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Agent skill

Tooluniverse Protein Structure Retrieval

by wu-yc in wu-yc/LabClaw

Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.

No licenceAuto-check passedResearch & Science

Install Tooluniverse Protein Structure Retrieval

skills CLI
$ npx skills add wu-yc/LabClaw --skill tooluniverse-protein-structure-retrieval -a claude-code

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

GitHub CLI
$ gh skill install wu-yc/LabClaw tooluniverse-protein-structure-retrieval --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/wu-yc/LabClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio/tooluniverse-protein-structure-retrieval .claude/skills/tooluniverse-protein-structure-retrieval && 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
tooluniverse-protein-structure-retrieval
GitHub stars
1.1k
Used in
2 other repos
Token cost
~2.8k tokens
SKILL.md length
566 words
Files
1
Skills in repo
68
Repo updated
First seen
Licence
None found

At a glance

Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.

  • Works in 4 steps: Clarification (When Needed) → Protein Disambiguation → Data Retrieval (Internal) → …
  • Users need protein structures
  • SKILL.md covers Workflow Overview, Phase 0: Clarification (When…, Phase 1: Protein Disambiguation and Phase 2: Data Retrieval…, plus 6 more sections
  • Reaches rcsb.org and ebi.ac.uk

What it does

Tooluniverse Protein Structure Retrieval is an agent skill from wu-yc/LabClaw. Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Creates detailed structure reports with experimental metadata, ligand information, and download links. Use when users need protein structures, 3D models, crystallography data, or mention PDB IDs (4-character codes like 1ABC) or UniProt accessions.

Its SKILL.md is about 2.8k 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 AlphaFold and UniProt. The repository describes itself as: LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists).

When your agent uses it

  • Users need protein structures
  • Crystallography data
  • Mention PDB IDs (4-character codes like 1ABC)
  • UniProt accessions

Example prompts

  • “Use the tooluniverse-protein-structure-retrieval skill to retrieve protein structure data from RCSB PDB, PDBe, and AlphaFold with protein…”
  • “/tooluniverse-protein-structure-retrieval”

Requirements

  • Python 3

Workflow steps

4 steps, taken from the step headings in SKILL.md.

  1. Clarification (When Needed)
  2. Protein Disambiguation
  3. Data Retrieval (Internal)
  4. Report Structure Profile

What it can do on your machine

Read from SKILL.md and the folder at commit df37802. 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

    No scripts in the folder and no shell commands in SKILL.md (its code samples are python and markdown).

    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:

    • rcsb.org
    • ebi.ac.uk
    • alphafold.ebi.ac.uk

    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

Tooluniverse Protein Structure Retrieval loads about 2.8k tokens when it runs. Until then it costs about 111 tokens; SKILL.md has 566 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~111
When it runs · the whole SKILL.md, loaded when a task matches
~2.8k

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

Without a licence we can't republish the file, so here is its outline and opening line. It has 566 words (~2,777 tokens).

“Retrieve protein structures with proper disambiguation, quality assessment, and comprehensive metadata.”

— opening of SKILL.md by wu-yc
name
tooluniverse-protein-structure-retrieval

Read the full SKILL.md on GitHub

Files

Just SKILL.md in skills/bio/tooluniverse-protein-structure-retrieval of wu-yc/LabClaw.

Open the folder on GitHubat commit df37802

Used in 2 other repositories

We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in wu-yc/LabClaw, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Tooluniverse Protein Structure Retrieval 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.

Tooluniverse Protein Structure Retrieval compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Tooluniverse Protein Structure Retrieval this skillwu-yc/LabClaw1.1k2 repos~2.8kAutomated safety check: PassNone
Alphafold Database Fetch And Analyzegoogle-deepmind/science-skills3.2k2 repos~1.2kAutomated safety check: PassApache-2.0
Bio DB ToolsDrugClaw/DrugClaw126—~1.4kAutomated safety check: PassApache-2.0
Ggetdavila7/claude-code-templates33k10 repos~6.3kAutomated safety check: PassMIT
Alphafold Databasedavila7/claude-code-templates33k10 repos~4kAutomated safety check: PassMIT
Foldseek Structural Searchgoogle-deepmind/science-skills3.2k1 repos~1.3kAutomated safety check: PassApache-2.0

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  • Tooluniverse Drug Repurposing

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  • Tooluniverse Gene Enrichment

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Works with

Categories

Questions about Tooluniverse Protein Structure Retrieval

What does Tooluniverse Protein Structure Retrieval do?

Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Tooluniverse Protein Structure Retrieval is an agent skill from wu-yc/LabClaw. Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles.

When should I use Tooluniverse Protein Structure Retrieval?

Tooluniverse Protein Structure Retrieval fits situations like: users need protein structures; crystallography data; mention PDB IDs (4-character codes like 1ABC); uniProt accessions.

How do I install Tooluniverse Protein Structure Retrieval in Claude Code?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-protein-structure-retrieval -a claude-code`. Or copy the skill folder (skills/bio/tooluniverse-protein-structure-retrieval in wu-yc/LabClaw) into .claude/skills/tooluniverse-protein-structure-retrieval in your project. Claude Code loads it when a task matches its description.

How do I install Tooluniverse Protein Structure Retrieval in Codex?

Run `npx skills add wu-yc/LabClaw --skill tooluniverse-protein-structure-retrieval -a codex`. Or copy the skill folder (skills/bio/tooluniverse-protein-structure-retrieval in wu-yc/LabClaw) into .agents/skills/tooluniverse-protein-structure-retrieval in your project. Codex loads it when a task matches its description.

Can I use Tooluniverse Protein Structure Retrieval 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 wu-yc/LabClaw --skill tooluniverse-protein-structure-retrieval -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/tooluniverse-protein-structure-retrieval, .gemini/skills/tooluniverse-protein-structure-retrieval, .github/skills/tooluniverse-protein-structure-retrieval and .opencode/skills/tooluniverse-protein-structure-retrieval in your project.

What does Tooluniverse Protein Structure Retrieval need to run?

SKILL.md names no scripts, command-line tools or credentials: Tooluniverse Protein Structure Retrieval is instructions for the agent only. Our summary lists: Python 3.

Does Tooluniverse Protein Structure Retrieval access the network?

SKILL.md names 3 domains. In commands or code: rcsb.org, ebi.ac.uk and alphafold.ebi.ac.uk; the agent is likely to contact these when it follows the instructions. This is read from the text; nothing was executed.

Is Tooluniverse Protein Structure Retrieval 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 Tooluniverse Protein Structure Retrieval use?

No licence was found for Tooluniverse Protein Structure Retrieval or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.

How many tokens does Tooluniverse Protein Structure Retrieval use?

About 2.8k tokens (SKILL.md is roughly 11k 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 Tooluniverse Protein Structure Retrieval?

Skills that share tags, products or a category with Tooluniverse Protein Structure Retrieval: Alphafold Database Fetch And Analyze (google-deepmind/science-skills, 3.2k stars), Bio DB Tools (DrugClaw/DrugClaw, 126 stars), Gget (davila7/claude-code-templates, 33k stars) and Alphafold Database (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Tooluniverse Protein Structure Retrieval?

wu-yc (a GitHub user) maintains it in wu-yc/LabClaw, which has 1,055 GitHub stars. The repository holds 68 skills in this directory. The repository was last updated on March 19, 2026.

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