基于修正的伪氨基酸组成预测氧化还原酶辅酶类型.doc

基于修正的伪氨基酸组成预测氧化还原酶辅酶类型张光亚李红春方柏山华侨大学生物工程与技术系泉州 362021: 从出发快速确定氧化还原酶的辅酶依赖类型对于了解其结构和功能、催化机制及构建辅酶再生体系具有重要指导作用。伪氨基酸组成方法并用于提取氧化还原酶序列特征值采用k-近邻算法预测其辅酶依赖类型。当λ=48, w=0.1时10倍交叉验证结果表明其ROC曲线下面积为0.9536预测精度达92.0比最优条件下伪氨基酸组成预测精度提高了3.5与其他7种常见特征值提取方法相比修正的伪氨基酸组成表现最好。结果从序列出发预测氧化还原酶辅酶依赖类型是可行的且修正的伪氨基酸组成可望成为一种新的有效提取蛋白质序列特征值方法。: 氧化还原酶辅酶依赖类型修正的伪氨基酸组成k-近邻ROC曲线下面积redicting the Cofactors of Oxidoreductases by the Modified Pseudo-amino Acid Composition Guangya Zhang, Hongchun Li, and Baishan Fang TInstitute of Industrial Biotechnology, Huaqiao University, Quanzhou 362021, ChinaT Abstract: Types of cofactor independency for newly found oxidoreductases sequences are usually determined by experimental analysis. These experimental methods are both time-consuming and costly. With the explosion of oxidoreductases sequences entering into the databanks, it is highly desirable to explore the feasibility of selectively classifying newly found oxidoreductases into their respective cofactor independency classes by means of an automated method. In this study, we proposed a modified Chou’s pseudo-amino acid composition method to extract features from sequences and the k-nearest neighbor was used as the classifier, and the results were very encouraging. When ?=48, w=0.1, the areas under the ROC curve of k-nearest neighbor in 10-fold cross-validation was 0.9536; and the success rate was 92.0%, which was 3.5% higher than that of pseudo-amino acid composition. It was also better than all the other 7 feature extraction methods. Our results showed that predicting the cofactors of oxidoreductases was feasible and the modified pseudo-amino acid composition method may be a useful method for extracting features from protein sequences. Keywords: oxidoreductases, cofactor independency type, modified pseudo-amino acid composition, k-nearest neighbor, areas under the ROC curve 在国际生物化学联合会划分的大类酶中, 约35%为氧化还原酶, 由于氧化还原酶在催化制备手性醇、羟基酸、氨基酸方面显示出极大的优势, 因此在制药、食品、精细化工、农药等领