Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark,Journal of Chemical Information and Modeling

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Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2018-07-10 00:00:00 , DOI: 10.1021/acs.jcim.8b00312
Thomas Gaillard ₁

Affiliation

Computer-aided protein–ligand binding predictions are a valuable help in drug discovery. Protein–ligand docking programs generally consist of two main components: a scoring function and a search algorithm. It is of interest to evaluate the intrinsic performance of scoring functions, independently of conformational exploration, to understand their strengths and weaknesses and suggest improvements. The comparative assessment of scoring functions (CASF) provides such an evaluation. Here we add the AutoDock and Vina scoring functions to the CASF-2013 benchmark. We find that these popular, free software docking programs are generally in the first half (AutoDock) and first quarter (Vina) among all methods tested in CASF-2013. Vina is the best of all methods in terms of docking power. We also find that ligand minimization has an important impact, reducing the performance difference between AutoDock and Vina.

中文翻译：

根据CASF-2013基准评估AutoDock和AutoDock Vina

计算机辅助的蛋白质-配体结合预测在药物发现中提供了宝贵的帮助。蛋白质-配体对接程序通常由两个主要部分组成：评分功能和搜索算法。评估计分功能的内在性能（与构象探索无关），以了解其优缺点并提出改进建议是很有意思的。评分功能的比较评估（CASF）提供了这样的评估。在这里，我们将AutoDock和Vina评分功能添加到CASF-2013基准测试中。我们发现，在CASF-2013中测试的所有方法中，这些流行的免费软件对接程序通常位于上半年（AutoDock）和第一季度（Vina）中。就对接电源而言，Vina是所有方法中最好的。我们还发现配体最小化具有重要影响，

更新日期：2018-07-10

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