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Tools · Computational Biology

MPNN Sequence Design

Design amino-acid sequences for a fixed protein backbone with ProteinMPNN, LigandMPNN or SolubleMPNN

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.

MPNN Sequence Design: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
Nvidia T4Default15 min$0.51$0.37$0.30$0.23
Nvidia L415 min$0.70$0.50$0.40$0.30
Nvidia A1015 min$0.96$0.68$0.55$0.41
Nvidia L40S15 min$1.71$1.22$0.97$0.73
Nvidia A100, 40 GB15 min$1.84$1.31$1.05$0.79
Nvidia A100, 80 GB15 min$2.19$1.57$1.25$0.94
Nvidia H10015 min$3.46$2.47$1.97$1.49
Nvidia H20015 min$3.97$2.83$2.27$1.70
Nvidia B20015 min$5.47$3.91$3.12$2.35

In workflows

Chain it with other steps.

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

Inputs

  • Structures (list) · optionalPDB, CIF
  • Protein structure (list) · optionalPDB, CIF

Outputs

  • ArchiveZIP
  • TableCSV
  • Protein sequencesFASTA

References

The method behind it.

  1. J. Dauparas, I. Anishchenko, N. Bennett et al. (2022). Robust deep learning–based protein sequence design using ProteinMPNN. Science. doi:10.1126/science.add2187 (opens in a new tab)
  2. Justas Dauparas, Gyu Rie Lee, Robert Pecoraro et al. (2025). Atomic context-conditioned protein sequence design using LigandMPNN. Nature Methods. doi:10.1038/s41592-025-02626-1 (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": "mpnn-design", "resource": "t4", "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": "mpnn-design-1", "job_type": "mpnn-design", "resource": "t4", "payload": { ... }}'
Payload fields and examples in the docs

Computational Biology

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