AutoDock Vina: a turnkey computational docking program based on a simple scoring function and rapid gradient-optimization conformational. Using AutoDock 4 and. Vina with. AutoDockTools: A Tutorial. Written by Ruth Huey, Garrett M. Morris and Stefano Forli. The Scripps Research. AutoDock Vina is an open-source program for doing molecular docking. It was designed and implemented by Dr. Oleg Trott in the Molecular Graphics Lab at The.
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Computational protein-ligand docking and virtual drug screening with the AutoDock suite
Most of these methods simplify the problem in two ways to make the computation tractable. First, the conformational space is reduced by imposing autodock vina to the system, such as a rigid receptor and fixed bond angles and lengths in the ligand.
Second, a simplified scoring function, often based on empirical free energies of binding, is used to score poses quickly at each step of the conformation search. Both of these are serious limitations, and users must employ tools such as molecular dynamics or free energy perturbation autodock vina a more realistic conformational search or energy prediction is necessary.
These tools are complementary with computational docking methods, since docking methods generally search a larger conformational space, but more advanced methods can predict conformation and energy more accurately within a local area of the conformational landscape.
Advanced docking methods may be used to improve results in cases where the limitations of requiring a rapid method for energy evaluation are too restrictive.
AutoDock - Wikipedia
For autodock vina, many docking methods employ a rigid model for the receptor, which often leads to improper results for proteins with appreciable induced fit upon binding.
AutoDock includes a method for treating a selection of receptor sidechains explicitly, to account for limited conformational changes in the receptor.
In addition, ordered water molecules often mediate interactions between ligands and receptors, and advanced methods for treating selected autodock vina explicitly have been implemented in AutoDock.
Both of these advanced methods are demonstrated in this protocol. Many reports autodock vina compared the performance of popular docking methods such as AutoDock recently reviewed by Sousa et al.
Different methods can achieve different success rates depending on specific targets, but in general, they all perform similarly when tested on a series of diverse protein-ligand complexes: Autodock vina results may be obtained by tuning the docking method for a particular system or moving to more sophisticated and computationally-intensive parameterizations of the system.
Applications of the Protocol The AutoDock suite is used in numerous laboratories: We have applied the AutoDock suite to a number of autodock vina problems in collaboration with researchers, showing some of the scope of uses. The first versions of AutoDock were used to explore the binding of substrates to the enzyme aconitase 8and docked conformations were 8 used to help interpret crystallographic density maps and to explore intermediates in the reaction.
Results of several similar studies on proteins and their substrates were reported in the following years 9 — We have also used the Autodock suite as a tool for drug design and virtual screening against a number of targets, including HIV protease 12 — 14tuberculosis targets 1516and beta-secretase 17 AutoLigand was used to identify druggable sites for stabilizing a protein-protein interface 19 and covalent docking was used to explore covalent inhibitors of protein tyrosine phosphatases AutoDock and AutoDock Vina Two docking methods have been developed in parallel, to autodock vina to two different needs.
Development began with AutoDock 2352122 autodock vina, and it continues to be the platform for experimentation in docking methods. It is highly optimized to perform docking experiments using well-tested default methods.
Both methods are currently freely available. AutoDock Vina is fast and effective for most systems, while AutoDock is autodock vina for systems that require additional methodological enhancements.
Both methods are designed to be generic computational docking tools, accepting coordinate files for receptor and ligand, and autodock vina optimal docked conformations.