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Pdb Database

Listed
drshailesh88·vlatest·database

Access and query protein structure data from the Protein Data Bank (PDB) using drshailesh88's specialized database 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 drshailesh88/integrated_content_os --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

drshailesh88

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/scientific/pdb-database/references/api_reference.md:52contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/entry/4HHB
    • skills/scientific/pdb-database/references/api_reference.md:55contacts data.rcsb.org
      curl https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB_1
    • skills/scientific/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 drshailesh88/integrated_content_os at 9e61937ad2.

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

Commit
9e61937ad2
Manifest
skills/scientific/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, drshailesh88-pdb-database, provides access to a PDB (Protein Data Bank) database. It allows users to query and retrieve information about protein structures, including coordinates, experimental details, and related publications. The skill can be used for tasks such as identifying specific proteins, analyzing structural data, or generating reports on protein characteristics.

When to use it

  • Research: A biologist needs to find the 3D structure of a particular enzyme for a research project.
  • Drug Discovery: A chemist wants to identify potential drug binding sites on a target protein.
  • Education: A student is learning about protein structures and wants to visualize different examples.
  • Structural Analysis: An engineer needs to analyze the stability of a protein under specific conditions.

Key capabilities

  • Accesses the Protein Data Bank (PDB) database.
  • Retrieves protein structure data.
  • Provides access to experimental details related to structures.
  • Offers information on publications associated with proteins.

Example prompts

  • "Find the PDB ID for insulin."
  • "What are the coordinates of residue 100 in the structure of hemoglobin?"
  • "Give me a list of all protein structures solved using X-ray diffraction."

Tips & gotchas

The skill relies on the availability and accuracy of data within the Protein Data Bank. Familiarity with PDB IDs and basic structural biology terminology will improve results.