mcpbeat

Query Pdb

biotender-max/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".

916 tokens
context cost
the whole folder, loaded on every use
1
files
instructions only
0
copies elsewhere
how many repositories repackaged it
132
stars on the repo
on the repository, not the skill itself

Install

one command, takes just this skill from the repository 
npx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill query-pdb

The instruction itself

5 sections, as written by the author

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

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_scientific_name",
                        "operator": "exact_match", "value": organism}}
    ]
    if method:
        nodes.append({"type": "terminal", "service": "text",
                      "parameters": {"attribute": "exptl.method", "operator": "exact_match", "value": method}})
    query = {
        "query": {"type": "group", "logical_operator": "and", "nodes": nodes},
        "return_type": "entry",
        "request_options": {"paginate": {"start": 0, "rows": max_results},
                           "sort": [{"sort_by": "rcsb_accession_info.deposit_date", "direction": "desc"}]}
    }
    r = requests.post("https://search.rcsb.org/rcsbsearch/v2/query", json=query)
    r.raise_for_status()
    return r.json()

# 3. Get entry details
def get_pdb_entry(pdb_id):
    url = f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}"
    r = requests.get(url)
    r.raise_for_status()
    return r.json()

# 4. Download structure
def download_pdb(pdb_id, output_dir="/workspace/group"):
    url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
    r = requests.get(url)
    r.raise_for_status()
    path = f"{output_dir}/{pdb_id}.pdb"
    with open(path, 'w') as f:
        f.write(r.text)
    return path

# Example
results = search_pdb("human insulin")
for hit in results.get("result_set", []):
    pdb_id = hit["identifier"]
    details = get_pdb_entry(pdb_id)
    title = details.get("struct", {}).get("title", "N/A")
    method = details.get("exptl", [{}])[0].get("method", "N/A")
    resolution = details.get("rcsb_entry_info", {}).get("resolution_combined", ["N/A"])[0]
    print(f"{pdb_id}: {title}")
    print(f"  Method: {method}, Resolution: {resolution} Å")

Common Methods

  • X-RAY DIFFRACTION — crystal structures
  • ELECTRON MICROSCOPY — cryo-EM
  • SOLUTION NMR — NMR in solution

Follow-up Suggestions

  • "Want me to download this structure and analyze binding sites?"
  • "Should I compare with the AlphaFold prediction?"
  • "Want me to find ligands bound in this structure?"

How to use it

Copy the folder

Take biotender-max/query-pdb from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

The agent identifies a skill by the name field in its header. Two skills with the same name cannot sit side by side — one of them will be ignored.