Deep-USIpred: identifying substrates of ubiquitin protein ligases E3 and deubiquitinases with pretrained protein embedding and bayesian neural network

Identifying the substrates of ubiquitin protein ligase (E3) and deubiquitinases (DUB) contributes to the discovery of potential therapeutic targets for diseases. However, experimental identification of E3/DUB-substrate interactions is costly and time-consuming. Current computational methods for predicting E3/DUB-substrate interactions rely heavily on specific domain knowledge and involve complex and diverse biological data processing. To address this challenge, we proposed a deep learning prediction model, named Deep-USIpred, which predicts E3/DUB-substrate interactions using protein sequences. The proposed Deep-USIpred model encodes protein sequences with a pretrained model and utilizes 1DCNN-BNN deep learning algorithm to make a robust prediction model. We evaluated the performance of the proposed model on real datasets, and our experimental results show that it can achieve excellent prediction performance on the tasks of ESI and DSI. Our proposed method provides a promising alternative for the prediction of E3/DUB-substrate interactions, which has the potential to accelerate drug discovery for various diseases. The source code and dataset are available at https://github.com/PGTSING/Deep-USIpred.