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protein-design-workflow

Maintainer FreedomIntelligence · Last updated April 1, 2026

End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools. For tool selection, use binder-design. For QC thresholds, use protein-qc.

OpenClawNanoClawAnalysisReproductionprotein-design-workflow🔬 omics & computational biologyprotein structure & designend

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/protein-design-workflow

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb".
  • modal run modal_colabfold.py \ --input-faa all_sequences.fasta \ --out-dir predictions/.
  • Output: AF2 predictions with pLDDT, ipTM, PAE.

Source Doc

Excerpt From SKILL.md

1.3 Select hotspots

  • Choose 3-6 exposed residues
  • Prefer charged/aromatic (K, R, E, D, W, Y, F)
  • Check surface accessibility
  • Verify residue numbering

Output: target_prepared.pdb, hotspot list

Option B: BindCraft (end-to-end)

Output: 100-500 backbone PDBs

For RFdiffusion backbones

Output: 8 sequences per backbone (800-4000 total)

Use cases

  • Use protein-design-workflow in research workflows aligned with this subject area.
  • Follow the upstream documentation for the full working procedure.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

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