LigandMPNN

LigandMPNN is an AI Engineering skill for Claude Code, published by BioTender-max in awesome-bio-agent-skills.

174 stars30 forkson BioTender-max/awesome-bio-agent-skillsAdded 2026/09/07+1% in starsRepository updated 2026/07/01

agent-skillsai-agentai-agentsawesomeawesome-listbioinformaticsbiomedicalclaudeclaude-codeclaude-skillscomputational-biologydrug-discoverygenomicsllmmcpprotein-designproteomicssingle-cellskillstranscriptomics

Install in seconds

Install LigandMPNN

Copy LigandMPNN into your Claude Code skills folder. Run the command in your terminal, or review the source on GitHub before installing.

terminal

npx degit https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/adaptyv/ligandmpnn ~/.claude/skills/ligandmpnn

Requires Node.js. Downloads this skill only — not the rest of the repository — into your Claude Code skills folder.

Without Node.js

git clone https://github.com/BioTender-max/awesome-bio-agent-skills.git

Clones the whole repository, then copy the skill’s own directory into your skills folder yourself.

In this catalog

Source file: skills/adaptyv/ligandmpnn/SKILL.md in BioTender-max/awesome-bio-agent-skills
Installs to: ~/.claude/skills/ligandmpnn
Collection: One of 25 skills cataloged from this repository
Category: AI Engineering — 3475 skills

What LigandMPNN does

LigandMPNN designs protein sequences around bound ligands, metals, cofactors, or nucleic acids. Use it for enzyme active sites, binding pocket optimization, and other ligand-aware sequence design tasks.

LigandMPNN is cataloged under AI Engineering on DirSkills. LigandMPNN comes from a repository tagged agent-skills, ai-agent, ai-agents, awesome and awesome-list.

Documentation

README

Excerpt

LigandMPNN Ligand-Aware Design

Prerequisites

Requirement	Minimum	Recommended
Python	3.8+	3.10
CUDA	11.0+	11.7+
GPU VRAM	8GB	16GB (T4)
RAM	8GB	16GB

How to run

First time? See Installation Guide to set up Modal and biomodals.

cd biomodals
modal run modal_ligandmpnn.py \
  --pdb-path protein_ligand.pdb \
  --num-seq-per-target 16 \
  --sampling-temp 0.1

GPU: T4 (16GB) | Timeout: 600s default

Option 2: Local installation

git clone https://github.com/dauparas/LigandMPNN.git
cd LigandMPNN

python run.py \
  --pdb_path protein_ligand.pdb \
  --out_folder output/ \
  --num_seq_per_target 16

This is the opening of the README. Read the full README on GitHub.

Frequently asked about LigandMPNN

What else does BioTender-max publish alongside LigandMPNN?
LigandMPNN is one of 25 skills that DirSkills catalogs from BioTender-max/awesome-bio-agent-skills, the repository it ships in. Its siblings there include ATAC Seq, AlphaFold and BindCraft Binder Design. Each one is a separate skill with its own page in this directory, installs the same way LigandMPNN does, and is maintained by BioTender-max in that same repository. The rest of the collection is listed on the BioTender-max/awesome-bio-agent-skills page.
How does LigandMPNN compare to other AI Engineering skills?
LigandMPNN ranks #3224 by stars among the 3475 AI Engineering skills in this catalog. The most-starred ones next to it are Architecture Decision Records, AI-First Engineering and Agentic OS. DirSkills ranks by the star count of the repository each skill ships in, so that order reflects how popular those repositories are rather than any review of LigandMPNN against them. Open each page to compare what they document and how they install.