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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
TLDR
AutoDock Vina achieves an approximately two orders of magnitude speed‐up compared with the molecular docking software previously developed in the lab, while also significantly improving the accuracy of the binding mode predictions, judging by tests on the training set used in AutoDock 4 development. Expand
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
TLDR
AutoDock4 incorporates limited flexibility in the receptor and its utility in analysis of covalently bound ligands is reported, using both a grid‐based docking method and a modification of the flexible sidechain technique. Expand
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
TLDR
It is shown that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckerian genetic algorithm is the most efficient, reliable, and successful of the three. Expand
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
TLDR
It is shown that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckia genetic algorithm is the most efficient, reliable, and successful of the three. Expand
A semiempirical free energy force field with charge‐based desolvation
The authors describe the development and testing of a semiempirical free energy force field for use in AutoDock4 and similar grid‐based docking methods. The force field is based on a comprehensiveExpand
Reduced surface: an efficient way to compute molecular surfaces.
TLDR
A program called MSMS is shown to be fast and reliable in computing molecular surfaces, which relies on the use of the reduced surface that is briefly defined here and from which the solvent-accessible and solvent-excluded surfaces are computed. Expand
Automated docking of flexible ligands: Applications of autodock
TLDR
AutoDock is a suite of C programs used to predict the bound conformations of a small, flexible ligand to a macromolecular target of known structure and the enhancements included in the current release are described. Expand
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
TLDR
It is shown that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallography conformation when there are more degrees offreedom. Expand
Small-molecule library screening by docking with PyRx.
TLDR
This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems. Expand
Computational protein–ligand docking and virtual drug screening with the AutoDock suite
TLDR
This protocol covers the docking and virtual screening methods provided by the AutoDock suite of programs, including a basic docking of a drug molecule with an anticancer target, a virtual screen of this target with a small ligand library, docking with selective receptor flexibility, active site prediction and docking with explicit hydration. Expand
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