Detection of Interactions between Proteins through Rotation Forest and Local Phase Quantization Descriptors

doi:10.3390/ijms17010021

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	Detection of Interactions between Proteins through Rotation Forest and Local Phase Quantization Descriptors
	Wong, Leon 1; You, Zhu-Hong 2; Ming, Zhong 1; Li, Jianqiang 1; Chen, Xing 3; Huang, Yu-An 1
	2016
发表期刊	INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN	1422-0067
卷号	17 期号:1 页码:11
摘要	Protein-Protein Interactions (PPIs) play a vital role in most cellular processes. Although many efforts have been devoted to detecting protein interactions by high-throughput experiments, these methods are obviously expensive and tedious. Targeting these inevitable disadvantages, this study develops a novel computational method to predict PPIs using information on protein sequences, which is highly efficient and accurate. The improvement mainly comes from the use of the Rotation Forest (RF) classifier and the Local Phase Quantization (LPQ) descriptor from the Physicochemical Property Response (PR) Matrix of protein amino acids. When performed on three PPI datasets including Saccharomyces cerevisiae, Homo sapiens, and Helicobacter pylori, we obtained good results of average accuracies of 93.8%, 97.96%, and 89.47%, which are much better than in previous studies. Extensive validations have also been explored to evaluate the performance of the Rotation Forest ensemble classifier with the state-of-the-art Support Vector Machine classifier. These promising results indicate that the proposed method might play a complementary role for future proteomics research.
关键词	protein-protein interaction Rotation Forest Physicochemical Property Response Matrix (PR) Local Phase Quantization
DOI	10.3390/ijms17010021
语种	英语
资助项目	National Science Foundation of China[61373086] ; National Science Foundation of China[61401385] ; National Science Foundation of China[11301517] ; Guangdong Natural Science Foundation[2014A030313555] ; Shenzhen Scientific Research and Development Funding Program[JCYJ20140418095735569]
WOS研究方向	Biochemistry & Molecular Biology ; Chemistry
WOS类目	Biochemistry & Molecular Biology ; Chemistry, Multidisciplinary
WOS记录号	WOS:000374583800021
出版者	MDPI AG
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/22811
专题	中国科学院数学与系统科学研究院
通讯作者	You, Zhu-Hong
作者单位	1.Shenzhen Univ, Coll Comp Sci & Software Engn, Shenzhen 518060, Peoples R China 2.China Univ Min & Technol, Sch Comp Sci & Technol, Xuzhou 221116, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Wong, Leon,You, Zhu-Hong,Ming, Zhong,et al. Detection of Interactions between Proteins through Rotation Forest and Local Phase Quantization Descriptors[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2016,17(1):11.
APA	Wong, Leon,You, Zhu-Hong,Ming, Zhong,Li, Jianqiang,Chen, Xing,&Huang, Yu-An.(2016).Detection of Interactions between Proteins through Rotation Forest and Local Phase Quantization Descriptors.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,17(1),11.
MLA	Wong, Leon,et al."Detection of Interactions between Proteins through Rotation Forest and Local Phase Quantization Descriptors".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 17.1(2016):11.