DiffDock: Diffusion Steps, Twists and Turns for Molecular Docking and Beyond!

presented on March 8th 2023 by Gabriele Corso, Bowen Jing, and Hannes Stärk
abstract:
Predicting the binding structure of a small molecule ligand to a protein is critical to drug design. Unlike previous work, we frame molecular docking as a generative modeling problem and develop DiffDock, a diffusion generative model over the non-Euclidean manifold of ligand poses. Empirically, DiffDock significantly outperforms the previous state-of-the-art traditional docking and deep learning methods on both crystal and computationally folded structures.

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Thank you for explaining how DiffDock works. How does DiffDock deal with non standard molecules in pdb? Do we need to remove them before docking?