GraphPhos: Predict Protein-Phosphorylation Sites Based on Graph Neural Networks

Phosphorylation is one of the most common protein post-translational modifications. The identification of phosphorylation sites serves as the cornerstone for protein-phosphorylation-related research. This paper proposes a protein-phosphorylation site-prediction model based on graph neural networks named GraphPhos, which combines sequence features with structure features. Sequence features are derived from manual extraction and the calculation of protein pre-trained language models, and the structure feature is the secondary structure contact map calculated from protein tertiary structure. These features are then innovatively applied to graph neural networks. By inputting the features of the entire protein sequence and its contact graph, GraphPhos achieves the goal of predicting phosphorylation sites along the entire protein. Experimental results indicate that GraphPhos improves the accuracy of serine, threonine, and tyrosine site prediction by at least 8%, 15%, and 12%, respectively, exhibiting an average 7% improvement in accuracy compared to individual amino acid category prediction models.