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Pdb Database

Listed
moosegoose0701·vlatest·database·Apache-2.0

Queries and analyzes Protein Data Bank (PDB) databases for structural biology data and insights.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add dp-archive/archive --skill pdb-database -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

moosegoose0701

Taken from the source listing. We haven't verified who controls this account.

Install target

Live repository

Not pinned. Installing fetches whatever the repository holds at the time you run the command.

No human has reviewed this code. The checks below are a static scan of the files at one commit — nobody has run this skill or judged whether it works. A skill runs with whatever access you give your agent, so read the source before you install it.

Automated safety checks

scanned

This skill failed 1 of 6 checks. A failure is not proof of bad intent; it means something in the code needs a human to look at it before you run it.

  • No undeclared network calls: failed

    Contacts 1 host that is neither well-known infrastructure nor declared in the skill's frontmatter: data.rcsb.org.

    Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.

    Hosts contacted

    data.rcsb.orgundeclared

    What it found

    • seed_skills/pdb-database/references/api_reference.md:52contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/entry/4HHB
    • seed_skills/pdb-database/references/api_reference.md:55contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB_1
    • seed_skills/pdb-database/references/api_reference.md:58contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/assembly/4HHB/1

  • Declares what it does: passed

    SKILL.md parses and declares a name and a description.

    SKILL.md exists, its frontmatter parses, and it declares a name and a description.

  • No obfuscated payloads: passed

    No encoded or obfuscated payloads.

    No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.

  • No credential access: passed

    Reads no keys, tokens, keychains or credential files.

    Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.

  • No pipe-to-shell installers: passed

    No pipe-to-shell or download-and-run installers.

    No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.

  • Pinned to a commit: passed

    Scanned moosegoose0701/skill-compose at f8bf8cab69.

    The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.

Commit
f8bf8cab69
Manifest
seed_skills/pdb-database/SKILL.md
Scanned
2 files, 847 lines
This is a static scan, not a review. It reads the skill's files; it does not run them, and it cannot tell you whether the skill is any good or whether the code does what its description says. A skill runs with whatever access you give your agent.
What each check looks for →

About this skill

What it does

This skill allows AI agents to interact with a PDB (Protein Data Bank) database. It can retrieve information about protein structures, including experimental data and metadata. The agent can use this skill to answer questions related to specific proteins or perform analyses based on structural data.

When to use it

  • Scientific Research: An agent assisting researchers in finding relevant protein structure data for a study.
  • Drug Discovery: An agent identifying potential drug targets by analyzing the structures of target proteins.
  • Education: An agent explaining protein structures and related concepts to students.
  • Bioinformatics Analysis: An agent automating tasks involving querying and retrieving information from PDB entries.

Key capabilities

  • Accesses Protein Data Bank (PDB) data.
  • Retrieves experimental data for protein structures.
  • Provides metadata associated with PDB entries.

Example prompts

  • "Find the PDB entry for insulin."
  • "What is the resolution of the structure in PDB ID 1AKE?"
  • "Give me a list of all proteins containing hemoglobin."

Tips & gotchas

The skill's effectiveness depends on accurate and complete PDB identifiers (IDs). Ensure that prompts include valid PDB IDs for optimal results.