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Pdb Database

Listed
aminoanalytica·vlatest·database·Apache-2.0

Access and query amino acid sequence data, structural information, and related details from a comprehensive Protein Data Bank (PDB) database.

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 aminoanalytica/amina-skills --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

aminoanalytica

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 2 hosts that are neither well-known infrastructure nor declared in the skill's frontmatter: data.rcsb.org, search.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.orgundeclaredsearch.rcsb.orgundeclared

    What it found (3 of 5)

    • skills/pdb-database/SKILL.md:88contacts data.rcsb.org
      resp = requests.get(f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}")
    • skills/pdb-database/SKILL.md:99contacts data.rcsb.org
      resp = requests.get(f"https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{entity_id}")
    • skills/pdb-database/SKILL.md:168contacts data.rcsb.org
      resp = requests.get(f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}")

  • 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 aminoanalytica/amina-skills at e0ff001af3.

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

Commit
e0ff001af3
Manifest
skills/pdb-database/SKILL.md
Scanned
2 files, 508 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 and querying capabilities of the Protein Data Bank (PDB) database. It allows users to retrieve information about protein structures, including atomic coordinates, experimental details, and related publications. The skill facilitates analysis and understanding of 3D molecular structures for research or educational purposes.

When to use it

  • Researching a specific protein: Find detailed structural data for proteins involved in biological processes.
  • Educational exploration: Visualize and learn about the 3D structure of various biomolecules.
  • Analyzing experimental results: Compare your findings with existing PDB entries.
  • Drug discovery: Identify potential binding sites on target proteins based on their structures.

Key capabilities

  • PDB database access
  • Structure retrieval
  • Atomic coordinate data
  • Experimental details
  • Related publication information

Example prompts

  • "Get the structure of hemoglobin from the PDB."
  • "What are the experimental conditions for PDB ID 1AKE?"
  • "Find all proteins with a resolution better than 2 Angstroms in the PDB."

Tips & gotchas

The skill requires familiarity with PDB identifiers (e.g., 1AKE, 4HHB) to effectively retrieve data. Results are dependent on the completeness and accuracy of the information available within the Protein Data Bank itself.