DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.
DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions.
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DOI：
10.1093/nar/gkn332
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发表时间：
2008-07
影响因子：
14.9
通讯作者：
Skolnick, Jeffrey
中科院分区：
文献类型：
--
作者：
Gao, Mu;Skolnick, Jeffrey
DNA - 蛋白质复合物的结构阐明了不同蛋白质家族所示的DNA - 蛋白结合机制的多样性。基于DNA结合结构域（DBD猎人）的方法，用于识别DNA结合蛋白和相关的结合位点。我们得出的统计潜力的评估是为了描述DNA碱基对和蛋白质保留之间的相互作用。从相应的模板中推断出约4000蛋白的基准测试，我们的方法的精度为98％，精度为84％三种方法。最终，我们将方法应用于约1700个结构基因组学靶标，并预测37个具有以前未知功能的靶标可能是DNA结合蛋白。 DBD-Hunter免费提供，请访问http://cssb.biology.gatech.edu/skolnick/webservice/dbd-hunter/。
The structures of DNA–protein complexes have illuminated the diversity of DNA–protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge for predicting DNA–protein interactions. To address this issue, we have developed a knowledge-based method, DNA-binding Domain Hunter (DBD-Hunter), for identifying DNA-binding proteins and associated binding sites. The method combines structural comparison and the evaluation of a statistical potential, which we derive to describe interactions between DNA base pairs and protein residues. We demonstrate that DBD-Hunter is an accurate method for predicting DNA-binding function of proteins, and that DNA-binding protein residues can be reliably inferred from the corresponding templates if identified. In benchmark tests on ∼4000 proteins, our method achieved an accuracy of 98% and a precision of 84%, which significantly outperforms three previous methods. We further validate the method on DNA-binding protein structures determined in DNA-free (apo) state. We show that the accuracy of our method is only slightly affected on apo-structures compared to the performance on holo-structures cocrystallized with DNA. Finally, we apply the method to ∼1700 structural genomics targets and predict that 37 targets with previously unknown function are likely to be DNA-binding proteins. DBD-Hunter is freely available at http://cssb.biology.gatech.edu/skolnick/webservice/DBD-Hunter/.
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