alphafold-database
Access and analyze over 200 million AI-predicted protein structures for drug discovery and structural biology.
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The alphafold-database skill was audited on Jun 3, 2026 and we found 18 security issues across 2 threat categories. Review the findings below before installing.
Categories Tested
Security Issues
medium line 248
Python subprocess execution
SourceSKILL.md
| 248 | subprocess.run(cmd, shell=True, check=True) |
low line 61
External URL reference
SourceSKILL.md
| 61 | api_url = f"https://alphafold.ebi.ac.uk/api/prediction/{uniprot_id}" |
low line 79
External URL reference
SourceSKILL.md
| 79 | url = 'https://www.uniprot.org/uploadlists/' |
low line 113
External URL reference
SourceSKILL.md
| 113 | model_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.cif" |
low line 119
External URL reference
SourceSKILL.md
| 119 | confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_{version}.json" |
low line 124
External URL reference
SourceSKILL.md
| 124 | pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_{version}.json" |
low line 133
External URL reference
SourceSKILL.md
| 133 | pdb_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-model_{version}.pdb" |
low line 151
External URL reference
SourceSKILL.md
| 151 | confidence_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" |
low line 176
External URL reference
SourceSKILL.md
| 176 | pae_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-predicted_aligned_error_v4.json" |
low line 336
External URL reference
SourceSKILL.md
| 336 | conf_url = f"https://alphafold.ebi.ac.uk/files/{alphafold_id}-confidence_v4.json" |
low line 386
External URL reference
SourceSKILL.md
| 386 | url = f"https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/{uniprot_id}.json" |
low line 495
External URL reference
SourceSKILL.md
| 495 | - **AlphaFold DB Website:** https://alphafold.ebi.ac.uk/ |
low line 496
External URL reference
SourceSKILL.md
| 496 | - **API Documentation:** https://alphafold.ebi.ac.uk/api-docs |
low line 497
External URL reference
SourceSKILL.md
| 497 | - **Google Cloud Dataset:** https://cloud.google.com/blog/products/ai-machine-learning/alphafold-protein-structure-database |
low line 498
External URL reference
SourceSKILL.md
| 498 | - **3D-Beacons API:** https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/ |
low line 500
External URL reference
SourceSKILL.md
| 500 | - Nature (2021): https://doi.org/10.1038/s41586-021-03819-2 |
low line 501
External URL reference
SourceSKILL.md
| 501 | - Nucleic Acids Research (2024): https://doi.org/10.1093/nar/gkad1011 |
low line 502
External URL reference
SourceSKILL.md
| 502 | - **Biopython Documentation:** https://biopython.org/docs/dev/api/Bio.PDB.alphafold_db.html |
Scanned on Jun 3, 2026
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Categorydevelopment
UpdatedJune 15, 2026
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