Improving ligand-ranking of AutoDock Vina by changing the empirical parameters.
Sign Up to like & getrecommendations! Published in 2021 at "Journal of computational chemistry"
DOI: 10.1002/jcc.26779
Abstract: AutoDock Vina (Vina) achieved a very high docking-success rate, p ^ , but give a rather low correlation coefficient, R , for binding affinity with respect to experiments. This low correlation can be an obstacle… read more here.
Keywords: version; correlation; empirical parameters; autodock vina ... See more keywords
Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina
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DOI: 10.1002/minf.202200188
Abstract: Structure‐based virtual high‐throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographic structure, i. e.,… read more here.
Keywords: accuracy; exhaustiveness; ligand; size ... See more keywords
PeptoGrid—Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries
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DOI: 10.3390/molecules24020277
Abstract: Peptides are promising drug candidates due to high specificity and standout safety. Identification of bioactive peptides de novo using molecular docking is a widely used approach. However, current scoring functions are poorly optimized for peptide… read more here.
Keywords: autodock vina; peptogrid rescoring; peptide; peptide libraries ... See more keywords
Accelerating AutoDock Vina with GPUs
Sign Up to like & getrecommendations! Published in 2022 at "Molecules"
DOI: 10.3390/molecules27093041
Abstract: AutoDock Vina is one of the most popular molecular docking tools. In the latest benchmark CASF-2016 for comparative assessment of scoring functions, AutoDock Vina won the best docking power among all the docking tools. Modern… read more here.
Keywords: vina gpus; accelerating autodock; acceleration; autodock vina ... See more keywords