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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


Abstract:

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.

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