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3D Shape Similarity

3D shape and pharmacophore virtual screening: rank libraries against a query conformer with USRCAT and Gaussian shape + color overlay to find scaffold hops

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.

3D Shape Similarity: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
CPUDefault5 min$0.042$0.024$0.015$0.009

In workflows

Chain it with other steps.

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

Inputs

  • Molecules (list)SDF, MOLBLOCK
  • MoleculesSDF, MOLBLOCK

Outputs

  • ArchiveZIP
  • MoleculesSDF
  • TableCSV

References

The method behind it.

  1. Greg Landrum, Paolo Tosco, Ricardo Rodriguez et al. (2026). RDKit: Open-source cheminformatics. Zenodo. doi:10.5281/zenodo.591637 (opens in a new tab)
  2. Adrian M Schreyer, Tom Blundell (2012). USRCAT: real-time ultrafast shape recognition with pharmacophoric constraints. Journal of Cheminformatics. doi:10.1186/1758-2946-4-27 (opens in a new tab)
  3. J. A. Grant, M. A. Gallardo, B. T. Pickup (1996). A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape. Journal of Computational Chemistry. doi:10.1002/(sici)1096-987x(19961115)17:14<1653::aid-jcc7>3.0.co;2-k (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": "shape-similarity", "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": "shape-similarity-1", "job_type": "shape-similarity", "resource": "cpu", "payload": { ... }}'
Payload fields and examples in the docs

Cheminformatics & Structure

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