Docking & MD overview
Locate the pocket, generate candidate poses for a small molecule, then rescore them by binding free energy — run as much of the arc as your question needs.
Docking answers whether and how a small molecule binds a target. It's a three-step arc — locate the pocket, generate candidate poses, then rescore them by binding free energy — and you run as much of it as your question needs. This is the core of structure-based hit finding and lead optimization.
Availability
These tools are metered by credits and gated by your plan — plans set your monthly credits, available model families, and which modal-app tools you can run. See Plans & tiers.
What you can achieve here
- Find where a ligand could bind on a structure
- Predict a small molecule's binding pose
- Rescore poses by physics-based binding free energy
- Screen a set of compounds against one target
For which tool fits each, see What you can achieve.
Tools in this section
| Tool | What it does |
|---|---|
| DiffDock on the platform | Run blind, diffusion-based protein–ligand docking with DiffDock-L — confidence-ranked poses, not binding energies. |
| MM-GBSA | Calculate binding free energies with GPU-accelerated MM-GBSA using OpenMM. |
| P2Rank | Predict protein binding sites with ML-based pocket detection and druggability scoring. |
Recipes using these tools
Fold, find pockets, dock, triage
From a protein sequence to a druggable pocket with a verified docking pose and an ADMET read — the standard structure-first entry point.
Hit to lead
Dock a hit against a target, rescore the pose, screen ADMET, plan a synthesis route, and check vendor availability — the hit-to-lead pass.
Read next
Reading a result against the bench
How predicted poses, pockets, and binding energies compare to co-crystal structures and assays.
What you can achieve
The outcomes these tools deliver — and which to pick when several do the same thing.
Which tool?
Match a scientific goal to a tool across every domain.
Concept clusters
How tools, jobs, and results fit together.
Workflows
Guided pipelines and copy-and-adapt prompt recipes for common goals.
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Troubleshooting BLAST
Fix a missing .nin or .pin index, an out-of-memory run, NCBI 429 throttling on -remote, and an empty hit list — plus when to re-run and when to stop.
DiffDock on the platform
Run blind, diffusion-based protein–ligand docking with DiffDock-L — confidence-ranked poses, not binding energies.