Poster
in
Workshop: Machine Learning for Drug Discovery (MLDD)
DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models
Mohamed Amine Ketata · Cedrik Laue · Ruslan Mammadov · Hannes Stärk · Rachel (Menghua) Wu · Gabriele Corso · Céline Marquet · Regina Barzilay · Tommi Jaakkola
in
Workshop: Machine Learning for Drug Discovery (MLDD)
Understanding how proteins structurally interact is crucial to modern biology, with applications in drug discovery and protein design. Recent machine learning methods have formulated protein-small molecule docking as a generative problem with significant performance boosts over both traditional and deep learning baselines. In this work, we propose a similar approach for rigid protein-protein docking: DiffDock-PP is a diffusion generative model that learns to translate and rotate unbound protein structures into their bound conformations. We achieve state-of-the-art performance on DIPS with a median C-RMSD of 4.85, outperforming all considered baselines. Additionally, DiffDock-PP is faster than all search-based methods and generates reliable confidence estimates for its predictions.