diffdock
DiffDock is a diffusion-based molecular docking tool that predicts protein-ligand binding poses without requiring a predefined binding site. Use it when the binding site is unknown, when traditional docking fails, or when exploring multiple binding modes. Pipeline: prepare protein (PDB) and ligand (SMILES/SDF) inputs → run DiffDock inference → analyze confidence-ranked poses → visualize in PyMOL or NGLview.
Installation and usage
DiffDock is a diffusion-based molecular docking tool that predicts protein-ligand binding poses without requiring a predefined binding site. Use it when the binding site is unknown, when traditional docking fails, or when exploring multiple binding modes. Pipeline: prepare protein (PDB) and ligand (SMILES/SDF) inputs → run DiffDock inference → analyze confidence-ranked poses → visualize in PyMOL or NGLview.
Once installed, you can use this skill by running the following command in your terminal:
skills use diffdock