Benchmarking sets for molecular docking
Benchmarking sets for molecular docking
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DOI：
10.1021/jm0608356
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发表时间：
2006-11-16
影响因子：
7.3
通讯作者：
Irwin, John J.
中科院分区：
文献类型：
--
作者：
Huang, Niu;Shoichet, Brian K.;Irwin, John J.
配体富集是分子对接的关键指标。为了避免偏差，诱饵应该在物理上类似于配体，这样富集就不是简单地分离表面特征，而是在化学上与它们不同，因此它们不太可能是粘合剂。我们已经组装了一个有用的诱饵目录（DUD），包含2950个配体，用于40个不同的目标。每个配体都有36个物理上相似但拓扑结构不同的诱饵分子，从而形成了一个包含98 266种化合物的数据库。对于大多数目标，使用未校正的数据库（如MDDR）的富集程度至少比使用DUD高半个log，这是前者存在偏差的证据。这些计算还允许40 x 40交叉对接，其中每个配体集的富集程度可以对所有40个靶标进行比较，从而实现对接筛选的特异性度量。DUD作为对接的基准测试集可以在http://blaster.docking.org/dud/上免费在线获得。
Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys ( DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98 266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40 x 40 cross- docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/.