Equivariant flow matching for molecular docking guided by ligand-protein interactions

Molecular docking is a key technique in drug discovery, but existing deep learning-based methods still struggle to generate physically valid binding poses consistently. Post-processing with empirical force fields can partially improve physical plausibility, yet it breaks end-to-end modeling, increases computational cost, and often weakens ligand-protein interactions and leads to pose deviations. Diffusion-based docking methods have recently shown improved accuracy and physical realism, but they typically require many sampling steps, leading to low inference efficiency. Approaches based on internal coordinates reduce sampling steps but suffer from complex pipelines and high per-step computational cost. In addition, many docking models rely heavily on extensive sampling and external scoring functions to identify reliable poses, further increasing inference time. To address these challenges, we propose an equivariant flow matching approach for molecular docking guided by ligand-protein interactions in Cartesian space (IFMDock). IFMDock guides the flow matching model to generate physically plausible docking poses with favorable repeated-sampling behavior, while substantially reducing the number of inference steps and improving docking accuracy and physical validity. Experiments on the PoseBusters and DeepDockingDare benchmarks demonstrate its effectiveness and superior performance.