Comparative study of several algorithms for flexible ligand docking
Comparative study of several algorithms for flexible ligand docking
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DOI：
10.1023/b:jcam.0000017496.76572.6f
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发表时间：
2003-11-01
影响因子：
3.5
通讯作者：
Brooks, CL
中科院分区：
文献类型：
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作者：
Bursulaya, BD;Totrov, M;Brooks, CL
我们已经对几种用于柔性分子对接的程序进行了比较评估：DOCK 4.0、FlexX 1.8、AutoDock 3.0、GOLD 1.2和ICM 2.8。这是通过两项不同的研究完成的：对37种蛋白质-配体复合物的数据集进行对接实验，并筛选包含10，037个条目的文库。基于相应的秩一解判断方法的对接精度。我们已经发现，对于AutoDock、DOCK、FlexX、GOLD和ICM，以可接受的准确度对接的分子分数分别为0.47、0.31、0.35、0.52和0.93。因此，ICM在配体对接这些受体时提供了最高的准确性。从其他程序的结果被发现是不太准确，大约相同的质量。速度比较表明，FlexX是最快的，AutoDock是最慢的测试对接程序。使用DOCK、FlexX和ICM进行数据库筛选。ICM能够在17个案例中识别总文库的前1%内的原始配体。DOCK和FlexX的相应数字分别为7和8。我们估计，在虚拟数据库筛选中，50%的潜在活性化合物将在ICM发现的约1.5%的最高评分溶液中以及DOCK和FlexX产生的约9%的最高评分溶液中发现。
We have performed a comparative assessment of several programs for flexible molecular docking: DOCK 4.0, FlexX 1.8, AutoDock 3.0, GOLD 1.2 and ICM 2.8. This was accomplished using two different studies: docking experiments on a data set of 37 protein-ligand complexes and screening a library containing 10,037 entries against 11 different proteins. The docking accuracy of the methods was judged based on the corresponding rank-one solutions. We have found that the fraction of molecules docked with acceptable accuracy is 0.47, 0.31, 0.35, 0.52 and 0.93 for, respectively, AutoDock, DOCK, FlexX, GOLD and ICM. Thus ICM provided the highest accuracy in ligand docking against these receptors. The results from the other programs are found to be less accurate and of approximately the same quality. A speed comparison demonstrated that FlexX was the fastest and AutoDock was the slowest among the tested docking programs. The database screening was performed using DOCK, FlexX and ICM. ICM was able to identify the original ligands within the top 1% of the total library in 17 cases. The corresponding number for DOCK and FlexX was 7 and 8, respectively. We have estimated that in virtual database screening, 50% of the potentially active compounds will be found among approximate to 1.5% of the top scoring solutions found with ICM and among approximate to 9% of the top scoring solutions produced by DOCK and FlexX.