Lightweight lookup for a PDB entry by 4-char ID: tries the RCSB UniProt endpoint first, falls back to the core entry record. Returns title, experimental method, resolution, and deposition date without the full polymer/ligand detail of
AI agents call summary to retrieve information from Mcp Rcsb Pdb without modifying anything — typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
This tool queries the RCSB Protein Data Bank to fetch metadata about a protein structure entry. It retrieves information only (no creation, modification, deletion, or execution of arbitrary code). The blast radius of misuse is minimal: an attacker could enumerate PDB entries or gather structural biology research data, but cannot modify databases, execute commands, or cause financial harm.
From the tool's definition Tool performs 'Lightweight lookup' and 'Returns title, experimental method, resolution, and deposition date' — retrieves and queries data with no modification or side effects.
Attacks that exploit this kind of access
Lightweight lookup for a PDB entry by 4-char ID: tries the RCSB UniProt endpoint first, falls back to the core entry record. Returns title, experimental method, resolution, and deposition date without the full polymer/ligand detail of. It is categorised as a Read tool in the Mcp Rcsb Pdb MCP Server, which means it retrieves data without modifying state.
Register the Mcp Rcsb Pdb MCP server in PolicyLayer and add a rule for summary: allow, deny, rate-limit, or require approval. Point your MCP client at the PolicyLayer proxy URL and the rule is enforced on every call, before it reaches Mcp Rcsb Pdb. Nothing to install.
summary is a Read tool with low risk. Read-only tools are generally safe to allow by default.
Yes. Add a rate_limit block to the summary rule in your PolicyLayer policy. For example, setting max: 10 and window: 60 limits the tool to 10 calls per minute. Rate limits are tracked per agent session and reset automatically.
Set action: deny in the PolicyLayer policy for summary. The AI agent will receive a policy violation error and cannot call the tool. You can also include a reason field to explain why the tool is blocked.
summary is provided by the Mcp Rcsb Pdb MCP server (pipeworx-io/mcp-rcsb-pdb). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
Every MCP server has a record like this.
Type a name, get the same breakdown: verified identity, auth posture, risk grade, capabilities, recommended policy.
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