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. 2020 Oct 24;21(21):7891.
doi: 10.3390/ijms21217891.

GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System

Chi-Wei Chen  1   2 , Lan-Ying Huang  2 , Chia-Feng Liao  2 , Kai-Po Chang  3   4 , Yen-Wei Chu  2   5   6   7   8   9
Affiliations

GasPhos: Protein Phosphorylation Site Prediction Using a New Feature Selection Approach with a GA-Aided Ant Colony System

Chi-Wei Chen et al. Int J Mol Sci. .

Abstract

Protein phosphorylation is one of the most important post-translational modifications, and many biological processes are related to phosphorylation, such as DNA repair, transcriptional regulation and signal transduction and, therefore, abnormal regulation of phosphorylation usually causes diseases. If we can accurately predict human phosphorylation sites, this could help to solve human diseases. Therefore, we developed a kinase-specific phosphorylation prediction system, GasPhos, and proposed a new feature selection approach, called Gas, based on the ant colony system and a genetic algorithm and used performance evaluation strategies focused on different kinases to choose the best learning model. Gas uses the mean decrease Gini index (MDGI) as a heuristic value for path selection and adopts binary transformation strategies and new state transition rules. GasPhos can predict phosphorylation sites for six kinases and showed better performance than other phosphorylation prediction tools. The disease-related phosphorylated proteins that were predicted with GasPhos are also discussed. Finally, Gas can be applied to other issues that require feature selection, which could help to improve prediction performance. GasPhos is available at http://predictor.nchu.edu.tw/GasPhos.

Keywords: ant colony system; feature selection; genetic algorithms; kinase; phosphorylation.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Comparison of conserved sequences and feature subsets.
Figure 2
Figure 2
Gas flowchart.
Figure 3
Figure 3
The path selection strategy adopted by Gas.
Figure 4
Figure 4
GasPhos flow chart.
See this image and copyright information in PMC

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