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.Graphical Abstract

Keywords

Deep Forest; Feature Extraction; Machine Learning; Prediction; Protein Phosphorylation

Published in

Journal of Biochemistry
2023,
Publisher: OXFORD UNIV PRESS

SLU Authors

• Mehrshad, Maliheh

  • Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences
    

UKÄ Subject classification

Biochemistry and Molecular Biology
Bioinformatics and Systems Biology


Publication identifier

DOI: https://doi.org/10.1093/jb/mvad116

Permanent link to this page (URI)

https://res.slu.se/id/publ/128278