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RCSB PDB for 3D protein structures, resolution, and experimental methods
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Based on SOC occupation classification
| name | pdb |
| description | RCSB PDB for 3D protein structures, resolution, and experimental methods |
RCSB PDB hosts experimentally determined 3D structures of biological macromolecules solved by X-ray crystallography, cryo-EM, and NMR.
import requests
# Text search
url = "https://search.rcsb.org/rcsbsearch/v2/query"
query = {
"query": {
"type": "terminal",
"service": "text",
"parameters": {"attribute": "struct.title", "operator": "contains_words", "value": "kinase"}
},
"return_type": "entry"
}
r = requests.post(url, json=query)
pdb_ids = [hit["identifier"] for hit in r.json()["result_set"]]
# Fetch entry summary
r = requests.get("https://data.rcsb.org/rest/v1/core/entry/4HHB")
entry = r.json()
# Get polymer entities
r = requests.get("https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB/1")
query_gql = '{ entry(entry_id: "4HHB") { struct { title } rcsb_entry_info { resolution_combined } } }'
r = requests.post("https://data.rcsb.org/graphql", json={"query": query_gql})
https://files.rcsb.org/download/{PDB_ID}.cif (or .pdb).PDBParser or MMCIFParser for local structure analysis.Shared operational contract for all MedSci agents: sequential execution, planning phase, retry limits, evidence standards.
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