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Tools · Computational Biology

Structure QC Report

Grade protein model geometry: Ramachandran and rotamer outliers, atomic clashes, cis-peptides, C-beta deviation and ligand bond geometry

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.

Structure QC Report: reservation per run, USD
HardwareTypical runtimeBasicStarterProEnterprise
CPUDefault30 min$0.25$0.14$0.09$0.054

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) · optionalPDB, CIF

Outputs

  • ArchiveZIP
  • TableCSV
  • TableCSV
  • StructuresPDB

References

The method behind it.

  1. Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang et al. (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. doi:10.1093/bioinformatics/btp163 (opens in a new tab)
  2. Simon C. Lovell, Ian W. Davis, W. Bryan Arendall et al. (2003). Structure validation by Cα geometry: ϕ,ψ and Cβ deviation. Proteins: Structure, Function, and Bioinformatics. doi:10.1002/prot.10286 (opens in a new tab)
  3. Simon C. Lovell, J. Michael Word, Jane S. Richardson et al. (2000). The penultimate rotamer library. Proteins: Structure, Function, and Genetics. doi:10.1002/1097-0134(20000815)40:3<389::aid-prot50>3.0.co;2-2 (opens in a new tab)
  4. J. Michael Word, Simon C. Lovell, Thomas H. LaBean et al. (1999). Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. Journal of Molecular Biology. doi:10.1006/jmbi.1998.2400 (opens in a new tab)
  5. Thomas A. Halgren (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of Computational Chemistry. doi:10.1002/(sici)1096-987x(199604)17:5/6<490::aid-jcc1>3.0.co;2-p (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": "structure-qc", "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": "structure-qc-1", "job_type": "structure-qc", "resource": "cpu", "payload": { ... }}'
Payload fields and examples in the docs

Computational Biology

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