Pdb Database

If you're working with protein structures, this gives Claude direct access to the RCSB Protein Data Bank through a proper API integration. It handles the setup through uv and makes sure you're aware of RCSB's usage policies before pulling any data. Coming from DeepMind's science skills collection, it's built for computational biology workflows where you need to query, retrieve, or analyze protein structure data without manually downloading PDB files. The 1K installs and solid audit scores suggest it's stable enough for real research work. Just know you'll need to review RCSB's terms on first use, which the skill enforces by creating a license file in your workspace.

skills.sh installs: 2.3K
GitHub stars: 3.4K
last updated: Aug 21, 2026

View on GitHub

Install

$ npx -y skills add google-deepmind/science-skills --skill pdb-database --agent claude-code

Installs into .claude/skills of the current project.

Files

RCSB Protein Data Bank skill

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If .licenses/pdb_database_LICENSE.txt does not already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://www.rcsb.org/pages/usage-policy, then (2) create the file recording the notification text and timestamp.

Core Rules

Always prefer to use the provided scripts. Only as a last resort use curl, urllib, raw HTTP requests, or any other method to access PDB APIs. The scripts automatically enforce required rate limits.
Always redirect output to a file. Parse output with e.g. jq, grep, or a short Python snippet. Do NOT print large API responses to stdout to avoid truncation.
Notification: If this skill is used, ensure this is mentioned in the output.
Explain your queries On completing a task that used PDB JSON/GraphQL queries, explain in clear language what your query did so the user can correct any bad assumptions.