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Tools · Computational Biology

Docking Protocol Validator

Redock co-crystallized ligands and score pose RMSD and enrichment to validate a docking setup before screening

Open in the appRun via API

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.

Docking Protocol Validator: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
CPUDefault2 min$0.017$0.0096$0.006$0.0036

In workflows

Chain it with other steps.

Each input and output has a data kind, so the builder only connects steps that fit.

Inputs

  • Table · optionalJSON
  • Docked poses (list) · optionalSDF, PDBQT, PDB
  • Table · optionalCSV
  • Docked poses (list)SDF, PDBQT, PDB
  • Protein structurePDB, CIF
  • Molecules · optionalSDF

Outputs

  • ArchiveZIP
  • TableJSON
  • TableCSV

Ready-made workflows that use it

References

The method behind it.

  1. Michael J. Hartshorn, Marcel L. Verdonk, Gianni Chessari et al. (2007). Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance. Journal of Medicinal Chemistry. doi:10.1021/jm061277y (opens in a new tab)
  2. Jean-François Truchon, Christopher I. Bayly (2007). Evaluating Virtual Screening Methods: Good and Bad Metrics for the “Early Recognition” Problem. Journal of Chemical Information and Modeling. doi:10.1021/ci600426e (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": "docking-validate", "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": "docking-validate-1", "job_type": "docking-validate", "resource": "cpu", "payload": { ... }}'
Payload fields and examples in the docs

Computational Biology

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