Incorporating post translational modification information for enhancing the predictive performance of membrane transport proteins

Nguyen Quoc Khanh Le, Green Arther Sandag, Yu Yen Ou

研究成果: 雜誌貢獻文章同行評審

6 引文 斯高帕斯(Scopus)

摘要

Transporters involved in the cellular entry and exit of ions or molecules throughout the membrane proteins and thereby play an essential role in recognizing the immune system and energy transducers. According to their relevance in proteomics, numerous studies have been conducted to analyze the transporters; especially the discrimination of their classes and subfamilies. We realized that post translational modification information had a critical role in the process of transport proteins. Therefore, in this study, we aim to incorporate post translational information with radial basis function networks to improve the predictive performance of transport proteins in major classes (channels/pores, electrochemical transporters, and active transporters) and six different families (α-type channels, β-barrel porins, pore-forming toxins, porters, P–P bond hydrolysis-driven transporters, and oxidoreduction-driven transporters). The experiment results by using PSSM profiles combined with PTM information could classify the transporters into three classes and six families with five-fold cross-validation accuracy of 87.6% and 92.5%, respectively. For the independent dataset of 444 proteins, the performance with post translational modification attained the accuracy of 82.13% and 89.34% for classifying three classes and six families, respectively. Compared with the other methods and previous works, our result shows that the predictive performance is better with the accuracy improvement by 12%. We suggest that our study could become a robust model for biologists to discriminate transport proteins with high performance and understand better the function of transport proteins. Further, the contributions of this study could be fundamental for further research that can use PTM information to enhance numerous computational biology problems.
原文英語
頁(從 - 到)251-260
頁數10
期刊Computational Biology and Chemistry
77
DOIs
出版狀態已發佈 - 十二月 1 2018
對外發佈Yes

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

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