Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark
Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark
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DOI：
10.1021/acs.jcim.8b00312
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发表时间：
2018-08-01
影响因子：
5.6
通讯作者：
Gaillard, Thomas
中科院分区：
文献类型：
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作者：
Gaillard, Thomas
计算机辅助蛋白质配体结合预测在药物发现中是有价值的帮助。蛋白质配体对接程序通常由两个主要部分组成：评分函数和搜索算法。这是感兴趣的评价评分功能的内在性能，独立于构象探索，了解他们的长处和短处，并提出改进建议。评分函数的比较评估（CASF）提供了这样的评价。这里我们将AutoDock和维纳评分功能添加到CASF-2013基准测试中。我们发现，这些流行的，免费的软件对接程序一般是在上半年（AutoDock）和第一季度（维纳）在CASF-2013测试的所有方法。维纳在对接功率方面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，减少了AutoDock和维纳之间的性能差异。
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.