Current status and future perspectives of computational studies on human–virus protein–protein interactions

Abstract

Abstract The protein–protein interactions (PPIs) between human and viruses mediate viral infection and host immunity processes. Therefore, the study of human–virus PPIs can help us understand the principles of human–virus relationships and can thus guide the development of highly effective drugs to break the transmission of viral infectious diseases. Recent years have witnessed the rapid accumulation of experimentally identified human–virus PPI data, which provides an unprecedented opportunity for bioinformatics studies revolving around human–virus PPIs. In this article, we provide a comprehensive overview of computational studies on human–virus PPIs, especially focusing on the method development for human–virus PPI predictions. We briefly introduce the experimental detection methods and existing database resources of human–virus PPIs, and then discuss the research progress in the development of computational prediction methods. In particular, we elaborate the machine learning-based prediction methods and highlight the need to embrace state-of-the-art deep-learning algorithms and new feature engineering techniques (e.g. the protein embedding technique derived from natural language processing). To further advance the understanding in this research topic, we also outline the practical applications of the human–virus interactome in fundamental biological discovery and new antiviral therapy development.