Masters Lily, Eagon Scott, Heying Michael
Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, CA, 93407, USA.
Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, CA, 93407, USA.
J Mol Graph Model. 2020 May;96:107532. doi: 10.1016/j.jmgm.2020.107532. Epub 2020 Jan 13.
We investigated the application of consensus scoring using the freely available and open source structure-based virtual screening docking programs AutoDock Vina, smina and idock. These individual programs and several simple consensus scoring methods were tested for their ability to identify hits against 20 DUD-E benchmark targets using the AUC and EF1 metrics. We found that all of the consensus scoring methods, however normalized, fared worse, on average, than simply using the output from a single program, smina. Additionally, the effect of a significant increase in the run time of all three programs was tested to find if a longer run time yielded improved results. Our results indicated that a longer run time than the default had little impact on the performance of these three programs or on consensus scoring methods based on their output. Thus, we have found that using the smina program alone at default settings is the best approach for researchers that do not have access to a suite of commercial docking software packages.
我们研究了使用免费开源的基于结构的虚拟筛选对接程序AutoDock Vina、smina和idock进行一致性评分的应用。这些单独的程序和几种简单的一致性评分方法，通过AUC和EF1指标，针对20个DUD-E基准靶点识别命中化合物的能力进行了测试。我们发现，所有的一致性评分方法，无论如何归一化，平均而言，都比简单使用单个程序smina的输出结果要差。此外，还测试了这三个程序运行时间显著增加的影响，以确定更长的运行时间是否能产生更好的结果。我们的结果表明，比默认运行时间更长对这三个程序的性能或基于其输出的一致性评分方法几乎没有影响。因此，我们发现，对于无法使用一套商业对接软件包的研究人员来说，在默认设置下单独使用smina程序是最佳方法。
