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ligandmpnn

ligandmpnn is a skill for Claude Code, Codex from JimLiu/science-skills. It costs 100 tokens per session (3,185 once invoked), scanned A, original, no licence file.

A method for designing protein sequences around an existing three-dimensional backbone while considering bound molecules, nucleic acids, or metals.

In plain words
What is it for?
Use it to redesign residues around a small molecule or cofactor, or to design metal-binding sites.
Why use it?
It helps redesign binding pockets and coordinating sites while keeping the surrounding molecular geometry in view.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

not rated 229repo +1 changed 8d ago A scan 100 tokens no licence

Good fit Use it to redesign residues around a small molecule or cofactor, or to design metal-binding sites.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jimliu/science-skills/ligandmpnn
View source ↗ JimLiu/science-skills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add JimLiu/science-skills --skill ligandmpnn
Clone the repo
git clone --depth 1 https://github.com/JimLiu/science-skills

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
[![agentmods](https://agentmods.dev/badge/skills/jimliu/science-skills/ligandmpnn/github.svg)](https://agentmods.dev/skills/jimliu/science-skills/ligandmpnn)
Your own site
<a href="https://agentmods.dev/skills/jimliu/science-skills/ligandmpnn"><img src="https://agentmods.dev/badge/skills/jimliu/science-skills/ligandmpnn/github.svg" alt="Measured on agentmods" height="20"></a>

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/jimliu/science-skills/ligandmpnn"><img src="https://agentmods.dev/badge/skills/jimliu/science-skills/ligandmpnn.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 100 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,185 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown 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 $0.00100 $0.03185
Opus 5.5 $0.00040 $0.01274
Sonnet 5.5 $0.00020 $0.00637
Haiku 4.5 $0.00010 $0.00318

Measured 8d ago against content hash 1c1c3235511a, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

ligandmpnn scanned grade A with 1 finding 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 8d 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.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

| `checkpoint digest mismatch or missing: [...]` | A `.pt` is missing or did not match its pinned sha256 (truncated download, or the file changed upstream; a mismatched copy is renamed to `*.rejected` — or `*.rejected.1`
skills/ligandmpnn/SKILL.md · 167 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

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. 8d ago Changed · +43 lines 1c1c3235511a
  2. 2mo ago First seen · 124 lines · 100 tokens per session scan A 004f25fe7caa

Subscribe to this mod's changes

ligandmpnn is a skill published in the GitHub repository JimLiu/science-skills (229 stars, last pushed 8d ago), with no licence file. It adds 100 tokens to every session and 3,185 once invoked, about $0.0004 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Scientificbiomodels
Related

ligandmpnn compared with skills from other repositories

ligandmpnn next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
ligandmpnnJimLiu/science-skillsSkill2298d agononeA100Claude Code, Codex
esmfold2aipoch/open-scienceSkill5.5kyesterdayApache-2.0A223Claude Code, Codex
openfold3aipoch/open-scienceSkill5.5kyesterdayApache-2.0A60Claude Code, Codex
ligandmpnnaipoch/open-scienceSkill5.5kyesterdayApache-2.0A100Claude Code, Codex
alphafold2aipoch/open-scienceSkill5.5kyesterdayApache-2.0A117Claude Code, Codex
boltzaipoch/open-scienceSkill5.5kyesterdayApache-2.0A88Claude Code, Codex
chai1aipoch/open-scienceSkill5.5kyesterdayApache-2.0A98Claude Code, Codex