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Open AccessFeature PaperArticle

Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening

[email protected], BioSIM—Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal
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Appl. Sci. 2019, 9(21), 4538; https://doi.org/10.3390/app9214538
Received: 3 October 2019 / Revised: 18 October 2019 / Accepted: 21 October 2019 / Published: 25 October 2019
(This article belongs to the Section Applied Biosciences and Bioengineering)
AutoDock and Vina are two of the most widely used protein–ligand docking programs. The fact that these programs are free and available under an open source license, also makes them a very popular first choice for many users and a common starting point for many virtual screening campaigns, particularly in academia. Here, we evaluated the performance of AutoDock and Vina against an unbiased dataset containing 102 protein targets, 22,432 active compounds and 1,380,513 decoy molecules. In general, the results showed that the overall performance of Vina and AutoDock was comparable in discriminating between actives and decoys. However, the results varied significantly with the type of target. AutoDock was better in discriminating ligands and decoys in more hydrophobic, poorly polar and poorly charged pockets, while Vina tended to give better results for polar and charged binding pockets. For the type of ligand, the tendency was the same for both Vina and AutoDock. Bigger and more flexible ligands still presented a bigger challenge for these docking programs. A set of guidelines was formulated, based on the strengths and weaknesses of both docking program and their limits of validation. View Full-Text
Keywords: AutoDock 4; AutoDock Vina; molecular docking; CADD; virtual screening; computational chemistry AutoDock 4; AutoDock Vina; molecular docking; CADD; virtual screening; computational chemistry
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Vieira, T.F.; Sousa, S.F. Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening. Appl. Sci. 2019, 9, 4538.

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