Loading skill
Install any skill in seconds. Free to start, no credit card required.
Get Started Free →mkurman/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.
2 of 22 test cases passed with the skill.
Tokens, turns and time describe resource use, not a dollar price.
Lift withheld: 2 comparable cases; this report requires 8.
A test case the skill fixed. Same model, same prompt, with and without the skill.
Before performing any PDB data queries in a new environment where LICENSE_NOTIFICATION.txt is missing, what setup action must be taken regarding usage policies?
| Checked | Without skill | With skill |
|---|---|---|
| The response states that the user must be notified to check RCSB terms at https://www.rcsb.org/pages/usage-policy. | Missed | Passed |
| The response indicates that LICENSE_NOTIFICATION.txt must be created containing the notification text and timestamp. | Missed | Passed |
The instructions your model reads when the skill loads.
uv: Read the uv skill and follow its Setup instructions to ensure
uv is installed and on PATH.curl, urllib, raw HTTP requests, or any other method to access PDB APIs.
The scripts automatically enforce required rate limits.jq, grep,
or a short Python snippet. Do NOT print large API responses to stdout to
avoid truncation.Fetch the relevant schema to discover searchable attribute names. For
structure attributes: uv run scripts/fetch_schema.py --api search_structure --output schema_structure.txt For chemical attributes: uv run scripts/fetch_schema.py --api search_chemical --output schema_chemical.txt
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.
Compose and run a JSON search query using the discovered attributes: uv run scripts/search_pdb.py --query '<JSON>' --return_type <RETURN_TYPE> --output results.json Pass the --count_only flag to get just the number
of matching entries.
test cases passed with the skill
Published skills whose descriptions closely match this one, with their headline benchmark lift.
More skills from the same source and nearby in the registry, with their headline benchmark lift.