Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
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DOI：
10.1016/j.sbi.2013.01.009
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发表时间：
2013-04-01
影响因子：
6.8
通讯作者：
Gao, Mu
中科院分区：
文献类型：
--
作者：
Skolnick, Jeffrey;Zhou, Hongyi;Gao, Mu
最近发展起来的配体同源性建模（LHM）领域将蛋白质同源性建模的思想扩展到配体结合位点的预测和用于虚拟配体筛选，已经成为一种强大的新方法。与传统的对接方法不同，LHM可以应用于低到中等分辨率的预测以及实验结构，性能几乎没有降低，从而使平均蛋白质组的75%具有潜在的重要虚拟筛选预测。在大规模基准测试中，LHM能够预测脱靶配体结合。因此，尽管普遍认为相反，低至中等分辨率预测的结构具有相当大的实用性的生化功能预测。
The recently developed field of ligand homology modeling (LHM) that extends the ideas of protein homology modeling to the prediction of ligand binding sites and for use in virtual ligand screening has emerged as a powerful new approach. Unlike traditional docking methodologies, LHM can be applied to low-to-moderate resolution predicted as well as experimental structures with little if any diminution in performance; thereby enabling similar to 75% of an average proteome to have potentially significant virtual screening predictions. In large scale benchmarking, LHM is able to predict off-target ligand binding. Thus, despite the widespread belief to the contrary, low-to-moderate resolution predicted structures have considerable utility for biochemical function prediction.