Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina.
Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina.
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DOI：
10.1371/journal.pone.0011955
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发表时间：
2010-08-04
期刊：
影响因子：
3.7
通讯作者：
Torbett BE
中科院分区：
文献类型：
--
作者：
Chang MW;Ayeni C;Breuer S;Torbett BE
AutoDock 系列软件已广泛应用于蛋白质-配体对接研究。本研究在虚拟筛选的背景下比较了 AutoDock 4 和 AutoDock Vina，通过使用这些程序来选择对 HIV 蛋白酶具有活性的化合物。这两个程序都用于对两个化学库的成员进行排名，每个化学库都包含经过实验验证的 HIV 蛋白酶结合物。在 NCI Diversity Set II 的情况下，AutoDock 4 和 Vina 都能够比随机更好地选择活性化合物（AUC 分别= 0.69 和 0.68；p<0.001）。在这种情况下，结合能预测高度相关，r = 0.63 和ι = 0.82。对于通用诱饵目录中的一组更大、更灵活的化合物，结合能预测不相关，只有 Vina 能够比随机排序更好地对化合物进行排序。在对具有很少可旋转键的较小分子进行排序时，AutoDock 4 和 Vina 的能力相当，尽管两者在评分中都表现出与大小相关的偏差。然而，由于 Vina 的执行速度更快，并且能够更准确地对较大的分子进行排序，研究人员在进行虚拟屏幕时应该首先关注它。
The AutoDock family of software has been widely used in protein-ligand docking research. This study compares AutoDock 4 and AutoDock Vina in the context of virtual screening by using these programs to select compounds active against HIV protease. Both programs were used to rank the members of two chemical libraries, each containing experimentally verified binders to HIV protease. In the case of the NCI Diversity Set II, both AutoDock 4 and Vina were able to select active compounds significantly better than random (AUC = 0.69 and 0.68, respectively; p<0.001). The binding energy predictions were highly correlated in this case, with r = 0.63 and ι = 0.82. For a set of larger, more flexible compounds from the Directory of Universal Decoys, the binding energy predictions were not correlated, and only Vina was able to rank compounds significantly better than random. In ranking smaller molecules with few rotatable bonds, AutoDock 4 and Vina were equally capable, though both exhibited a size-related bias in scoring. However, as Vina executes more quickly and is able to more accurately rank larger molecules, researchers should look to it first when undertaking a virtual screen.
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影响因子：
5.6
作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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DOI：
10.1021/ci020055f
发表时间：
2003-01-01
期刊：
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
影响因子：
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作者：
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通讯作者：
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影响因子：
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作者：
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通讯作者：
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