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Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform
Chen, ZH (Chen, Zhan-Heng)[ 1,2 ]; You, ZH (You, Zhu-Hong)[ 1,2 ]; Li, LP (Li, Li-Ping)[ 1 ]; Wang, YB (Wang, Yan-Bin)[ 1 ]; Wong, L (Wong, Leon)[ 1,2 ]; Yi, HC (Yi, Hai-Cheng)[ 1,2 ]
2019
Source PublicationINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN1422-0067
Volume20Issue:4Pages:1-15
Abstract

It is significant for biological cells to predict self-interacting proteins (SIPs) in the field of bioinformatics. SIPs mean that two or more identical proteins can interact with each other by one gene expression. This plays a major role in the evolution of proteinprotein interactions (PPIs) and cellular functions. Owing to the limitation of the experimental identification of self-interacting proteins, it is more and more significant to develop a useful biological tool for the prediction of SIPs from protein sequence information. Therefore, we propose a novel prediction model called RP-FFT that merges the Random Projection (RP) model and Fast Fourier Transform (FFT) for detecting SIPs. First, each protein sequence was transformed into a Position Specific Scoring Matrix (PSSM) using the Position Specific Iterated BLAST (PSI-BLAST). Second, the features of protein sequences were extracted by the FFT method on PSSM. Lastly, we evaluated the performance of RP-FFT and compared the RP classifier with the state-of-the-art support vector machine (SVM) classifier and other existing methods on the human and yeast datasets; after the five-fold cross-validation, the RP-FFT model can obtain high average accuracies of 96.28% and 91.87% on the human and yeast datasets, respectively. The experimental results demonstrated that our RP-FFT prediction model is reasonable and robust.

Keywordself-interacting proteins position-specific scoring matrix fast Fourier transform random projection
DOI10.3390/ijms20040930
Indexed BySCI
WOS IDWOS:000460805400138
Citation statistics
Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.xjipc.cas.cn/handle/365002/5729
Collection多语种信息技术研究室
Corresponding AuthorYou, ZH (You, Zhu-Hong)[ 1,2 ]
Affiliation1.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi 830011, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
Recommended Citation
GB/T 7714
Chen, ZH ,You, ZH ,Li, LP ,et al. Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2019,20(4):1-15.
APA Chen, ZH ,You, ZH ,Li, LP ,Wang, YB ,Wong, L ,&Yi, HC .(2019).Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,20(4),1-15.
MLA Chen, ZH ,et al."Prediction of Self-Interacting Proteins from Protein Sequence Information Based on Random Projection Model and Fast Fourier Transform".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 20.4(2019):1-15.
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