{"title":"DF-Phos: Prediction of Protein Phosphorylation Sites by Deep Forest.","authors":"Zeynab Zahiri, Nasser Mehrshad, Maliheh Mehrshad","doi":"10.1093/jb/mvad116","DOIUrl":null,"url":null,"abstract":"<p><p>Phosphorylation is the most important and studied post-translational modification (PTM), which plays a crucial role in protein function studies and experimental design. Many significant studies have been performed to predict phosphorylation sites using various machine-learning methods. Recently, several studies have claimed that deep learning-based methods are the best way to predict the phosphorylation sites because deep learning as an advanced machine learning method can automatically detect complex representations of phosphorylation patterns from raw sequences and thus offers a powerful tool to improve phosphorylation site prediction. In this study, we report DF-Phos, a new phosphosite predictor based on the Deep Forest to predict phosphorylation sites. In DF-Phos, the feature vector taken from the CkSAApair method is as input for a Deep Forest framework for predicting phosphorylation sites. The results of 10-fold cross-validation show that the Deep Forest method has the highest performance among other available methods. We implemented a Python program of DF-Phos, which is freely available for non-commercial use at https://github.com/zahiriz/DF-Phos Moreover, users can use it for various PTM predictions.</p>","PeriodicalId":15234,"journal":{"name":"Journal of biochemistry","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of biochemistry","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/jb/mvad116","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Phosphorylation is the most important and studied post-translational modification (PTM), which plays a crucial role in protein function studies and experimental design. Many significant studies have been performed to predict phosphorylation sites using various machine-learning methods. Recently, several studies have claimed that deep learning-based methods are the best way to predict the phosphorylation sites because deep learning as an advanced machine learning method can automatically detect complex representations of phosphorylation patterns from raw sequences and thus offers a powerful tool to improve phosphorylation site prediction. In this study, we report DF-Phos, a new phosphosite predictor based on the Deep Forest to predict phosphorylation sites. In DF-Phos, the feature vector taken from the CkSAApair method is as input for a Deep Forest framework for predicting phosphorylation sites. The results of 10-fold cross-validation show that the Deep Forest method has the highest performance among other available methods. We implemented a Python program of DF-Phos, which is freely available for non-commercial use at https://github.com/zahiriz/DF-Phos Moreover, users can use it for various PTM predictions.
期刊介绍:
The Journal of Biochemistry founded in 1922 publishes the results of original research in the fields of Biochemistry, Molecular Biology, Cell, and Biotechnology written in English in the form of Regular Papers or Rapid Communications. A Rapid Communication is not a preliminary note, but it is, though brief, a complete and final publication. The materials described in Rapid Communications should not be included in a later paper. The Journal also publishes short reviews (JB Review) and papers solicited by the Editorial Board.