A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
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DOI：
10.1093/bioinformatics/btn099
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发表时间：
2008-05-01
期刊：
影响因子：
5.8
通讯作者：
Zhao, Xuechun
中科院分区：
文献类型：
--
作者：
Li, Haiquan;Dai, Xinbin;Zhao, Xuechun
动机：膜转运蛋白在离子、小分子或大分子跨生物膜的输入和输出中起着至关重要的作用。目前，发表的计算工具数量有限，可以在昂贵的实验验证之前系统地发现和分类转运蛋白。为了解决这个问题，我们使用了最近邻方法，该方法将同源搜索和拓扑分析无缝集成到机器学习框架中。结果：我们的方法令人满意地区分了转运蛋白分类数据库中的484个转运蛋白家族，这是一个有代表性的转运蛋白数据库。对数据库进行5次交叉验证，平均阳性分类率为72.3。此外，该方法成功检测了7种模式生物和4种非模式生物的转运蛋白，范围从古生代到哺乳动物。基于文献的初步验证交叉验证了我们对11种生物的65.8个预测，其中55.9个预测与TransportDB中预测的83.6个转运蛋白重叠。可用性和补充信息：http://www.w3.org/1999/xlink">http://bioinfo.noble.org/manuscript-support/transporter/Contact: pzhao@noble.org。
Motivation: Membrane transport proteins play a crucial role in the import and export of ions, small molecules or macromolecules across biological membranes. Currently, there are a limited number of published computational tools which enable the systematic discovery and categorization of transporters prior to costly experimental validation. To approach this problem, we utilized a nearest neighbor method which seamlessly integrates homologous search and topological analysis into a machine-learning framework.Results: Our approach satisfactorily distinguished 484 transporter families in the Transporter Classification Database, a curated and representative database for transporters. A five-fold cross-validation on the database achieved a positive classification rate of 72.3 on average. Furthermore, this method successfully detected transporters in seven model and four non-model organisms, ranging from archaean to mammalian species. A preliminary literature-based validation has cross-validated 65.8 of our predictions on the 11 organisms, including 55.9 of our predictions overlapping with 83.6 of the predicted transporters in TransportDB.Availability and Supplementary information: http://www.w3.org/1999/xlink">http://bioinfo.noble.org/manuscript-support/transporter/Contact: pzhao@noble.org.