query-pdb
Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".
npx skills add BioTender-max/awesome-bio-agent-skills --skill query-pdb --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# RCSB PDB Database Query Query the RCSB Protein Data Bank for experimental 3D structures. ## When to Use - User asks for experimental structures of a protein - User provides a PDB ID (e.g., "6LU7") - User wants to find structures solved by X-ray, cryo-EM, or NMR - User asks about resolution, ligands, or binding sites ## How to Execute ```python import requests import json # 1. Text search (simple keyword) def search_pdb(query_text, max_results=5): url = "https://search.rcsb.org/rcsbsearch/v2/query" query = { "query": { "type": "terminal", "service": "full_text", "parameters": {"value": query_text} }, "return_type": "entry", "request_options": {"paginate": {"start": 0, "rows": max_results}} } r = requests.post(url, json=query) r.raise_for_status() return r.json() # 2. Advanced search (by gene + organism + method) def advanced_search_pdb(gene_name, organism="Homo sapiens", method=None, max_results=5): nodes = [ {"type": "terminal", "service": "text", "parameters": {"attribute": "rcsb_entity_source_organism.rcsb_gene_name.value", "operator": "exact_match", "value": gene_name}}, {"type": "terminal", "service": "text", "parameters": {"attribute": "rcsb_entity_source_organism.ncbi_scien
- When to Use
- How to Execute
- Common Methods
- Follow-up Suggestions
What does the query-pdb skill do?
Query RCSB PDB for experimental protein structures. Use when user asks about crystal structures, X-ray, cryo-EM, NMR structures, or PDB IDs. Triggers on "pdb", "crystal structure", "cryo-em", "x-ray structure", "protein crystal", "experimental structure".
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill query-pdb --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 144 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.