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Agent skill

Proteinmpnn

by JimLiu in JimLiu/science-skills

Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al.

Apache-2.0Auto-check passedResearch & Science

Install Proteinmpnn

skills CLI
$ npx skills add JimLiu/science-skills --skill proteinmpnn -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install JimLiu/science-skills proteinmpnn --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/JimLiu/science-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/proteinmpnn .claude/skills/proteinmpnn && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
proteinmpnn
GitHub stars
227
Used in
4 other repos
Token cost
~1.1k tokens
SKILL.md length
493 words
Files
1
Skills in repo
27
Repo updated
First seen
Licence
Apache-2.0

At a glance

Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al.

  • Tasks that involve Protein structure and design
  • SKILL.md covers Running it, A flat chain map in…, Checkpoints — which one to pick and Errors worth recognizing
  • Calls pip, git and python; reaches github.com

What it does

Proteinmpnn is an agent skill from JimLiu/science-skills. Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Protein structure and design. It works with GitHub. The licence is Apache-2.0.

When your agent uses it

  • Tasks that involve Protein structure and design

Example prompts

  • “/proteinmpnn”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit fb309c3. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Shell commands in SKILL.md call:

    • pip
    • git
    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • github.com

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Proteinmpnn loads about 1.1k tokens when it runs. Until then it costs about 94 tokens; SKILL.md has 493 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~94
When it runs · the whole SKILL.md, loaded when a task matches
~1.1k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from JimLiu/science-skills at commit fb309c3, republished under its Apache-2.0 licence (© JimLiu). 493 words, ~1,139 tokens.

Download SKILL.mdSave it as .claude/skills/proteinmpnn/SKILL.md (or your agent's skills folder).
name
proteinmpnn
description
Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. 2022, github.com/dauparas/ProteinMPNN). Reach for this skill to run sequence design on RFdiffusion backbones, to redesign one chain of a PDB while holding interface residues fixed, or to generate a temperature-swept set of sequences for downstream folding.
license
Apache-2.0
category
biomodels
metadata.display-name
ProteinMPNN

ProteinMPNN

ProteinMPNN is the default inverse-folding step in the binder pipeline: a message-passing network that sees backbone geometry only, so it is the right choice when the design surface is protein–protein and the wrong one as soon as a ligand, nucleic acid, or metal is part of the interface — ligandmpnn adds those atoms to the graph with a near-identical CLI, and solublempnn swaps in weights trained on soluble structures for an expression-biased prior. Code and weights are MIT (github.com/dauparas/ProteinMPNN). The model is small enough to run on CPU — for a handful of sequences on one backbone that is seconds and usually faster than dispatching a remote job; a GPU helps for batched campaigns (hundreds of backbones or large --num_seq_per_target). Either way the repo is cloned in-job — there is no PyPI dist and the checkpoints are bundled in the repo.

Running it

bash
pip install torch numpy   # if not already present
git clone --depth 1 https://github.com/dauparas/ProteinMPNN.git proteinmpnn
cd proteinmpnn
python protein_mpnn_run.py \
  --pdb_path backbone.pdb --pdb_path_chains "A" \
  --out_folder out --num_seq_per_target 16 --sampling_temp "0.1"

Two flags trip almost everyone the first time. --sampling_temp is parsed as a space-separated string so one run can sweep several temperatures; a single value needs no quoting, but a multi-value sweep must be quoted ("0.1 0.2 0.3"), and commas never split — "0.1,0.2" fails the float cast. --pdb_path_chains is also space-separated inside one quoted argument ("A B"); a comma is kept as part of the chain ID.

Designs land in out/seqs/<pdb_stem>.fa. The first record is the input sequence; each design header carries score= (mean negative log-likelihood — lower is more confident), global_score=, and seq_recovery=. ProteinMPNN writes sequences only — it does not thread them back onto the backbone; if you need designed-sequence PDBs, the ligandmpnn runner writes them to backbones/ automatically and accepts --model_type protein_mpnn for the same weights.

Show full SKILL.md (225 more words)Show less

A flat chain map in --fixed_positions_jsonl silently redesigns every residue

--fixed_positions_jsonl expects one JSON object per line keyed by the PDB stem first, then chain, then a list of 1-indexed residue numbers: {"backbone": {"A": [10, 11, 12], "B": []}}. Passing the inner {"A": [...]} directly — the obvious guess — is silently treated as "no PDB matched," and every position is redesigned. The bundled helper_scripts/make_fixed_positions_dict.py writes the correct shape from a chain and range string and is worth the extra call; the same outer-stem rule applies to --chain_id_jsonl and --tied_positions_jsonl.

Checkpoints — which one to pick

--model_nametraining noiseuse
v_48_0020.02 Åhighest recovery; close-to-native redesigns
v_48_020 (default)0.20 Åde novo backbones — tolerates RFdiffusion imperfection
v_48_0300.30 Åvery rough backbones; lowest recovery
--use_soluble_model—swaps to the soluble-trained set; see solublempnn

Errors worth recognizing

You seeIt means / do this
KeyError: 'A'Chain letter not in the PDB — grep '^ATOM' file.pdb | cut -c22 | sort -u to see what is.
JSONDecodeError on a *_jsonl flagThe flag wants a file path, not inline JSON; write the file first.
All positions redesigned despite --fixed_positions_jsonlOuter PDB-stem key missing — see the gotcha above.
ModuleNotFoundError for relative importsScript run from the wrong cwd — cd into the cloned repo first; the imports are repo-relative.

Next: fold the designs in complex with the target via boltz, chai1, or esmfold2 and filter on ipTM.

© JimLiu, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in skills/proteinmpnn of JimLiu/science-skills.

Open the folder on GitHubat commit fb309c3

Used in 4 other repositories

We found 4 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 4 other GitHub owners. This page covers the copy in JimLiu/science-skills, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Proteinmpnn next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

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Alphafold Database Fetch And Analyzegoogle-deepmind/science-skills3.2k2 repos~1.2kAutomated safety check: PassApache-2.0
Alphafoldadaptyvbio/protein-design-skills1643 repos~1.2kAutomated safety check: PassMIT
Read GitHubAgentTeam-TaichuAI/ScienceClaw6712 repos~638Automated safety check: PassNone

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Works with

Categories

Questions about Proteinmpnn

What does Proteinmpnn do?

Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al. Proteinmpnn is an agent skill from JimLiu/science-skills. Inverse-fold a protein backbone (PDB structure) into amino-acid sequence with ProteinMPNN (Dauparas et al.

When should I use Proteinmpnn?

Proteinmpnn fits situations like: tasks that involve Protein structure and design.

How do I install Proteinmpnn in Claude Code?

Run `npx skills add JimLiu/science-skills --skill proteinmpnn -a claude-code`. Or copy the skill folder (skills/proteinmpnn in JimLiu/science-skills) into .claude/skills/proteinmpnn in your project. Claude Code loads it when a task matches its description.

How do I install Proteinmpnn in Codex?

Run `npx skills add JimLiu/science-skills --skill proteinmpnn -a codex`. Or copy the skill folder (skills/proteinmpnn in JimLiu/science-skills) into .agents/skills/proteinmpnn in your project. Codex loads it when a task matches its description.

Can I use Proteinmpnn in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add JimLiu/science-skills --skill proteinmpnn -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/proteinmpnn, .gemini/skills/proteinmpnn, .github/skills/proteinmpnn and .opencode/skills/proteinmpnn in your project.

What does Proteinmpnn need to run?

Going by SKILL.md and its folder, Proteinmpnn needs the command-line tools its instructions call (pip, git and python). Our summary lists: Python 3.

Does Proteinmpnn access the network?

SKILL.md names 1 domain. In commands or code: github.com; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Proteinmpnn safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Proteinmpnn use?

Proteinmpnn is published under the Apache-2.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Proteinmpnn use?

About 1.1k tokens (SKILL.md is roughly 4.6k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Proteinmpnn?

Skills that share tags, products or a category with Proteinmpnn: GitHub Deep Research (bytedance/deer-flow, 84k stars), Last30days (mvanhorn/last30days-skill, 64k stars), Alphafold Database Fetch And Analyze (google-deepmind/science-skills, 3.2k stars) and Alphafold (adaptyvbio/protein-design-skills, 164 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Proteinmpnn?

JimLiu (a GitHub user) maintains it in JimLiu/science-skills, which has 227 GitHub stars. The repository holds 27 skills in this directory. The repository was last updated on July 1, 2026.

Source: JimLiu/science-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.