A Structure-Aware Multimodal Framework for Drug-Target Interaction Prediction via Heterogeneous Graph Learning

Predicting drug-target interactions is critical for drug discovery, yet many deep learning methods overlook atom-residue-level relationships. We propose Protein Heterogeneous Graph learning for Drug-Target Interaction prediction (PHGDTI), a multimodal framework that integrates sequence and structural cues for binding prediction. Drug and protein sequences are embedded with Mol2Vec and Tasks Assessing Protein Embeddings (TAPE) and refined by a self-attention module. In parallel, a drug-protein graph encoder models three complementary graphs: a drug atom graph, a protein residue graph, and a heterogeneous atom-residue graph. Graph attention layers propagate intra- and intermolecular information, and SAGPooling yields compact structural representations. Fusing these structural and sequence features enables accurate affinity estimation. Experiments on the Davis kinase dataset and GalaxyDB dataset show PHGDTI surpasses competitive baselines, and ablation results highlight the benefit of heterogeneous graph modeling.