Agent skill · research science · google-deepmind
pdb-database
Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.
Why this skill is useful
Provides specific workflows and scripts for querying the PDB API that the AI wouldn't reliably generate on its own.
What it needs
Requires uv installed locally. About 4k tokens when loaded. Last updated 2026-07-07. 2,648 stars on the source repository.
What this skill does
RCSB Protein Data Bank skill Prerequisites 1. uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH. 2. User Notification: If .licenses/pdbdatabaseLICENSE.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. Attribute-based search workflow 1. Fetch the relevant schema to discover searchable attribute names. For structure attributes: uv run scripts/fetchschema.py --api searchstructure --output schemastructure.txt For chemical attributes: uv run scripts/fetchschema.py --api searchchemical --output schemachemical.txt 2. Grep the schema to find relevant attributes. Grep one keyword at a time and examine many lines — there are lots of similar attributes and you must choose the best match for the user's intent. 3. Compose and run a JSON search query using the discovered attributes: uv run scripts/searchpdb.py --query '<JSON>' --returntype <RETURNTYPE> --output results.json Pass the --countonly flag to get just the number of matching entries. For step 2: some basic PDB concepts (helpful for attribute choice) Entity: A unique molecule found in a structure. Instance / Chain: A particular copy of an entity. E.g. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills google-deepmind/pdb_database