FIGRDock: Fast Interaction-Guided Regression for Flexible Docking

Shikun Feng, Bicheng Lin, Yuanhuan Mo, Yuyan Ni, Wenyu Zhu, Bowen Gao, Wei-Ying Ma, haitao li, Yanyan Lan

Keywords: Flexible Docking, Protein-ligand interactions

Abstract: Flexible docking, which predicts the binding conformations of both proteins and small molecules by modeling their structural flexibility, plays a vital role in structure-based drug design. Although recent generative approaches, particularly diffusion-based models, have shown promising results, they require iterative sampling to generate candidate structures and depend on separate scoring functions for pose selection. This leads to an inefficient pipeline that is difficult to scale in real-world drug discovery workflows. To overcome these challenges, we introduce FIGRDock, a fast and accurate flexible docking framework that understands complicated interactions between molecules and proteins with a regression-based approach. FIGRDock leverages initial docking poses from conventional tools to distill interaction-aware distance patterns, which serve as explicit structural conditions to directly guide the prediction of the final protein-ligand complex via a regression model. This one-shot inference paradigm enables rapid and precise pose prediction without reliance on multi-step sampling or external scoring stages. Experimental results show that FIGRDock achieves up to 100× faster inference than diffusion-based docking methods, while consistently surpassing them in accuracy across standard benchmarks. These results suggest that FIGRDock has the potential to offer a scalable and efficient solution for flexible docking, advancing the pace of structure-based drug discovery.

Submission Number: 20