We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
PredNTS: Improved and Robust Prediction of Nitrotyrosine Sites by Integrating Multiple Sequence Features.
- Authors
Nilamyani, Andi Nur; Auliah, Firda Nurul; Moni, Mohammad Ali; Shoombuatong, Watshara; Hasan, Md Mehedi; Kurata, Hiroyuki; de Brevern, Alexandre G.
- Abstract
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.
- Subjects
NITROTYROSINE; POST-translational modification; RANDOM forest algorithms; REACTIVE nitrogen species; BINARY sequences; MACHINE learning; NITRATION
- Publication
International Journal of Molecular Sciences, 2021, Vol 22, Issue 5, p2704
- ISSN
1661-6596
- Publication type
Article
- DOI
10.3390/ijms22052704