Autpdock Vina as a new “generation” rather than “version” of AutoDock. However, for any given target, either program may provide a better result, even though AutoDock Vina is more likely to do so.
This is due to the fact that the scoring functions are different, and both autpdock inexact. It can also be used for viewing the results. Can I dock two proteins with AutoDock Vina?
You might be able to do that, but AutoDock Vina is designed only for receptor-ligand docking. There are better programs for protein-protein docking. Will Vina run on my bit machine? By design, modern bit machines can run bit binaries natively.
Why do I get “can not open vima. Oftentimes, file browsers hide the file tutorizl, so while you think you have a file ” conf. This setting can be changed in the control panel or system preferences.
You should also make sure that the file path you are providing is correct with respect to the directory folder you are in, e.
Why do I get “usage errors” when I try to follow the video tutorial? The command line options changed somewhat since the tutorial has been recorded. In particular, ” –out ” replaced ” –all “. Vina runs well on my machine, but when I run it on my exotic Linux cluster, I get a “boost thread resource” error.
Your Linux cluster is [inadvertantly] configured in such a way as to disallow spawning threads. Therefore, Vina can not run. Contact your system administrator.
Why is my docked conformation different from what you get in the video tutorial? The docking algorithm is non-deterministic.
Even though with this receptor-ligand pair, the minimum of the scoring function corresponds to the correct conformation, the docking algorithm sometimes fails to find it.
Try several times and see for yourself. Note that the probability of failing to find the mininum may be different with a different system. My docked conformation is the same, but my energies are different from what you get in the video tutorial. The scoring function has changed since the tutorial was recorded, but only in the part that is independent of the conformation: Why do my results look weird in PyMOL?
PDBQT is not a standard molecular structure format. The version of PyMOL used in the tutorial 0. This might not be the case for newer versions of PyMOL. Any other way to view the results?
As small as possible, but not smaller. The smaller the search space, the easier it is for the docking algorithm to explore it. On the other hand, it will not explore ligand and flexible side chain atom positions outside the search space.
You should probably avoid search spaces bigger than 30 x 30 x 30 Angstrom, unless you also increase ” –exhaustiveness “. This is probably because you intended to specify the search space sizes in “grid points” 0. The AutoDock Vina search space sizes are given in Angstroms instead.
If you really intended to use an unusually large search space, you can ignore this warning, but note that the search algorithm’s job may be harder.
AutoDock Vina – molecular docking and virtual screening program
You may need to increase the value of the exhaustiveness to make up for it. This will lead to longer run time.
The bound conformation looks reasonable, except for the hydrogens. AutoDock Vina actually uses a united-atom scoring function, i. Therefore, the positions of the hydrogens in the output are arbitrary. The hydrogens in the input file are used to decide which atoms can be hydrogen bond donors or acceptors though, so the correct protonation of the input structures is still important. What does “exhaustiveness” really control, under the hood?
In the current implementation, the docking calculation consists of a number of independent runsstarting from random conformations. Each of these runs consists of a number of sequential steps. Each step involves a random perturbation of the conformation followed by a local optimization using the Broyden-Fletcher-Goldfarb-Shanno algorithm and a selection in which the step is either accepted or not. Each local optimization involves many evaluations of the scoring function as well as its derivatives in the position-orientation-torsions coordinates.
The number of evaluations in a local optimization is guided by convergence and other criteria. The number of steps in a run is determined heuristically, depending on the size and flexibility of the ligand and the flexible side chains. However, the number of runs is set by the exhaustiveness parameter. Since the individual runs are executed in parallel, where appropriate, exhaustiveness also limits the parallelism.
These are merged, refined, clustered and sorted automatically to produce the final result. Why do I not get the correct bound conformation? It can be any of a number of things: If you are coming from AutoDock 4, a very common mistake is to specify the search space in “points” 0. Your ligand or receptor might not have been correctly protonated. Bad luck the search algorithm could have found the correct conformation with good probability, but was simply unlucky.
Try again with a different seed. The minimum of the scoring function correponds to the correct conformation, but the search algorithm has trouble finding it. In this case, higher exhaustiveness or smaller search space should help.
The minimum of the scoring function simply is not where the correct conformation is. Trying over and over again will not help, but may occasionally give the right answer if two wrongs inexact search and scoring make a right.
Docking autodokc an approximate approach. Related to the above, the culprit may also be the quality of the X-ray or NMR receptor structure. If you are not doing redocking, i.
The rings can only be rigid during docking.
AutoDock Vina Manual
Perhaps they have the wrong conformation, affecting the outcome. You are using a 2D flat ligand as input.
The actual bound conformation of the ligand may occasionally be different from what the X-ray or NMR structure shows. Other problems How can I tweak the scoring function? You can change the weights easily, by specifying them in the configuration file, or in the command line.