getcompanion-ai/ligandmpnn
skills/ligandmpnn/SKILL.md
Design protein sequences around ligand or small-molecule contexts with LigandMPNN-style workflows. Use when a task asks for ligand-aware protein design, residue redesign, constraints, or design ranking.
$ install --global
skillsauthnpx skillsauth add getcompanion-ai/feynman ligandmpnnInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- ligandmpnn
- description:
- Design protein sequences around ligand or small-molecule contexts with LigandMPNN-style workflows. Use when a task asks for ligand-aware protein design, residue redesign, constraints, or design ranking.
LigandMPNN
Use this skill for ligand-aware protein sequence design.
Workflow:
- Record the input structure, ligand identity, chain/residue design mask, fixed residues, symmetry, and design objective.
- Verify the execution route and model availability before running.
- Save input structure, ligand file, residue masks, command, seeds, model version, generated FASTA, and score tables.
- Filter outputs by constraint satisfaction, sequence diversity, known motifs, predicted structure confidence, and ligand-contact plausibility.
- Send shortlisted designs through an independent structural or literature/database check before presenting them as candidates.
Generated designs must remain tied to exact input structures and constraints.
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