diffdock-docking

name	diffdock-docking
description	Run a pinned DiffDock release for diffusion-based protein-ligand pose prediction. Use for candidate pose generation from receptor coordinates and ligand structures, especially without a fixed pocket; do not interpret DiffDock confidence as affinity.
license	MIT

DiffDock Docking

Gate and preflight

Follow $cx-compute-environment. Ask once before cloning/installing a pinned commit, downloading weights, and using GPU compute. Name all network hosts and never send private structures to a hosted service without approval.

Workflow

1. Prepare inputs with $cx-molecular-input-preparation; record receptor assembly/state and every ligand microstate.
2. Pin repository commit, environment lock, checkpoint checksum, inference configuration, seed, samples per complex, and hardware.
3. Smoke-test on the upstream example, then predict each complex into an isolated output directory. Preserve all generated poses and confidence values.
4. Convert outputs without changing atom order or stereochemistry; verify atom mapping and clashes.
5. Treat confidence as within-model pose ranking. Apply $cx-docking-validation; use an independent affinity model or experiment for affinity claims.

Boundaries

• Confidence is neither probability of binding nor binding affinity.
• Check training/template overlap for benchmark targets and ligands.
• For predicted receptors, report receptor uncertainty and avoid claiming precision in low-confidence pockets.