SMILES → 3D embed → dock
Convert SMILES to 3D structures, then dock with AutoDock Vina.
- Steps
- 2
- Jobs
- autodockvinaconvert-batch
- Complexity
- simple
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SMILES → DiffDock → top poses
Dock a SMILES library with DiffDock and keep the top-confidence poses.
- Steps
- 2
- Jobs
- diffdock
- Complexity
- simple
Free Wilson → 3D embed → dock
Enumerate analogs with Free Wilson, embed to 3D, then dock with AutoDock Vina.
- Steps
- 3
- Jobs
- autodockvinaconvert-batchfreewilson
- Complexity
- moderate
DrugFlow generate → dock
Generate pocket ligands with DrugFlow, cap the set, then dock with AutoDock Vina.
- Steps
- 3
- Jobs
- autodockvinadrugflow
- Complexity
- moderate
Sequence → fold → dock
Fold a protein sequence with ESMFold2, embed ligands to 3D, then dock with AutoDock Vina.
- Steps
- 3
- Jobs
- autodockvinaconvert-batchesmfold2
- Complexity
- moderate
Thompson Sampling → 3D embed → dock
Screen a combinatorial library with Thompson Sampling, embed hits to 3D, then dock with AutoDock Vina.
- Steps
- 3
- Jobs
- autodockvinaconvert-batchthompsonsampling
- Complexity
- moderate
Vina triage → GNINA rescore
Dock with AutoDock Vina, keep the top poses, and rescore with GNINA.
- Steps
- 4
- Jobs
- autodockvinaconvert-batchgnina
- Complexity
- moderate
Vina triage → Boltz-2 re-predict (batch)
Dock a ligand set, keep the top poses, and re-predict affinities with Boltz-2 in batch.
- Steps
- 4
- Jobs
- autodockvinaboltz2convert-batch
- Complexity
- moderate
Vina triage → SurfDock (scatter)
Dock with AutoDock Vina, keep the top hits, and re-dock each ligand with SurfDock (one GPU job per ligand).
- Steps
- 5
- Jobs
- autodockvinaconvert-batchsurfdock
- Complexity
- advanced