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Pdb Database

Listed
ovachiever·vlatest·database

Access, query, and analyze structured data within PDB databases using natural language prompts via this ovachiever agent skill.

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 ovachiever/droid-tings --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

ovachiever

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)

    • skills/pdb-database/references/api_reference.md:52contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/entry/4HHB
    • skills/pdb-database/references/api_reference.md:55contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB_1
    • 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 ovachiever/droid-tings at 7acd12a754.

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

Commit
7acd12a754
Manifest
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 provides access to a PDB (Protein Data Bank) database, allowing AI agents to retrieve information about protein structures. It enables querying of PDB entries by ID or keyword and retrieving associated data like experimental conditions and resolution. The agent can then utilize this structural data for various downstream tasks such as analysis and comparison.

When to use it

  • Research: An agent needs to find the structure of a specific protein (e.g., "Retrieve the PDB ID for human insulin").
  • Drug Discovery: An agent is comparing the structures of different proteins involved in a disease pathway.
  • Education: A student wants to learn about protein crystallography and access structural data.
  • Structural Biology Analysis: An agent needs to find all entries with a resolution below 2 Angstroms for a specific protein family.

Key capabilities

  • Query PDB by ID
  • Query PDB by keyword
  • Retrieve experimental conditions
  • Retrieve resolution data

Example prompts

  • "What is the PDB ID for hemoglobin?"
  • "Find all entries related to 'SARS-CoV-2 spike protein'."
  • “Give me the resolution of entry 6LUW.”

Tips & gotchas

The skill relies on accurate PDB identifiers. Ensure that the provided IDs or keywords are valid and correctly formatted to receive relevant results.