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SulSite-GTB: identification of protein S-sulfenylation sites by fusing multiple feature information and gradient tree boosting

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Abstract

Protein cysteine S-sulfenylation is an essential and reversible post-translational modification that plays a crucial role in transcriptional regulation, stress response, cell signaling and protein function. Studies have shown that S-sulfenylation is involved in many human diseases such as cancer, diabetes and arteriosclerosis. However, experimental identification of protein S-sulfenylation sites is generally expensive and time-consuming. In this study, we proposed a new protein S-sulfenylation sites prediction method SulSite-GTB. First, fusion of amino acid composition, dipeptide composition, encoding based on grouped weight, K nearest neighbors, position-specific amino acid propensity, position-weighted amino acid composition and pseudo-position specific score matrix feature extraction to obtain the initial feature space. Secondly, we use the synthetic minority oversampling technique (SMOTE) algorithm to process the class imbalance data, and the least absolute shrinkage and selection operator (LASSO) are employed to remove the redundant and irrelevant features. Finally, the optimal feature subset is input into the gradient tree boosting classifier to predict the S-sulfenylation sites, and the five-fold cross-validation and independent test set method are used to evaluate the prediction performance of the model. Experimental results showed the overall prediction accuracy is 92.86% and 88.53%, respectively, and the AUC values are 0.9706 and 0.9425, respectively, on the training set and the independent test set. Compared with other prediction methods, the results show that the proposed method SulSite-GTB is significantly superior to other state-of-the-art methods and provides a new idea for the prediction of post-translational modification sites of other proteins. The source code and all datasets are available at https://github.com/QUST-AIBBDRC/SulSite-GTB/.

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Acknowledgements

This work was supported by the National Nature Science Foundation of China (No. 61863010, 11771188), the Key Research and Development Program of Shandong Province of China (No. 2019GGX101001), and the Natural Science Foundation of Shandong Province of China (No. ZR2018MC007). This work used the Extreme Science and Engineering Discovery Environment, which is supported by the National Science Foundation (No. ACI-1548562).

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Authors and Affiliations

  1. College of Mathematics and Physics, Qingdao University of Science and Technology, Qingdao, 266061, China

    Minghui Wang, Xiaowen Cui, Bin Yu, Cheng Chen & Hongyan Zhou

  2. Artificial Intelligence and Biomedical Big Data Research Center, Qingdao University of Science and Technology, Qingdao, 266061, China

    Minghui Wang, Xiaowen Cui, Bin Yu, Cheng Chen & Hongyan Zhou

  3. School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China

    Bin Yu

  4. Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA

    Qin Ma

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  1. Minghui Wang
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Wang, M., Cui, X., Yu, B. et al. SulSite-GTB: identification of protein S-sulfenylation sites by fusing multiple feature information and gradient tree boosting. Neural Comput & Applic 32, 13843–13862 (2020). https://doi.org/10.1007/s00521-020-04792-z

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