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Pdb

Listed
adaptyvbio·vlatest·other·MIT

The PDB skill extracts protein structures from scientific papers, streamlining research by providing immediate structural data.

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 adaptyvbio/protein-design-skills --skill pdb -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

adaptyvbio

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

    • skills/pdb/SKILL.md:27contacts files.rcsb.org
      curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb"
    • skills/pdb/SKILL.md:30contacts files.rcsb.org
      curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif"

  • 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 adaptyvbio/protein-design-skills at 59dd633743.

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

Commit
59dd633743
Manifest
skills/pdb/SKILL.md
Scanned
1 file, 200 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

The pdb skill provides capabilities related to protein design. It allows users to interact with and manipulate protein structures, likely through a series of prompts and actions. The specific functionalities revolve around the manipulation and analysis of proteins within a computational environment.

When to use it

  • When you need to explore different protein sequences for potential modifications.
  • To analyze existing protein structures and identify areas suitable for design interventions.
  • For generating variations of a protein structure based on specified criteria.
  • If you're working with protein engineering workflows that require iterative design cycles.

Key capabilities

  • Protein sequence manipulation
  • Structure analysis
  • Design intervention suggestions
  • Variation generation

Example prompts

  • "Suggest mutations to improve the stability of this protein."
  • "Analyze the structure and identify potential binding sites."
  • "Generate 10 variations of this protein with increased hydrophobicity."
  • "What are the key structural features influencing this protein's function?"

Tips & gotchas

This skill likely requires familiarity with protein structures and basic bioinformatics concepts to effectively utilize its capabilities. The specific input formats and output interpretations may require some experimentation to optimize results.