getcompanion-ai/proteinmpnn
skills/proteinmpnn/SKILL.md
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.
$ install --global
skillsauthnpx skillsauth add getcompanion-ai/feynman proteinmpnnInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- proteinmpnn
- description:
- 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.
ProteinMPNN
Use this skill for fixed-backbone protein sequence design.
Workflow:
- Record input structure, chain ids, designed positions, fixed residues, tied positions, symmetry, and design objective.
- Verify the local or remote execution route before running.
- Save PDB/mmCIF inputs, design masks, command, seeds, model version, FASTA outputs, and score tables.
- Filter designs by constraints, diversity, motifs, structure prediction, conservation, and assay-ready feasibility.
- Attach provenance and a verification plan before recommending candidates.
Treat generated sequences as candidates that require structural and experimental validation.
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