Enhancing Bioactivity Prediction via Spatial Emptiness Representation of Protein-ligand Complex and Union of Multiple Pockets

Predicting the bioactivity of candidate ligands remains a central challenge in drug discovery. Ligands and endogenous substrates often compete for the same binding sites on target proteins, and the extent to which a ligand can modulate protein function depends not only on its binding but also on how effectively it occupies the relevant pocket. However, most existing methods focus narrowly on local interactions within protein–ligand complexes and neglect spatial emptiness—the unoccupied regions within the binding site that may permit endogenous molecules to engage or interfere. Such unfilled space can diminish the ligand’s functional impact, regardless of binding affinity. To overcome this key limitation in protein–ligand modeling, we propose LigoSpace, a novel method integrating three core components. LigoSpace introduces GeoREC (Geometric Representation of Spatial Emptiness in Complexes) to quantify atomic-level empty space and Union-Pocket to unify multiple protein pockets, providing a global view of binding sites. Additionally, LigoSpace employs a pairwise loss instead of commonly used MSE loss, to better capture relative relationships critical for drug discovery. Extensive experiments on multiple datasets with diverse bioactivity types demonstrate that LigoSpace significantly improves performance when integrated into state-of-the-art models, highlighting the effectiveness of its novel components.