Proteinmpnn
OthersproteinmpnnProteinmpnn is an Agent Skill for general use published in the companion-inc/feynman repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.
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.
QUICK START
How to use this skill
Bring this guide into your coding agent with a prompt tailored to the tool you use.
- Open your project in Codex.
- Copy and paste the prompt below.
- Review files and risks before approving any action.
Prompt to paste
Inspect the Agent Skill at https://github.com/companion-inc/feynman/blob/HEAD/skills/proteinmpnn/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/proteinmpnn, but wait for my approval before writing files or running scripts.
Copying this prompt does not install or run the skill. Review third-party files before use.
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.