Construction and test of ligand decoy sets using MDock: community structure-activity resource benchmarks for binding mode prediction.
Construction and test of ligand decoy sets using MDock: community structure-activity resource benchmarks for binding mode prediction.
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DOI：
10.1021/ci200080g
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发表时间：
2011-09-26
影响因子：
5.6
通讯作者：
Zou X
中科院分区：
文献类型：
--
作者：
Huang SY;Zou X
针对CSAR （Community Structure-Activity Resource）基准，分别使用MDock和DOCK程序构建了两组配体结合诱饵，分别用于刚性配体和柔性配体对接。基准测试中为每个复合物生成的诱饵完全覆盖了结合位点，并且还包含一定数量的近原生结合模式。利用配体结合诱饵集对一些评分函数进行了评估，以评估它们预测近原生结合模式的能力。其中，如果考虑到得分最高的结合模式，ITScore对刚性配体诱饵的预测成功率为86.7%，对柔性配体诱饵的预测成功率为79.7%，而成功预测的定义是与天然结构的RMSD < 2.0 Å。诱饵集可以作为评分函数的绑定模式预测的基准，可在CSAR网站（http://www.csardock.org/）上获得。
Two sets of ligand binding decoys have been constructed for the CSAR (Community Structure-Activity Resource) benchmark by using the MDock and DOCK programs for rigid-ligand and flexible-ligand docking, respectively. The decoys generated for each complex in the benchmark thoroughly cover the binding site and also contain a certain number of near-native binding modes. A few scoring functions have been evaluated using the ligand binding decoy sets for their abilities of predicting near-native binding modes. Among them, ITScore achieved a success rate of 86.7% for the rigid-ligand decoys and 79.7% for the flexible-ligand decoys, under the common definition of a successful prediction as RMSD < 2.0 Å from the native structure if the top-scored binding mode was considered. The decoy sets may serve as benchmarks for binding mode prediction of a scoring function, which are available at the CSAR website (http://www.csardock.org/).