Revisiting drug–protein interaction prediction: a novel global–local perspective

Abstract Motivation Accurate inference of potential drug–protein interactions (DPIs) aids in understanding drug mechanisms and developing novel treatments. Existing deep learning models, however, struggle with accurate node representation in DPI prediction, limiting their performance. Results We propose a new computational framework that integrates global and local features of nodes in the drug–protein bipartite graph for efficient DPI inference. Initially, we employ pre-trained models to acquire fundamental knowledge of drugs and proteins and to determine their initial features. Subsequently, the MinHash and HyperLogLog algorithms are utilized to estimate the similarity and set cardinality between drug and protein subgraphs, serving as their local features. Then, an energy-constrained diffusion mechanism is integrated into the transformer architecture, capturing interdependencies between nodes in the drug–protein bipartite graph and extracting their global features. Finally, we fuse the local and global features of nodes and employ multilayer perceptrons to predict the likelihood of potential DPIs. A comprehensive and precise node representation guarantees efficient prediction of unknown DPIs by the model. Various experiments validate the accuracy and reliability of our model, with molecular docking results revealing its capability to identify potential DPIs not present in existing databases. This approach is expected to offer valuable insights for furthering drug repurposing and personalized medicine research. Availability and implementation Our code and data are accessible at: https://github.com/ZZCrazy00/DPI.