Papers › EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of...
EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions
Ngoc-Quang Nguyen
Accurate prediction of compound-protein interactions (CPI) remains a cornerstone challenge in computational drug discovery. While existing sequence-based approaches leverage molecular fingerprints or graph representations, they critically overlook three-dimensional (3D) structural determinants of binding affinity. To bridge this gap, we present EquiCPI, an end-to-end geometric deep learning framework that synergizes first-principles structural modeling with SE(3)-equivariant neural networks. Our pipeline transforms raw sequences into 3D atomic coordinates via ESMFold for proteins and DiffDock-L for ligands, followed by physics-guided conformer re-ranking and equivariant feature learning. At its core, EquiCPI employs SE(3)-equivariant message passing over atomic point clouds, preserving symmetry under rotations, translations, and reflections, while hierarchically encoding local interaction patterns through tensor products of spherical harmonics. The proposed model is evaluated on BindingDB (affinity prediction) and DUD-E (virtual screening), EquiCPI achieves performance on par with or exceeding the state-of-the-art deep learning competitors.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections