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Tools · Computational Biology

Protein Preparer

PDBFixer cleanup, PDB2PQR protonation, and dock-ready structures without MD solvation

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.

Protein Preparer: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
CPUDefault3 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

Outputs

  • ArchiveZIP
  • TableCSV
  • Protein structurePDBQT
  • Protein structurePDB

Ready-made workflows that use it

References

The method behind it.

  1. Peter Eastman, Jason Swails, John D. Chodera et al. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLOS Computational Biology. doi:10.1371/journal.pcbi.1005659 (opens in a new tab)
  2. Elizabeth Jurrus, Dave Engel, Keith Star et al. (2017). Improvements to the APBS biomolecular solvation software suite. Protein Science. doi:10.1002/pro.3280 (opens in a new tab)
  3. Mats H. M. Olsson, Chresten R. Søndergaard, Michal Rostkowski et al. (2011). PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. Journal of Chemical Theory and Computation. doi:10.1021/ct100578z (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": "protein-prepare", "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": "protein-prepare-1", "job_type": "protein-prepare", "resource": "cpu", "payload": { ... }}'
Payload fields and examples in the docs

Computational Biology

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