Mathematical Biosciences and Engineering (Oct 2021)

Predicting S-nitrosylation proteins and sites by fusing multiple features

  • Wang-Ren Qiu ,
  • Qian-Kun Wang ,
  • Meng-Yue Guan,
  • Jian-Hua Jia,
  • Xuan Xiao

DOI
https://doi.org/10.3934/mbe.2021450
Journal volume & issue
Vol. 18, no. 6
pp. 9132 – 9147

Abstract

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Protein S-nitrosylation is one of the most important post-translational modifications, a well-grounded understanding of S-nitrosylation is very significant since it plays a key role in a variety of biological processes. For an uncharacterized protein sequence, it is a very meaningful problem for both basic research and drug development when we can firstly identify whether it is a S-nitrosylation protein or not, and then predict the specific S-nitrosylation site(s). This work has proposed two models for identifying S-nitrosylation protein and its PTM sites. Firstly, three kinds of features are extracted from protein sequence: KNN scoring of functional domain annotation, PseAAC and bag-of-words based on the physical and chemical properties of amino acids. Secondly, the synthetic minority oversampling technique is used to balance the data sets, and some state-of-the-art classifiers and feature fusion strategies are performed on the balanced data sets. In the five-fold cross-validation for predicting S-nitrosylation proteins, the results of Accuracy (ACC), Matthew's correlation coefficient (MCC) and area under ROC curve (AUC) are 81.84%, 0.5178, 0.8635, respectively. Finally, a model for predicting S-nitrosylation sites has been constructed on the basis of tripeptide composition (TPC) and the composition of k-spaced amino acid pairs (CKSAAP). To eliminate redundant information and improve work efficiency, elastic nets are employed for feature selection. The five-fold cross-validation tests have indicated the promising success rates of the proposed model. For the convenience of related researchers, the web-server named "RF-SNOPS" has been established at http://www.jci-bioinfo.cn/RF-SNOPS

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