Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures
Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures
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DOI：
10.1002/prot.22067
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发表时间：
2008-11-01
影响因子：
2.9
通讯作者：
Shimizu, Kentaro
中科院分区：
文献类型：
--
作者：
Morita, Mizuki;Nakamura, Shugo;Shimizu, Kentaro
本文介绍了一种预测蛋白质配体结合位点的新方法。该方法包括计算蛋白质与放置在蛋白质表面的探针之间的范德华相互作用能，然后将具有吸引相互作用的探针聚类，以找到能量最有利的位点。在80%（28/35）的测试案例中，成功预测配体结合位点在配体结合的蛋白质结构上，77%（27/35）的测试案例成功预测非配体结合结构上的配体结合位点。我们的方法被用来成功地预测不受诱导拟合影响的配体结合位点，只要它的尺度不是很大，它有助于显著提高对非结合状态蛋白质结构的预测。这代表了在检测非特征蛋白质上的配体结合位点方面的传统方法的重大进步。此外，与传统方法相比，我们的方法可以预测更窄的配体结合位点。
This article describes a new method for predicting ligand-binding sites of proteins. The method involves calculating the van der Waals interaction energy between a protein and probes placed on the protein surface, and then clustering the probes with attractive interaction to find the energetically most favorable locus. In 80% (28/35) of the test cases, the ligand-binding site was successfully predicted on a ligand-bound protein structure, and in 77% (27/35) was successfully predicted on an unbound structure. Our method was used to successfully predict ligand-binding sites unaffected by induced-fit as long as its scales were not very large, and it contributed to a significant improvement in prediction with unbound state protein structures. This represents a significant advance over conventional methods in detecting ligand-binding sites on uncharacterized proteins. Moreover, our method can predict ligand-binding sites with a narrower locus than those achieved using conventional methods.