A simple statistical method for discriminating outer membrane proteins with better accuracy
A simple statistical method for discriminating outer membrane proteins with better accuracy
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DOI：
10.1093/bioinformatics/bti126
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发表时间：
2005-04-01
期刊：
影响因子：
5.8
通讯作者：
Suwa, M
中科院分区：
文献类型：
--
作者：
Gromiha, MM;Suwa, M
动机：区分外膜蛋白从其他折叠类型的球状蛋白和膜蛋白是一个重要的任务，无论是从基因组序列中识别外膜蛋白，并成功地预测其二级和三级structure.Results：我们已经系统地分析了不同结构类别的球状蛋白和外膜蛋白的氨基酸组成。结果表明，外膜蛋白和球状蛋白的氨基酸残基Glu、His、Ile、Cys、Gln、Asn和Ser存在显著差异。基于这些信息，我们设计了一种统计方法，用于区分外膜蛋白与其他球状蛋白和膜蛋白。我们的方法正确地选择了外膜蛋白，对于337种蛋白质的训练集，准确率为89%。另一方面，我们的方法在674个蛋白质的非冗余数据集中以79%的准确度正确地排除了球状蛋白质。此外，本方法能够正确排除α-螺旋膜蛋白，准确度高达80%。这些准确度水平与文献中的其他方法相当，这是一种简单的方法，可用于从基因组序列中分离外膜蛋白。蛋白质的大小，结构类和特定残基的歧视的影响进行了讨论。
Motivation: Discriminating outer membrane proteins from other folding types of globular and membrane proteins is an important task both for identifying outer membrane proteins from genomic sequences and for the successful prediction of their secondary and tertiary structures.Results: We have systematically analyzed the amino acid composition of globular proteins from different structural classes and outer membrane proteins. We found that the residues, Glu, His, Ile, Cys, Gln, Asn and Ser, show a significant difference between globular and outer membrane proteins. Based on this information, we have devised a statistical method for discriminating outer membrane proteins from other globular and membrane proteins. Our approach correctly picked up the outer membrane proteins with an accuracy of 89% for the training set of 337 proteins. On the other hand, our method has correctly excluded the globular proteins at an accuracy of 79% in a non-redundant dataset of 674 proteins. Furthermore, the present method is able to correctly exclude alpha-helical membrane proteins up to an accuracy of 80%. These accuracy levels are comparable to other methods in the literature, and this is a simple method, which could be used for dissecting outer membrane proteins from genomic sequences. The influence of protein size, structural class and specific residues for discrimination is discussed.