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Tools · Computational Biology

Protein Structure Ensemble Comparator

Compare predicted or designed protein structures by TM-score and RMSD, cluster them, and pick one representative per fold

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 Structure Ensemble Comparator: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
CPUDefault1 h$0.50$0.29$0.18$0.11

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

Outputs

  • ArchiveZIP
  • TableCSV
  • Protein structurePDB
  • TableCSV
  • StructuresPDB

References

The method behind it.

  1. Yang Zhang, Jeffrey Skolnick (2004). Scoring function for automated assessment of protein structure template quality. Proteins: Structure, Function, and Bioinformatics. doi:10.1002/prot.20264 (opens in a new tab)
  2. Patrick Kunzmann, Kay Hamacher (2018). Biotite: a unifying open source computational biology framework in Python. BMC Bioinformatics. doi:10.1186/s12859-018-2367-z (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-structure-cluster", "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-structure-cluster-1", "job_type": "protein-structure-cluster", "resource": "cpu", "payload": { ... }}'
Payload fields and examples in the docs

Computational Biology

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