Agent Skills › companion-inc/feynman › ligandmpnn

ligandmpnn

GitHub

用于配体感知蛋白质序列设计的技能，涵盖基于小分子环境的残基重设计、约束设置及设计评分。通过记录结构信息、验证模型可用性、过滤输出并独立校验，生成符合特定配体接触和结构置信度的候选序列。

skills/ligandmpnn/SKILL.md companion-inc/feynman

Trigger Scenarios

配体感知蛋白质设计残基重设计带约束的蛋白质设计设计评分与筛选

Install

npx skills add companion-inc/feynman --skill ligandmpnn -g -y

More Options

Use without installing

npx skills use companion-inc/feynman@ligandmpnn

指定 Agent (Claude Code)

npx skills add companion-inc/feynman --skill ligandmpnn -a claude-code -g -y

安装 repo 全部 skill

npx skills add companion-inc/feynman --all -g -y

预览 repo 内 skill

npx skills add companion-inc/feynman --list

SKILL.md

Frontmatter

{
    "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.