IPs-GRUAtt: An attention-based bidirectional gated recurrent unit network for predicting phosphorylation sites of SARS-CoV-2 infection

Abstract

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has generated tremendous concern and poses a serious threat to international public health. Phosphorylation is a common post-translational modification affecting many essential cellular processes and is inextricably linked to SARS-CoV-2 infection. Hence, accurate identification of phosphorylation sites will be helpful to understand the mechanisms of SARS-CoV-2 infection and mitigate the ongoing COVID-19 pandemic. In the present study, an attention-based bidirectional gated recurrent unit network, called IPs-GRUAtt, was proposed to identify phosphorylation sitesin SARS-CoV-2-infected host cells. Comparative results demonstrated that IPs-GRUAtt surpassed both state-of-the-art machine-learning methods and existing models for identifying phosphorylation sites. Moreover, the attention mechanism made IPs-GRUAtt able to extract the key features from protein sequences. These results demonstrated that the IPs-GRUAtt is a powerful tool for identifying phosphorylation sites. For facilitating its academic use, a freely available online web server for IPs-GRUAtt is provided at http://cbcb.cdutcm.edu.cn/phosphory/.