DiffDock: protein-small-molecule docking

DiffDock-L generates candidate ligand poses and ranks them by model confidence. Confidence is neither a measured probability of correctness nor binding affinity. Use this skill for one pair, batches, or separate receptor conformations; treat library-wide confidence sorting as pose triage, not hit identification.

Verified scope

Targets the current v1.1.3 release. Released source and current main's identical inference.py were checked on 2026-09-30. Bundled helpers were tested on tiny synthetic inputs; pretrained docking, ESMFold, CUDA, Docker, GNINA, and hosted-demo execution were not run in this review. Commands requiring those components are source-verified recipes, not successful end-to-end demonstrations.

Set up the upstream environment