pdb-database

pdb-database is a skill for Claude Code, Codex from wu-yc/LabClaw. It costs 49 tokens per session (2,426 once invoked), scanned A, original, no licence file.

A connection to the RCSB Protein Data Bank, a public database of three-dimensional structures of proteins and nucleic acids. It provides structure files and related information.

In plain words
What is it for?
Use it to search structures by text, sequence, or shape; retrieve metadata; and download PDB or mmCIF coordinate files.
Why use it?
It avoids searching for structure records and downloading coordinate files by hand. This helps when studying molecular shape or evaluating drug targets.

Skill for Claude CodeCodex

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.

agentmods
npx agentmods add skills/wu-yc/labclaw/pdb-database
Any agent
npx skills add wu-yc/LabClaw --skill pdb-database
Clone the repo
git clone --depth 1 https://github.com/wu-yc/LabClaw

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 pdb-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/wu-yc/labclaw/pdb-database.svg)](https://agentmods.dev/skills/wu-yc/labclaw/pdb-database)
Your own site
<a href="https://agentmods.dev/skills/wu-yc/labclaw/pdb-database"><img src="https://agentmods.dev/badge/skills/wu-yc/labclaw/pdb-database.svg" alt="Measured on agentmods" height="20"></a>
Per session 49 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,426 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. Scan, not verified.
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 $0.00049 $0.02426
Opus 5 $0.00024 $0.01213
Sonnet 5 $0.00010 $0.00485
Haiku 4.5 $0.00005 $0.00243

Measured 3d ago against content hash 43566e867689, method: parsed. Prices are Anthropic first-party input rates as of 2026-08-30, from the pricing page.

Security

Grade A, and why

pdb-database 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 3d 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.

data = fetch(query_type="graphql", query=query)
skills/bio/pdb-database/SKILL.md · 309 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. 3d ago First seen · 309 lines · 49 tokens per session scan A 43566e867689

Subscribe to this mod's changes

pdb-database is a skill published in the GitHub repository wu-yc/LabClaw (1,048 stars, last pushed 5mo ago), with no licence file. It adds 49 tokens to every session and 2,426 once invoked, about $0.0002 per session on Opus 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.

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