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Prediction of Drug-Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures
Meng, FR (Meng, Fan-Rong); You, ZH (You, Zhu-Hong); Chen, X (Chen, Xing); Zhou, Y (Zhou, Yong); An, JY (An, Ji-Yong)
2017
Source PublicationMOLECULES
ISSN1420-3049
Volume22Issue:7Pages:1-13
Abstract

Knowledge of drug-target interaction (DTI) plays an important role in discovering new drug candidates. Unfortunately, there are unavoidable shortcomings; including the time-consuming and expensive nature of the experimental method to predict DTI. Therefore, it motivates us to develop an effective computational method to predict DTI based on protein sequence. In the paper, we proposed a novel computational approach based on protein sequence, namely PDTPS (Predicting Drug Targets with Protein Sequence) to predict DTI. The PDTPS method combines Bi-gram probabilities (BIGP), Position Specific Scoring Matrix (PSSM), and Principal Component Analysis (PCA) with Relevance Vector Machine (RVM). In order to evaluate the prediction capacity of the PDTPS, the experiment was carried out on enzyme, ion channel, GPCR, and nuclear receptor datasets by using five-fold cross-validation tests. The proposed PDTPS method achieved average accuracy of 97.73%, 93.12%, 86.78%, and 87.78% on enzyme, ion channel, GPCR and nuclear receptor datasets, respectively. The experimental results showed that our method has good prediction performance. Furthermore, in order to further evaluate the prediction performance of the proposed PDTPS method, we compared it with the state-of-the-art support vector machine (SVM) classifier on enzyme and ion channel datasets, and other exiting methods on four datasets. The promising comparison results further demonstrate that the efficiency and robust of the proposed PDTPS method. This makes it a useful tool and suitable for predicting DTI, as well as other bioinformatics tasks.

KeywordDti Rvm Bigp Pca
DOI10.3390/molecules22071119
Indexed BySCI
WOS IDWOS:000406621300093
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Document Type期刊论文
Identifierhttp://ir.xjipc.cas.cn/handle/365002/5056
Collection多语种信息技术研究室
Corresponding AuthorYou, ZH (You, Zhu-Hong)
Affiliation1.China Univ Min & Technol, Sch Comp Sci & Technol, Xuzhou 21116, Peoples R China
2.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi 830011, Peoples R China
3.China Univ Min & Technol, Sch Informat & Control Engn, Xuzhou 21116, Peoples R China
Recommended Citation
GB/T 7714
Meng, FR ,You, ZH ,Chen, X ,et al. Prediction of Drug-Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures[J]. MOLECULES,2017,22(7):1-13.
APA Meng, FR ,You, ZH ,Chen, X ,Zhou, Y ,&An, JY .(2017).Prediction of Drug-Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures.MOLECULES,22(7),1-13.
MLA Meng, FR ,et al."Prediction of Drug-Target Interaction Networks from the Integration of Protein Sequences and Drug Chemical Structures".MOLECULES 22.7(2017):1-13.
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