Tools · Computational Biology
Binding-Site Detector
Find ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflows
Hardware and price
Price per run
What a typical run reserves from your wallet: the catalog's expected runtime on each piece of hardware × your plan's per-second rate. Larger inputs reserve more, and you're charged only for the seconds the job actually runs.
| Hardware | Typical runtime | Basic | Starter | Pro | Enterprise |
|---|---|---|---|---|---|
| CPUDefault | 3 min | $0.025 | $0.014 | $0.009 | $0.0054 |
In workflows
Chain it with other steps.
Each input and output has a data kind, so the builder only connects steps that fit.
Inputs
- Protein structurePDB, CIF
- Molecules · optionalSDF
Outputs
- ArchiveZIP
- TableJSON
- MoleculesSDF
Ready-made workflows that use it
- Screen a compound library against a targetSMILES → 3D embed → dockVirtual screening
- Dock analogs enumerated from your SAR dataFree Wilson → 3D embed → dockLibrary design
- Grow analogs from your SAR table with matched pairs, then dockMatched pairs → analogs → dockLibrary design
- Generate and dock new ligands for a pocketDrugFlow generate → dockLibrary design
- Dock against a protein with no solved structureSequence → fold → dockStructure prediction to docking
- Screen an ultra-large combinatorial libraryThompson Sampling → 3D embed → dockVirtual screening
- Rescore docking hits with a CNN scoring functionVina triage → GNINA rescoreVirtual screening
- Re-predict docking hits with Boltz-2 affinitiesVina triage → Boltz-2 re-predict (batch)Virtual screening
- Re-dock top hits with surface-aware diffusionVina triage → SurfDock (scatter)Virtual screening
- Dock into a cleaned predicted structure and see the contactsSequence → fold → prepare → dock → PLIPStructure prediction to docking
- Compare docking against a wild type and its point mutantsPoint mutants vs wild type → fold → dock → compareStructure prediction to docking
- Build a library from building blocks, filter it, then dockReaction enumerate → filter → diversity pick → dockLibrary design
References
The method behind it.
- Radoslav Krivák, David Hoksza (2018). P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. Journal of Cheminformatics. doi:10.1186/s13321-018-0285-8 (opens in a new tab)
Run via API
Submit it from your own code.
Use an API key from your account. The estimate uses your plan's rates; submitting reserves that amount from your wallet.
# Estimate the reservation for your plan (payload fields: see the API reference)
curl -X POST https://api.cognichem.com/api/v1/jobs/estimate \
-H "X-Api-Key: $COGNICHEM_API_KEY" \
-H "Content-Type: application/json" \
-d '{"job_type": "pocket-detect", "resource": "cpu", "payload": {}}'
# Submit (retrying with the same Idempotency-Key never submits twice)
curl -X POST https://api.cognichem.com/api/v1/jobs/submit \
-H "X-Api-Key: $COGNICHEM_API_KEY" \
-H "Idempotency-Key: $(uuidgen)" \
-H "Content-Type: application/json" \
-d '{"job_name": "pocket-detect-1", "job_type": "pocket-detect", "resource": "cpu", "payload": { ... }}'Computational Biology
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