pdb-database
Access RCSB PDB for 3D protein structures, enabling searches, downloads, and metadata retrieval for structural biology and drug discovery.
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The pdb-database skill was audited on May 12, 2026 and we found 13 security issues across 2 threat categories. Review the findings below before installing.
Categories Tested
Security Issues
low line 116
Fetch to external URL
SourceSKILL.md
| 116 | entry_data = fetch("4HHB", schema=Schema.ENTRY) |
low line 125
Fetch to external URL
SourceSKILL.md
| 125 | entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY) |
low line 212
Fetch to external URL
SourceSKILL.md
| 212 | data = fetch("4HHB", schema=Schema.ENTRY) |
low line 160
External URL reference
SourceSKILL.md
| 160 | - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb` |
low line 161
External URL reference
SourceSKILL.md
| 161 | - **mmCIF format** (modern standard): `https://files.rcsb.org/download/{PDB_ID}.cif` |
low line 163
External URL reference
SourceSKILL.md
| 163 | - **Biological assembly**: `https://files.rcsb.org/download/{PDB_ID}.pdb1` (for assembly 1) |
low line 173
External URL reference
SourceSKILL.md
| 173 | pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb" |
low line 179
External URL reference
SourceSKILL.md
| 179 | cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif" |
low line 325
External URL reference
SourceSKILL.md
| 325 | - **RCSB PDB Website:** <https://www.rcsb.org> |
low line 326
External URL reference
SourceSKILL.md
| 326 | - **PDB-101 Educational Portal:** <https://pdb101.rcsb.org> |
low line 327
External URL reference
SourceSKILL.md
| 327 | - **API Documentation:** <https://www.rcsb.org/docs/programmatic-access/web-apis-overview> |
low line 328
External URL reference
SourceSKILL.md
| 328 | - **Python Package Docs:** <https://rcsbapi.readthedocs.io/> |
low line 329
External URL reference
SourceSKILL.md
| 329 | - **Data API Documentation:** <https://data.rcsb.org/> |
Scanned on May 12, 2026
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Categoryeducation research
UpdatedMay 21, 2026
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