Versioned security assessment

Report ID: SA-2EAF90F9

6/30/2026, 5:49:53 AM

pdb-database security assessment v5

Skill Security Certification Report

Audit History

Audit model: codex Historical report

Skill name: pdb-database
Version: v5
Maintainer: K-Dense-AI
Source: github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pdb-database
Coverage: 3 Files scanned · 1,140 Lines analyzed
Policy version: Unavailable

Highest confirmed finding severity

Low

2 confirmed security findings require 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 severe patterns, but review found they are mostly documentation false positives or expected access to public RCSB PDB services. The real residual risks are low: examples perform public network requests, save downloaded structure files, and include one hardcoded curl subprocess debugging snippet. No evidence found of credential theft, obfuscation, prompt injection, malicious endpoints, or user-controlled command execution.

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

3 Files scanned · 1,140 Lines analyzed

2 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.

Source

Binding unavailable
Artifact

Identity incomplete
Audit

Complete
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 4 evidence locations

Filesystem access

May read or write local files.

Observed in 2 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

Risk findings

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

Confirmed security concerns (2)

RISK-001 Low

SKILL.md:157-164 references/api_reference.md:113-115 references/api_reference.md:401-404 references/api_reference.md:447

Expected Public RCSB Network Access

The skill documents requests to public RCSB PDB endpoints for search, metadata retrieval, and coordinate downloads. This is expected for the skill, but users should know it requires internet access.

The network calls and hardcoded URLs are directly visible and point to RCSB PDB services. No evidence shows credential exfiltration, hidden endpoints, or unrelated third-party destinations.

RISK-002 Low

SKILL.md:159-165 references/api_reference.md:392-408

Documented Local File Writes for Structure Downloads

Example code writes downloaded PDB and mmCIF files to local paths. This is normal for coordinate downloads, but callers should validate PDB IDs and output directories in production code.

The file writes are explicit and serve the documented purpose of saving structure files. Risk is limited because the examples use known PDB IDs, although the helper accepts output_dir and pdb_id parameters.

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 (3)

Low

references/api_reference.md:600-604 evaluation_result.json:21-24

Hardcoded Curl Subprocess Example

The reference includes a debugging example that runs curl through subprocess.run against a fixed RCSB URL. It is not command injection because command arguments are fixed and no user input is interpolated.

The subprocess call is present, but it uses a fixed argv list and a public RCSB endpoint. I found no shell=True usage or user-controlled command construction.

Low

SKILL.md:31-36 references/api_reference.md:32-37 references/api_reference.md:589-608

Markdown Backticks Misclassified as Shell Execution

Many external command alerts are caused by markdown code fences and inline code in SKILL.md and the API reference. These are documentation delimiters, not Ruby shell backtick execution.

The cited locations are markdown examples and code fences in documentation. They are not executable Ruby source and do not create shell execution behavior by themselves.

Low

SKILL.md:57 references/api_reference.md:239 references/api_reference.md:3-7

Static Scanner False Positives in Scientific Documentation

The Windows SAM and weak cryptography alerts are false positives. The cited content is scientific documentation, amino acid sequences, API text, or markdown code formatting, not credential access or cryptographic logic.

The cited lines are in a structural biology skill and contain protein sequence text, API documentation, or markdown examples. I found no evidence of Windows credential access, cryptographic operations, or malicious intent.

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