Annotating nucleic acid-binding function based on protein structure
Annotating nucleic acid-binding function based on protein structure
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DOI：
10.1016/s0022-2836(03)00031-7
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发表时间：
2003-02-28
影响因子：
5.6
通讯作者：
Mandel-Gutfreund, Y
中科院分区：
文献类型：
--
作者：
Stawiski, EW;Gregoret, LM;Mandel-Gutfreund, Y
结构基因组学的许多目标将是与目前数据库中的蛋白质几乎或根本没有结构相似性的蛋白质。因此，需要新的功能预测方法，这种方法不依赖于与其他已知蛋白质的序列或折叠相似性。我们提出了一种自动化的方法来预测核酸结合(NA结合)蛋白，特别是DNA结合蛋白。该方法是基于表征DNA结合蛋白表面大的带正电荷的静电斑块的结构和序列性质，这些性质通常与DNA结合位点重合。使用从这些静电斑块中提取的特征集，我们可以高精度地预测DNA结合蛋白。我们表明，我们的方法不依赖于序列或结构同源性，并且能够预测新结合基序的蛋白质和在未结合状态下解决的蛋白质结构。我们的方法还可以将NA结合蛋白与其他蛋白质区分开来，这些蛋白质表面有类似的大正电荷斑，但不与核酸结合。(C)2003爱思唯尔科学有限公司。保留所有权利。
Many of the targets of structural genomics will be proteins with little or no structural similarity to those currently in the database. Therefore, novel function prediction methods that do not rely on sequence or fold similarity to other known proteins are needed. We present an automated approach to predict nucleic-acid-binding (NA-binding) proteins, specifically DNA-binding proteins. The method is based on characterizing the structural and sequence properties of large, positively charged electrostatic patches on DNA-binding protein surfaces, which typically coincide with the DNA-binding-sites. Using an ensemble of features extracted from these electrostatic patches, we predict DNA-binding proteins with high accuracy. We show that our method does not rely on sequence or structure homology and is capable of predicting proteins of novel-binding motifs and protein structures solved in an unbound state. Our method can also distinguish NA-binding proteins from other proteins that have similar, large positive electrostatic patches on their surfaces, but that do not bind nucleic acids. (C) 2003 Elsevier Science Ltd. All rights reserved.