期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 22, 期 5, 页码 -出版社
MDPI
DOI: 10.3390/ijms22052704
关键词
nitrotyrosine; post-translational modification; feature encoding; RFE feature selection; machine learning
资金
- Japan Society for the Promotion of Science (JSPS) [19H04208, 19F19377]
- Grants-in-Aid for Scientific Research [19F19377] Funding Source: KAKEN
Nitrotyrosine, a type of protein post-translational modification, is generated by reactive nitrogen species. Computational prediction, such as the PredNTS predictor developed in this study, plays a vital role in understanding nitrated proteins before biological experimentation. The PredNTS predictor outperforms existing predictors and provides a useful computational resource for predicting nitrotyrosine sites.
Nitrotyrosine, which is generated by numerous reactive nitrogen species, is a type of protein post-translational modification. Identification of site-specific nitration modification on tyrosine is a prerequisite to understanding the molecular function of nitrated proteins. Thanks to the progress of machine learning, computational prediction can play a vital role before the biological experimentation. Herein, we developed a computational predictor PredNTS by integrating multiple sequence features including K-mer, composition of k-spaced amino acid pairs (CKSAAP), AAindex, and binary encoding schemes. The important features were selected by the recursive feature elimination approach using a random forest classifier. Finally, we linearly combined the successive random forest (RF) probability scores generated by the different, single encoding-employing RF models. The resultant PredNTS predictor achieved an area under a curve (AUC) of 0.910 using five-fold cross validation. It outperformed the existing predictors on a comprehensive and independent dataset. Furthermore, we investigated several machine learning algorithms to demonstrate the superiority of the employed RF algorithm. The PredNTS is a useful computational resource for the prediction of nitrotyrosine sites. The web-application with the curated datasets of the PredNTS is publicly available.
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