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Pdb Database

Listed
jackspace·vlatest·database·MIT

Access and query Jackspace's PDB protein structure database directly through this AI agent for research 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 jackspace/claudeskillz --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

jackspace

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: files.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

    files.rcsb.orgundeclared

    What it found (3 of 5)

    • skills/scientific-db-pdb-database/SKILL.json:8contacts files.rcsb.org
      "content": "### 1. Searching for Structures\r\n\r\nFind PDB entries using various search criteria:\r\n\r\n**Text Search:** Search by protein name, keywords, or…
    • skills/scientific-db-pdb-database/SKILL.json:8contacts files.rcsb.org
      "content": "### 1. Searching for Structures\r\n\r\nFind PDB entries using various search criteria:\r\n\r\n**Text Search:** Search by protein name, keywords, or…
    • skills/scientific-db-pdb-database/SKILL.json:8contacts files.rcsb.org
      "content": "### 1. Searching for Structures\r\n\r\nFind PDB entries using various search criteria:\r\n\r\n**Text Search:** Search by protein name, keywords, or…

  • 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 jackspace/claudeskillz at aef4e299d1.

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

Commit
aef4e299d1
Manifest
skills/scientific-db-pdb-database/SKILL.md
Scanned
2 files, 299 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, jackspace-pdb-database, allows AI agents to interact with a PDB (Protein Data Bank) database. It enables retrieval of protein structure data, including atomic coordinates and experimental details. The agent can query the database based on various criteria like PDB ID or keywords related to the protein.

When to use it

  • Scientific Research: An AI agent needs to gather information about a specific protein for research purposes.
  • Drug Discovery: Retrieve structural data of target proteins to aid in drug design and analysis.
  • Educational Purposes: A student or educator wants to explore protein structures and learn about their properties.
  • Bioinformatics Analysis: An agent needs to process and analyze a large dataset of protein structures.

Key capabilities

  • Query PDB database by ID
  • Retrieve atomic coordinates
  • Access experimental details for proteins
  • Search using keywords related to the protein

Example prompts

  • "Get me the structure data for PDB ID 1AKE."
  • "Find all proteins with 'kinase' in their description."
  • “What are the experimental conditions used to determine the structure of 4HHB?”

Tips & gotchas

The skill relies on a stable connection to the Protein Data Bank. Ensure your agent has appropriate network access for optimal performance.