Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge

arXiv:2402.11459v1 Announce Type: cross
Abstract: Accurate prediction of protein-ligand binding structures, a task known as molecular docking is crucial for drug design but remains challenging. While deep learning has shown promise, existing methods often depend on holo-protein structures (docked, and not accessible in realistic tasks) or neglect pocket sidechain conformations, leading to limited practical utility and unrealistic conformation predictions. To fill these gaps, we introduce an under-explored task, named flexible docking to predict poses of ligand and pocket sidechains simultaneously …

abstract arxiv bridge cs.ai cs.lg deep learning design diffusion drug design molecular docking physics.chem-ph prediction protein protein structures q-bio.bm tasks type