Taming Generative Co-Folding Prior for Molecular Docking with Diffusion Bridge

Molecular docking aims to predict the three-dimensional structure of a protein–ligand complex; in the conventional structure-based setting, it is conditioned on an input protein structure and ligand, often starting from an apo receptor in flexible docking or a holo receptor in rigid docking. Recent co-folding models exemplified by AlphaFold 3 achieve strong accuracy in protein–ligand complex prediction, but they typically generate complexes from sequence-derived inputs and therefore do not directly use apo structures as structural priors in docking, leading to a larger conformational search space and weaker robustness in difficult or few-step settings. We present BridgeDock, a framework that adapts pretrained co-folding backbones to flexible docking by modeling the apo-to-holo transition as a diffusion bridge, allowing generation from the initial protein–ligand state rather than from Gaussian noise. To make this bridge formulation compatible with pretrained denoisers, we introduce an alignment mechanism that maps bridge states to the original denoising schedule of the pretrained model. Experiments on standard flexible docking benchmarks show that BridgeDock consistently outperforms strong co-folding baselines. Moreover, BridgeDock is computationally efficient at inference time and remains effective even with very few denoising steps.