Andi Nur NilamyaniFirda Nurul AuliahMohammad Ali MoniWatshara ShoombuatongMd Mehedi HasanHiroyuki KurataKyushu Institute of TechnologyJapan Society for the Promotion of ScienceMahidol UniversityUNSW Medicine2022-08-042022-08-042021-03-01International Journal of Molecular Sciences. Vol.22, No.5 (2021), 1-1114220067166165962-s2.0-85102048754https://repository.li.mahidol.ac.th/handle/20.500.14594/76264Nitrotyrosine, which is generated by numerous reactive nitrogen species, is a type of protein post-translational modification. Identification of site-specific nitration modification on tyro-sine 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.Mahidol UniversityBiochemistry, Genetics and Molecular BiologyChemical EngineeringChemistryComputer ScienceArticleSCOPUS10.3390/ijms22052704