LigandMPNN
SkillMediaLets your agent design protein sequences that fit around ligands and small molecules using LigandMPNN-style workflows.
Available today. Use it from your connected AI after setup.
No other account needed.
Connect ahel once, and every AI you use reads what you have installed.
Then ask your AI: use the LigandMPNN skill
About this capability
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.
What this skill tells your AI
The instructions your AI receives, as published by companion-inc/feynman in skills/ligandmpnn/SKILL.md and read by ahel’s review.
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.
Signals
- GitHub stars
- 9k
- Forks
- 1k
- Last commit
- Sep 2026
Advanced
- Catalog kind
- skill
- Gateway key
ligandmpnn-companion-inc- Source
- github.com/companion-inc/feynman