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Agent Skill

Proteinmpnn skill

proteinmpnnaipoch/open-scienceresources/skills/proteinmpnn/SKILL.md

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.

5.3kApache-2.0

always on

89 tokname + description

once used

1,059 tokSKILL.md body

bundled files

11 KB

repo stars

5.3kGitHub

Install the Proteinmpnn skill

Skills CLI (Claude Code, Codex, Cursor and others)

npx skills add https://github.com/aipoch/open-science --skill proteinmpnn

Claude Code, by hand (all projects)

git clone --depth 1 https://github.com/aipoch/open-science.git /tmp/open-science
mkdir -p ~/.claude/skills
cp -R /tmp/open-science/resources/skills/proteinmpnn ~/.claude/skills/proteinmpnn

For one project only, copy the folder into .claude/skills/ in that project instead. The agent picks it up when a task matches its description.

What it costs your context

Agent Skills load in three steps. Tokens counted with the o200k tokenizer; your model's count will differ a little.

WhenWhat loadsCost
Every sessionName and description89 tok
When the agent uses itThe SKILL.md instructions1,059 tok
Only if opened1 bundled files (1 KB)varies

Until it is used, proteinmpnn costs about 15× less than the median MCP server we measured (1,362 tokens on every turn). Installing all 25 skills from aipoch/open-science would load 2,130 tokens of descriptions. Skills vs MCP study

Checks

Our checks found nothing to flag: it follows the Agent Skills specification's naming and size guidelines and doesn't pipe downloads into a shell.

Checked 2026-10-22 · method

What's inside

The headings of its SKILL.md. Read the full file on GitHub.

  • ProteinMPNN
  • Running it
  • A flat chain map in --fixedpositionsjsonl silently redesigns every residue
  • Checkpoints — which one to pick
  • Errors worth recognizing

More skills from aipoch/open-science

All skills in this repo
  1. alphafold2aipoch/open-science

    Predict protein structure for monomers and multimers with AlphaFold2 via the ColabFold runner (Mirdita et al. 2022, github.com/sokrypton/ColabFold; AlphaFold2 Jumper et al. 2021). Reach for this skill to fold a sequence or complex with the AF2/AF2-Multimer evoformer, to validate designed sequences by self-consistency pLDDT, ipTM, and RMSD, or to run a quick MSA-backed prediction using the public MMseqs2 server.

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  2. boltzaipoch/open-science

    Structure prediction for protein, nucleic-acid, and small-molecule complexes with Boltz-2 (Passaro & Wohlwend et al. 2025, github.com/jwohlwend/boltz). Reach for this skill to validate designed binders against a target, to co-fold a protein with a SMILES or CCD ligand, or to get an open-source AlphaFold3 alternative with optional binding-affinity prediction.

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  3. borzoiaipoch/open-science

    Predict genome-wide functional tracks (RNA-seq, CAGE, DNase, ChIP) from DNA sequence with Borzoi. Use this skill when: (1) Scoring the regulatory effect of a variant on expression/accessibility, (2) Generating predicted coverage tracks for a locus, (3) Prioritising non-coding variants by predicted track delta.

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  4. chai1aipoch/open-science

    Structure prediction for protein, nucleic-acid, and small-molecule complexes with the Chai-1 foundation model (Chai Discovery 2024, github.com/chaidiscovery/chai-lab). Reach for this skill to predict an antibody-antigen or protein-ligand complex from a single FASTA, to re-fold designed binders as an AlphaFold-multimer alternative, or to drive co-folding from Python for batched campaigns on a GPU.

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  5. compute-env-setupaipoch/open-science

    Prepare reproducible setup instructions and validate a user-managed named software environment on an Open-Science SSH Compute Host, including direct SSH and Slurm hosts. Use when a remote job needs packages, modules, cache variables, or a repeatable activation that the host does not already provide.

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  6. customizeaipoch/open-science

    Use when the user wants to create or manage a Specialist agent or create, revise, publish, or delete a Skill through the conversational `/Customize` entry. Routes Skill work to the internal skill-creator and handles Specialist work through the JavaScript host.agents SDK.

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  7. diffdockaipoch/open-science

    Predict small-molecule binding poses with DiffDock-L (Corso et al. 2023/2024, github.com/gcorso/DiffDock) — blind diffusion docking that places a ligand into a protein pocket without a predefined search box and ranks the samples with a learned confidence model. Reach for this skill to dock a SMILES or SDF against a PDB, to generate ranked 3D poses for a small fragment library, or to get a starting pose for downstream rescoring. DiffDock predicts geometry, not affinity.

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  8. env-managementaipoch/open-science

    Use when a notebook run fails on a missing package (ImportError, ModuleNotFoundError, "there is no package called"), when you need to inspect an installed package version, or when you need to install, add, or manage Python or R packages for the notebook runtime. Covers inspect_packages, routing Python vs R through manage_packages, why in-cell %pip/!pip/install.packages() and OS installers are forbidden, restarting the kernel after an install, and when to stop and ask the user.

    5.3k curl|sh105 tok idle · 1,362 in use