A Novel Capsule Network with Attention Routing to Identify Prokaryote Phosphorylation Sites

Abstract

By denaturing proteins and promoting the formation of multiprotein complexes, protein phosphorylation has important effects on the activity of protein functional molecules and cell signaling. The regulation of protein phosphorylation allows microbes to respond rapidly and reversibly to specific environmental stimuli or niches, which is closely related to the molecular mechanisms of bacterial drug resistance. Accurate prediction of phosphorylation sites (p-site) of prokaryotes can contribute to addressing bacterial resistance and providing new perspectives for developing novel antibacterial drugs. Most existing studies focus on human phosphorylation sites, while tools targeting phosphorylation site identification of prokaryotic proteins are still relatively scarce. This study designs a capsule network-based prediction technique for p-site in prokaryotes. To address the poor scalability and unreliability of dynamic routing processes in the output space of capsule networks, a more reliable way is introduced to learn the consistency between capsules. We incorporate a self-attention mechanism into the routing algorithm to capture the global information of the capsule, reducing the computational effort while enriching the representation capability of the capsule. Aiming at the weak robustness of the model, EcapsP improves the prediction accuracy and stability by introducing shortcuts and unconditional reconfiguration. In addition, the study compares and analyzes the prediction performance based on word vectors, physicochemical properties, and mixing characteristics in predicting serine (Ser/S), threonine (Thr/T), and tyrosine (Tyr/Y) p-site. The comprehensive experimental results show that the accuracy of the developed technique is close to 70% for the identification of the three phosphorylation sites in prokaryotes. Importantly, in side-by-side comparisons with other state-of-the-art predictors, our method improves the Matthews correlation coefficient (MCC) by approximately 7%. The results demonstrate the superiority of EcapsP in terms of high performance and reliability.