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diffdock-molecular-docking

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Diffusion-based molecular docking to predict 3D ligand–protein binding poses (blind docking) with confidence scoring; use when you need pose prediction for drug discovery or virtual screening.

When to use

• **Blind docking** when you have a protein structure (PDB) and a ligand (SMILES) but no known binding site.
• **Pose prediction** to generate multiple plausible 3D binding conformations and rank them.
• **Virtual screening support** to quickly evaluate candidate ligands by predicted binding poses and confidence.
• **Drug discovery workflows** where you need automated docking outputs (SDF poses + scores) for downstream analysis.
• **Batch/advanced docking** when running many ligand–protein pairs or using alternative inputs (e.g., sequence-based workflows; see `references/workflows_examples.md`).

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