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ligandmpnn

ligandmpnn is a skill for Claude Code, Codex from zongtingwei/Bioclaw_Skills_Hub. It costs 86 tokens per session (1,529 once invoked), scanned A, original, MIT.

A protein-design tool that proposes amino-acid sequences for a protein structure containing a small molecule, metal, or cofactor. It uses the molecule’s surrounding context when designing the sequence.

In plain words
What is it for?
Use it to design enzyme active sites, optimize ligand-binding pockets, create metal-coordination sites, or design cofactor-binding proteins from PDB structure files.
Why use it?
It helps design or improve proteins whose function depends on binding another molecule or coordinating a metal. Without ligand-aware design, the proposed sequence may not support the binding site properly.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one. Also seen: positional $N argument.

Needs its repository: it reads a path above its own folder, which exists only inside the repository. The line is **First time?** See [Installation Guide](../../docs/installation.md) to set up Modal and biomodals..

not rated 26repo 5mo ago A scan 86 tokens original MIT

Good fit Use it to design enzyme active sites, optimize ligand-binding pockets, create metal-coordination sites, or design cofactor-binding proteins from PDB structure files.

Compare 6 skills from other repositories ↓
View source ↗ zongtingwei/Bioclaw_Skills_Hub
Install

Getting it into your agent

It runs from inside its repository, so the clone comes first — what it calls does not travel with the file alone.

Clone the repo
git clone --depth 1 https://github.com/zongtingwei/Bioclaw_Skills_Hub
agentmods
npx agentmods add skills/zongtingwei/bioclaw_skills_hub/ligandmpnn

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for ligandmpnn

README.md
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Your own site
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Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for ligandmpnn

Your own site · 80×15
<a href="https://agentmods.dev/skills/zongtingwei/bioclaw_skills_hub/ligandmpnn"><img src="https://agentmods.dev/badge/skills/zongtingwei/bioclaw_skills_hub/ligandmpnn.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 86 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,529 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00086 $0.01529
Opus 5 $0.00043 $0.00764
Sonnet 5 $0.00017 $0.00306
Haiku 4.5 $0.00009 $0.00153

Measured 12d ago against content hash 0af35d40b00b, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

ligandmpnn scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/protein-design/skills/ligandmpnn/SKILL.md · 187 lines

How it starts

The opening of the file, as written. The whole thing — 187 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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.

Option 1: Modal (recommended)

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

Key parameters

Parameter Default Range Description
--pdb_path required path PDB with ligand
--num_seq_per_target 1 1-1000 Sequences per structure
--sampling_temp "0.1" "0.0001-1.0" Temperature (string!)
--ligand_mpnn_use_side_chain_context true bool Use ligand context

Ligand Specification

In PDB File

Ligand must be present as HETATM records:

ATOM    ...protein atoms...
HETATM  1  C1  LIG A 999      x.xxx  y.yyy  z.zzz  1.00  0.00           C

Supported Ligand Types

  • Small molecules (HETATM)
  • Metals (Zn, Fe, Mg, Ca, etc.)
  • Cofactors (NAD, FAD, ATP)
  • DNA/RNA

Output format

output/
├── seqs/
│   └── protein.fa          # FASTA sequences
└── protein_pdb/
    └── protein_0001.pdb    # PDBs with designed sequence

Sample output

Successful run

$ python run.py --pdb_path enzyme_substrate.pdb --out_folder output/ --num_seq_per_target 8
Loading LigandMPNN model weights...
Processing enzyme_substrate.pdb
Found ligand: LIG (12 atoms)
Generated 8 sequences in 3.1 seconds

output/seqs/enzyme_substrate.fa:
>enzyme_substrate_0001, score=1.45, global_score=1.38
MKTAYIAKQRQISFVKSHFSRQLE...
>enzyme_substrate_0002, score=1.52, global_score=1.41
MKTAYIAKQRQISFVKSQFSRQLD...

Read the full file on GitHub · 187 lines

Files

What ships with it

1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 12d ago First seen · 187 lines · 86 tokens per session scan A 0af35d40b00b

Subscribe to this mod's changes

ligandmpnn is a skill published in the GitHub repository zongtingwei/Bioclaw_Skills_Hub (26 stars, last pushed 5mo ago), licensed MIT. It adds 86 tokens to every session and 1,529 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientificagentbioinformaticsdesign-toolsinverse-foldingligand-awareopenclawsequence-designskills
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