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Security audit

Protein Docking Configurator

Security checks for vulnerabilities and agentic risk

Overview

This skill is a local molecular-docking configuration helper with some documentation gaps, but no hidden network, persistence, credential, or destructive behavior was found.

Reasonable to install for generating docking configuration files. Use it on non-sensitive input files in a normal project workspace, and provide explicit output paths you are comfortable writing to. Do not rely on advertised MOL or non-Vina/non-AutoDock4 support unless the skill is updated.

A.I.G

Vulnerability Patterns
  • Skill Instruction HijackingAlters the agent's session goals or safety constraints when the skill loads
  • Agent Memory PoisoningWrites attacker-controlled rules into memory that affect later sessions
  • Remote Payload Retrieval and ExecutionFetches external code whose behavior can change after review
  • Embedded Malicious CodeShips malicious scripts inside the skill and executes them locally
  • Unauthorized Access and Privilege EscalationObtains permissions beyond the task's legitimate needs

SkillSpector

Vulnerability Patterns
  • MCP Least PrivilegeUnderdeclared Capability, Wildcard Permission, Missing Permission Declaration
  • MCP Tool PoisoningHidden Instructions, Unicode Deception, Parameter Description Injection
  • Prompt InjectionInstruction Override, Hidden Instructions, Exfiltration Commands
  • Data ExfiltrationExternal Transmission, Env Variable Harvesting, File System Enumeration
  • Privilege EscalationExcessive Permissions, Sudo/Root Execution, Credential Access
Findings (4)

Undeclared Tool Scope

Medium
Category
MCP Least Privilege
Confidence
91% confidence
Finding

The skill documentation describes file read and file write behavior, but it does not declare any explicit tool scope such as permissions or allowed-tools. This creates an authorization ambiguity where an agent or reviewer cannot clearly determine the intended filesystem boundaries, increasing the risk of unintended file access, path traversal, or writing outside the workspace if the implementation is permissive.

Content

No source excerpt is available for this finding.

Description-Behavior Mismatch

Medium
Category
Not specified by scanner
Confidence
96% confidence
Finding

The module description says the skill supports AutoDock Vina, AutoDock4, and other mainstream docking tools. In practice, the CLI restricts --software to vina and autodock4, and the code only contains writers for Vina config and AutoDock4 GPF files. The implemented behavior is narrower than the advertised support.

Content

No source excerpt is available for this finding.

Intent-Code Divergence

Medium
Category
Not specified by scanner
Confidence
93% confidence
Finding

The docstring for from_ligand states that ligand_file may be a PDB/MOL file, and the CLI help for --reference-ligand makes the same claim. However, the method immediately calls PDBParser.parse, which only extracts atoms from PDB ATOM/HETATM records and has no MOL parser. This is an active documentation-to-code contradiction about supported input formats.

Content

No source excerpt is available for this finding.

Natural-Language Policy Violations

Low
Category
Not specified by scanner
Confidence
91% confidence
Finding

The top-level natural-language description is written entirely in Chinese, which signals a fixed language/locale choice in the skill's user-facing documentation. There is no indication that users may choose another language or that the locale restriction is required for a region-specific purpose.

Content

No source excerpt is available for this finding.

Static analysis

No suspicious patterns detected.