Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters.
Characterization and prediction of the binding site in DNA-binding proteins: improvement of accuracy by combining residue composition, evolutionary conservation and structural parameters.
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DOI：
10.1093/nar/gks405
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发表时间：
2012-08
影响因子：
14.9
通讯作者：
Chakrabarti P
中科院分区：
文献类型：
--
作者：
Dey S;Pal A;Guharoy M;Sonavane S;Chakrabarti P
我们提出了一组四个参数，在组合中可以预测DNA结合蛋白质结构上的残基的高度准确性。这些是进化保守残基的数量（Ncons）及其空间聚类（ρe）、氢键供体能力（Dp）和残基倾向（Rp）。我们首先使用这些参数来表征一组126个DNA结合蛋白（DBP）中的130个界面。然后分析这些参数单独和组合的适用性，以区分真正的结合区域与蛋白质表面的其余部分。在83%的情况下，RP显示出识别真实接口的最佳性能，排名第一。重要的是，我们还使用了蛋白质-DNA对接基准的未绑定-绑定测试用例来测试我们方法的有效性。当应用于非结合形式的DBPs时，Rp可以区分86%的情况。最后，我们应用支持向量机的方法来识别界面区域使用上述参数沿着与个人的氨基酸组成作为属性。预测的准确性为90.5%的结合结构和93.6%的未结合形式的蛋白质。
We present a set of four parameters that in combination can predict DNA-binding residues on protein structures to a high degree of accuracy. These are the number of evolutionary conserved residues (Ncons) and their spatial clustering (ρe), hydrogen bond donor capability (Dp) and residue propensity (Rp). We first used these parameters to characterize 130 interfaces in a set of 126 DNA-binding proteins (DBPs). The applicability of these parameters both individually and in combination, to distinguish the true binding region from the rest of the protein surface was then analyzed. Rp shows the best performance identifying the true interface with the top rank in 83% cases. Importantly, we also used the unbound-bound test cases of the protein–DNA docking benchmark to test the efficacy of our method. When applied to the unbound form of the DBPs, Rp can distinguish 86% cases. Finally, we have applied the SVM approach for recognizing the interface region using the above parameters along with the individual amino acid composition as attributes. The accuracy of prediction is 90.5% for the bound structures and 93.6% for the unbound form of the proteins.
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影响因子：
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作者：
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