Proteinmpnn

Design protein sequences from fixed backbone structures with ProteinMPNN-style workflows. Use when a task asks for backbone-conditioned sequence design, mutation suggestions, fixed residues, or design filtering.

advaitpaliwal Updated

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ProteinMPNN

Use this skill for fixed-backbone protein sequence design.

Workflow:

  1. Record input structure, chain ids, designed positions, fixed residues, tied positions, symmetry, and design objective.
  2. Verify the local or remote execution route before running.
  3. Save PDB/mmCIF inputs, design masks, command, seeds, model version, FASTA outputs, and score tables.
  4. Filter designs by constraints, diversity, motifs, structure prediction, conservation, and assay-ready feasibility.
  5. Attach provenance and a verification plan before recommending candidates.

Treat generated sequences as candidates that require structural and experimental validation.

advaitpaliwal/feynman/tree/main/skills/proteinmpnn commit 8f4296f456

Frequently asked questions

npx skillmds@latest add advaitpaliwal/proteinmpnn