ViraHinter: a dual-modal artificial intelligence framework for predicting virus-host interactions

TL;DR

ViraHinter is a dual-modal deep learning framework that predicts virus-host protein interactions, outperforming existing methods and aiding antiviral discovery by integrating structural and sequence data.

Contribution

It introduces a novel dual-modal deep learning approach combining structure generation and sequence embeddings for accurate virus-host interaction prediction.

Findings

Outperforms RoseTTAFold2-PPI, AlphaFold 3, and RoseTTAFold2-Lite in benchmarks.

Successfully identifies novel host factors relevant to viral infection.

Reveals 33 shared host factors across influenza subtypes.

Abstract

Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-host associations, much of the virus-host interactome remains uncharacterized due to the labor-intensive nature of experimental screens, the inherent difficulty in capturing transient interactions, and the limited sequence homology across divergent viral families. Here, we introduce ViraHinter, a dual-modal deep learning framework for the precise prediction of virus-host interactions and large-scale inference of interaction landscapes. ViraHinter couples a structure-generation branch with a sequence-representation branch, integrating structure-informed pair representations with ESM-derived embeddings to learn generalizable interaction rules across unseen viruses. We benchmark ViraHinter on pathogenic coronaviruses and influenza A viruses and show that it consistently outperforms RoseTTAFold2-PPI, AlphaFold 3 and RoseTTAFold2-Lite in prioritizing high-confidence candidates even under severe class imbalance and across diverse interface regimes. Notably, it successfully identifies novel functionally relevant host factors and recapitulates the structural plasticity of the complex interfaces. By intersecting predictions across multiple influenza subtypes, ViraHinter reveals 33 shared host factors, offering a roadmap for broad-spectrum antiviral discovery. ViraHinter therefore serves as a robust computational approach for studying virus-host interactions, enabling systematic screening of host factors for all known human-infecting viruses, providing new insights into the shared mechanisms of viral pathogenesis, and accelerating the discovery of novel therapeutic targets and the development of broad-spectrum antivirals.