using amino acid physicochemical distance transformation for fast protein remote homology detection使用氨基酸理化距离变换快速远程同源蛋白质检测.pdfVIP

Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection 1,2 1,2 1,2 3 4 Bin Liu *, Xiaolong Wang , Qingcai Chen , Qiwen Dong , Xun Lan 1 School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, People’s Republic of China, 2 Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, People’s Republic of China, 3 School of Computer Science, Fudan University, Shanghai, People’s Republic of China, 4 Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America Abstract Protein remote homology detection is one of the most important problems in bioinformatics. Discriminative methods such as support vector machines (SVM) have shown superior performance. However, the performance of SVM-based methods depends on the vector representations of the protein sequences. Prior works have demonstrated that sequence-order effects are relevant for discrimination, but little work has explored how to incorporate the sequence-order information along with the amino acid physicochemical properties into the prediction. In order to incorporate the sequence-order effects into the protein remote homology detection, the physicochemical distance transformation (PDT) method is proposed. Each protein sequence is converted into a series of numbers by using the physicochemical property scores in the amino acid index (AAIndex), and then the sequence is converted into a fixed length vector by PDT. The sequence-order information can be efficiently included into the feature vector with little com