pdb-database
Access and retrieve 3D protein and nucleic acid structures from RCSB PDB for research in structural biology and drug discovery.
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The pdb-database skill was audited on May 23, 2026 and we found 13 security issues across 2 threat categories. Review the findings below before installing.
Categories Tested
Security Issues
low line 104
Fetch to external URL
SourceSKILL.md
| 104 | entry_data = fetch("4HHB", schema=Schema.ENTRY) |
low line 112
Fetch to external URL
SourceSKILL.md
| 112 | entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY) |
low line 194
Fetch to external URL
SourceSKILL.md
| 194 | data = fetch("4HHB", schema=Schema.ENTRY) |
low line 145
External URL reference
SourceSKILL.md
| 145 | - **PDB format** (legacy text format): `https://files.rcsb.org/download/{PDB_ID}.pdb` |
low line 146
External URL reference
SourceSKILL.md
| 146 | - **mmCIF format** (modern standard): `https://files.rcsb.org/download/{PDB_ID}.cif` |
low line 148
External URL reference
SourceSKILL.md
| 148 | - **Biological assembly**: `https://files.rcsb.org/download/{PDB_ID}.pdb1` (for assembly 1) |
low line 157
External URL reference
SourceSKILL.md
| 157 | pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb" |
low line 163
External URL reference
SourceSKILL.md
| 163 | cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif" |
low line 301
External URL reference
SourceSKILL.md
| 301 | - **RCSB PDB Website:** https://www.rcsb.org |
low line 302
External URL reference
SourceSKILL.md
| 302 | - **PDB-101 Educational Portal:** https://pdb101.rcsb.org |
low line 303
External URL reference
SourceSKILL.md
| 303 | - **API Documentation:** https://www.rcsb.org/docs/programmatic-access/web-apis-overview |
low line 304
External URL reference
SourceSKILL.md
| 304 | - **Python Package Docs:** https://rcsbapi.readthedocs.io/ |
low line 305
External URL reference
SourceSKILL.md
| 305 | - **Data API Documentation:** https://data.rcsb.org/ |
Scanned on May 23, 2026
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Categoryeducation research
UpdatedMay 25, 2026
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