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PDB Explorer

Search 200K+ protein structures from the RCSB Protein Data Bank. Full-text search via RCSB Search API v2, with detailed entry metadata (resolution, R-factor, authors, unit cell, polymer entities with sequences). No API key needed — the app proxies RCSB REST API calls.

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Overview

Data Source

RCSB PDB REST API — search.rcsb.org (search) + data.rcsb.org (entry metadata + polymer entities).

Endpoints

POST /pdb_explorer/search — Search materials

curl -X POST "https://atomgpt.org/pdb_explorer/search" \
  -H "Authorization: Bearer sk-XYZ" \
  -H "Content-Type: application/json" \
  -d '{"formula": "MoS2"}'
Field Type Description
query string Full-text search query (e.g. 'insulin', 'kinase')
max_results int Max results (default 20, max 50)

Response: pdb_id, score, title, method, resolution, deposition_date, organism, authors, spacegroup.

GET /pdb_explorer/data/{jid} — Full record

curl "https://atomgpt.org/pdb_explorer/data/JVASP-664" \
  -H "Authorization: Bearer sk-XYZ"

Response: pdb_id, title, method, resolution, r_factor, r_free, deposition/release dates, authors, journal, doi, pub_year, cell (a/b/c/α/β/γ), spacegroup, z_value, polymer/nonpolymer/assembly counts, molecular_weight, polymers (entity_id, name, type, sequence, length, organism, weight).

Python Examples

import requests

response = requests.get(
    "https://atomgpt.org/pdb_explorer/data/JVASP-1002",
    headers={"Authorization": "Bearer sk-XYZ"},
)
data = response.json()
print(f"{data['pdb_id']}: {data['title']}")
print(f"  Method: {data['method']}, Resolution: {data['resolution']} Å")
for p in data["polymers"]:
    print(f"  Chain {p['entity_id']}: {p['name']} ({p['length']} residues)")

AGAPI Agent

from agapi.agents import AGAPIAgent
import os
agent = AGAPIAgent(api_key=os.environ.get("AGAPI_KEY"))
response = agent.query_sync("Show pdb explorer data")
print(response)

References