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MCP server wrapping AlphaFold DB and 8 other biomedical data sources, with a local SQLite knowledge graph.
The publisher performed an authenticated act of publication — proving control of a namespace in the official MCP registry, or appearing in a first-party catalogue an operator curates. That establishes WHO published it. It is not a security finding, and attested artifacts carry Flagged verdicts too.
7 critical findings reported by agent-audit-kit, 6 of them in the installed artifact. The composite score alone does not reflect this — read the per-scanner reports below.
This artifact ships from 3 sources and their verdicts differ. The worst is github (Flagged). Installing from a cleaner source does not mean the others are safe — check the source you actually install from.
github: https://github.com/smaniches/alphafold-sovereign-mcp, 185 findings
Choose your runtime: the CLI writes the mcpServers config entry for that target.
nerlo install --target claude-code -- alphafold-sovereign-mcp
Install respects the composite badge: Clean proceeds, Caution prompts for confirmation, and Flagged is refused. Write operations require an API token.
5 of 11 scanners examined this package. The rest do not apply to it — language, ecosystem and packaging decide which analyzers can say anything, and a scanner that cannot examine an artifact reports nothing rather than passing it.
v2.0.11
90 findings · 130.3s
v0.3.26
81 findings · 118.7s
v0.1.0
0 findings · 83.3s
v0.1.0
1 finding · 83.3s
v0.1.0
2 findings · 47.6s
v1.4.0
This scanner found nothing in this artifact that it assesses. What each scanner covers
0 findings · 1.0s
No report in this scan: capslock, govulncheck, osv-scanner, trivy, trivy_image.
1 scan on record. Every scan's full results are retained immutably for 24 months.
| Completed | Composite | Change | Scanners | Status |
|---|---|---|---|---|
| Aug 2, 2026 | Scan Halted | — | agentshield ·n/a: not applicablecisco-skill-scanner: completeagent-audit-kit: completenerlo-behavioral: completenerlo-install-instruction: completenerlo-multi-source: complete | rejected |
Findings in files this artifact installs stand as reported; a model re-read the rest and said which ones it believes are false positives. This is a second opinion published beside the evidence, not a correction to it: the per-scanner reports above are unchanged, every dismissed finding is still listed there at its original severity, and the score and the Flagged badge are computed from those raw severities alone. Nothing below moved them.
Out of 174 findings across every scanner that examined this package. 1 of 7 findings rated critical by their scanner was among the dismissals.
Not reviewed is not the same as clean. Those 1 finding stand exactly as their scanners reported them, at full severity, as they would have without this review.
Two keys had to turn. The model had to name a reason from a fixed list of six, and a deterministic check of ours — over which files this artifact actually installs — had to independently agree. Anything it could not corroborate is in “not reviewed” above, at full severity.
49 Documentation or example — The match is in documentation or sample code, confirmed by our own check to be outside the installed artifact.
Rules: AAK-HEALTHCARE-AI-004, SOCIAL_ENG_VAGUE_DESCRIPTION, MANIFEST_MISSING_LICENSE and 1 more · Files: examples/README.md, docs/index.md, docs/threat-model.md and 30 more · reported by agent-audit-kit, cisco-skill-scanner
6 Test or fixture file — The match is in a test or fixture. Our own check confirmed the file is not part of what gets installed.
Rules: AAK-SSRF-001, AAK-SECRET-004, AAK-SSRF-005 and 2 more · Files: tests/test_tool_disease.py, tests/test_client_clinvar.py, tests/test_knowledge_graph.py and 1 more · reported by agent-audit-kit
1 CI or editor configuration — The match is in build, CI or editor configuration, confirmed by our own check to be outside the installed artifact.
Rules: AAK-GHA-IMMUTABLE-001 · Files: .github/workflows/release.yml · reported by agent-audit-kit
These findings are in files this artifact installs and are not placeholder values. No false-positive basis can be corroborated for such a finding, so this review never dismisses one; they were not sent to the model and stand at their scanner's severity.
40 DATA_EXFIL_NETWORK_REQUESTS
Files: /repo/_archive/legacy/alphafold_mcp.py, /repo/_archive/legacy/fetcher.py · reported by cisco-skill-scanner
24 AAK-LOGINJ-001
Files: src/alphafold_sovereign/tools/disease.py, _archive/legacy/alphafold_mcp.py · reported by agent-audit-kit
13 AAK-HEALTHCARE-AI-004
Files: ARCHITECTURE.md, .zenodo.json, LIMITATIONS.md and 10 more · reported by agent-audit-kit
7 HIDDEN_DATA_FILE
Files: /repo/.clusterfuzzlite/project.yaml, /repo/.pre-commit-config.yaml, /repo/.release-please-manifest.json and 4 more · reported by cisco-skill-scanner
5 AAK-SSRF-001
Files: src/alphafold_sovereign/tools/knowledge_graph_tools.py, src/alphafold_sovereign/tools/disease.py, src/alphafold_sovereign/tools/precision_medicine.py and 2 more · reported by agent-audit-kit
5
1 The model did not answer for these findings.
Rules: FILE_MAGIC_MISMATCH · Files: /repo/tests/__init__.py · reported by cisco-skill-scanner
Critical network egress and credential access risks identified.
The artifact contains critical findings related to network egress, specifically Server-Side Request Forgery (SSRF) vulnerabilities in multiple `alphafold_sovereign` tool files and a legacy archive. It also presents a critical risk of credential access within a legacy archive file. High severity findings include potential supply chain compromise, additional SSRF vulnerabilities, and a hidden executable script.
Concern level assessed by the review: Critical. This is the review's scale, not the registry badge.
Reviewed by gemini-2.5-flash. The model sees the findings, not your code, and cannot change a score.
Files: src/alphafold_sovereign/tools/knowledge_graph_tools.py, src/alphafold_sovereign/tools/disease.py, src/alphafold_sovereign/tools/precision_medicine.py and 2 more · reported by agent-audit-kit
3 MANIFEST_MISSING_LICENSE
Files: /repo/SKILL.md, /repo/benchmarks/SKILL.md, /repo/_archive/legacy/SKILL.md · reported by cisco-skill-scanner
3 SOCIAL_ENG_VAGUE_DESCRIPTION
Files: /repo/SKILL.md, /repo/benchmarks/SKILL.md, /repo/_archive/legacy/SKILL.md · reported by cisco-skill-scanner
2 nerlo-malware-obfuscated_blob
Files: github_release:alphafold_sovereign_mcp-1.4.3.tar.gz.sigstore, github_release:alphafold_sovereign_mcp-1.4.3-py3-none-any.whl.sigstore · reported by nerlo-malware
2 PIPELINE_TAINT_FLOW
Files: /repo/CONTRIBUTING.md, /repo/SKILL.md · reported by cisco-skill-scanner
2 TOOL_ABUSE_UNDECLARED_NETWORK
Files: /repo/repo/ARCHITECTURE.md, /repo/_archive/legacy/repo/_archive/legacy/README.md · reported by cisco-skill-scanner
1 AAK-MCP-005
Files: .mcp.json · reported by agent-audit-kit
1 AAK-MCP-007
Files: .mcp.json · reported by agent-audit-kit
1 AAK-MCP-015
Files: _archive/legacy/alphafold_mcp.py · reported by agent-audit-kit
1 AAK-METIS-SCORING-SINK-001
Files: src/alphafold_sovereign/storage/knowledge_graph.py · reported by agent-audit-kit
1 AAK-STATE-PRIVACY-001
Files: PRIVACY.md · reported by agent-audit-kit
1 AAK-STATE-PRIVACY-002
Files: PRIVACY.md · reported by agent-audit-kit
1 AAK-STATE-PRIVACY-003
Files: PRIVACY.md · reported by agent-audit-kit
1 AAK-SUPPLY-001
Files: .mcp.json · reported by agent-audit-kit
1 EXCESSIVE_FILE_COUNT
Files: /repo/. · reported by cisco-skill-scanner
1 HIDDEN_EXECUTABLE_SCRIPT
Files: /repo/.clusterfuzzlite/build.sh · reported by cisco-skill-scanner
1 opt.nerlo-rules.nerlo-install-pipe-to-shell
Files: /repo/CONTRIBUTING.md · reported by nerlo-install-instruction