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Pdb Database

Listed
jimmc414·vlatest·database

Access and query protein structure data from the Protein Data Bank (PDB) for research and analysis.

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 jimmc414/kosmos --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

jimmc414

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 (3 of 4)

    • kosmos-claude-scientific-skills/scientific-skills/pdb-database/references/api_reference.md:52contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/entry/4HHB
    • kosmos-claude-scientific-skills/scientific-skills/pdb-database/references/api_reference.md:55contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB_1
    • kosmos-claude-scientific-skills/scientific-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 jimmc414/kosmos at 6cfe7f690d.

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

Commit
6cfe7f690d
Manifest
kosmos-claude-scientific-skills/scientific-skills/pdb-database/SKILL.md
Scanned
2 files, 842 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 and query a PostgreSQL database. It facilitates tasks such as retrieving specific data based on criteria, updating existing records, and executing complex SQL queries. The agent can use the skill to manage and analyze data stored within the database.

When to use it

  • Data Retrieval: An agent needs to find customer orders placed after a certain date for reporting purposes.
  • Inventory Management: An agent requires real-time stock levels of products in a warehouse.
  • Customer Support: An agent needs to access customer details and purchase history to resolve an inquiry.
  • Data Updates: An agent is tasked with updating product prices based on external market data.

Key capabilities

  • Connects to PostgreSQL databases.
  • Executes SQL queries.
  • Retrieves data from tables.
  • Updates existing records.

Example prompts

  • "Retrieve all customers who live in California."
  • "Update the price of product ID 123 to $19.99."
  • “What is the total number of orders placed this month?”

Tips & gotchas

  • Requires database connection credentials (host, username, password).
  • The agent must have appropriate permissions within the PostgreSQL database to perform the requested actions.