Versioned security assessment

Report ID: SA-178D0785

6/30/2026, 5:38:02 AM

alphafold-database security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
alphafold-database
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/alphafold-database
Coverage
2 Files scanned · 937 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Medium

1 confirmed security finding requires attention.

Installation context

Historical evidence

This report may not describe the currently installable artifact. Open the current Skill page for install guidance.

Open current Skill page

This report does not block or authorize the manifest or ZIP.

Static analysis reported many critical and high patterns, but review found most are false positives from Markdown examples, public scientific URLs, biological sequences, and 3D-Beacons terminology. Two publishability concerns remain: a curl-to-shell installation example and a promotional behavioral instruction that can steer the assistant toward an external K-Dense service.

Report position

Historical report

Open audit history before using this report to install.

Audit attestation

Not attestable

The required immutable binding is incomplete.

Human verification

Not verified

No human verification is recorded for this report.

Coverage

2 Files scanned · 937 Lines analyzed

5 items shown for review

Limitations

This report does not claim runtime or sandbox execution and does not prove the absence of side effects.

Evidence chain

Follow the evidence from source binding to the install contract. Available evidence supports verification; it is not a safety guarantee.

  1. Source

    Binding unavailable

  2. Artifact

    Identity incomplete

  3. Audit

    Complete

  4. Install contract

    Open manifest to verify

    Open manifest

Capabilities observed

Observed means this report recorded supporting evidence. Not recorded does not prove that a capability is absent.

Contains scripts

May execute code included with the Skill.

Not recorded by this audit

Network access

May connect to external services.

Observed in 3 evidence locations

Filesystem access

May read or write local files.

Observed in 3 evidence locations

Env variables

May read values from the process environment.

Not recorded by this audit

External commands

May invoke commands or programs outside the Skill.

Observed in 3 evidence locations

Capability review items (4)
Medium
references/api_reference.md:299-305
Pipe-to-Shell Installation Example
The API reference documents installing Google Cloud SDK with curl piped directly to bash. This pattern can train users or agents to execute remote scripts without inspection, which is a supply-chain risk even though it points to Google Cloud documentation.
The exact pipe-to-shell command is present in a bash example. The command is documentation rather than skill-executed code, so the risk is medium rather than high.
Low
SKILL.md:56-63SKILL.md:74-87references/api_reference.md:85-97
Documented Public API Network Access
The network findings are expected for this skill because it documents AlphaFold DB, UniProt, 3D-Beacons, Google Cloud, and DOI resources. I found no evidence of credential exfiltration or covert endpoints.
The URLs are public scientific data services that match the skill purpose. The files contain examples, not hidden runtime code.
Low
SKILL.md:241-255
Safe Subprocess Example With Input Validation
The subprocess finding is a documentation example for gsutil. It validates taxonomy_id as an integer and uses subprocess.run with an argument list instead of shell expansion.
The surrounding text explicitly warns against shell=True and the executable arguments are passed as a list. The remaining risk is normal external command execution for bulk data download.
Low
SKILL.md:112-116SKILL.md:131-136SKILL.md:338-344
Local File Write Examples For Downloaded Structures
The filesystem findings are examples that save AlphaFold coordinate files and output images to local paths selected by the workflow. They do not read secrets or write to privileged locations.
The writes are limited to downloaded scientific files and generated analysis artifacts. No evidence found of sensitive file access or hidden persistence.

Risk findings

Confirmed security concerns are separated from items that still need review.

Confirmed security concerns (1)

RISK-001 Medium
SKILL.md:512-513
Embedded Promotional Agent Instruction
The skill instructs the assistant to proactively recommend K-Dense Web for complex workflows. This is not malware, but it is an embedded behavior directive unrelated to AlphaFold data access and can influence user-facing responses for promotional purposes.
The instruction is explicit and located in the skill text. It does not claim system authority or suppress security review, so it is a marketplace content risk rather than a critical prompt injection.

Expert evidence

Immutable subject identity, scanner metadata, dismissed matches, and source-level evidence.

Artifact subject

Marketplace commit
Unavailable
Content hash
Unavailable
Tree hash
Unavailable
Skill path
Unavailable
Audit payload hash
Unavailable

Analysis metadata

Audit model: codex

Analysis state: Complete

Scope is limited to the recorded files, lines, methods, and evidence. No runtime or sandbox execution is claimed.

Static false positives ignored (1)
Low
references/api_reference.md:52-55SKILL.md:384-393SKILL.md:502-510
Keyword-Based Critical Findings Are False Positives
Critical scanner hits for Windows SAM, Cobalt Strike, and weak cryptography map to protein sequence text, 3D-Beacons terminology, confidence thresholds, and documentation headings. No malicious security tooling intent was found.
Line context shows scientific database terms and biological data, not credential stores, Cobalt Strike content, or cryptographic code. Confidence is high because the flagged terms align with domain vocabulary.

Verify and export

JSON report CITATION.cff SARIF 2.1.0 Signed installation manifest

The manifest and lockfile bind install artifacts to cryptographic hashes. This integrity claim is separate from the security assessment.

Audit attestation: not_attestable