science.pdb.search
Search 220K+ macromolecular 3D structures in the Protein Data Bank by keyword, protein name, organism, or author. Returns PDB IDs with relevance scores. The canonical database for structural biology, X-ray crystallography, cryo-EM, and NMR structures (RCSB PDB)
This record as markdown: /tools/io-github-whiteknightonhorse-apibase/science.pdb.search.md
What science.pdb.search does on Apibase
AI agents call science.pdb.search to retrieve information from Apibase without modifying anything. It is typically the context-gathering step in research, monitoring, and reporting workflows, before the agent takes action elsewhere.
| Parameter | Type | Required | Description |
|---|---|---|---|
limit | integer | — | Maximum number of results (1-50). Default: 10 |
query | string | Yes | Search query — keyword, protein name, organism, or author (e.g. "insulin", "hemoglobin", "Homo sapiens", "Watson") |
Parameters from the server's own tool schema.
Why science.pdb.search is rated Low
Retrieves public structural biology data without modification or side effects.
From the tool's definition Search 220K+ macromolecular 3D structures, returns PDB IDs with relevance scores.
Attacks that exploit this kind of access
The rule that runs science.pdb.search safely
PolicyLayer is an MCP gateway: it sits between your AI agents and Apibase, and checks every tool call against a rule you set before the call runs. Nothing changes on the server itself. For science.pdb.search, this is the rule to start with:
science.pdb.search is read-only, so it stays allowed. Everything else on the server is denied unless you say otherwise.
The button opens the PolicyLayer dashboard: create your workspace, connect Apibase, apply this rule, and every science.pdb.search call is checked against it from then on.
Questions about science.pdb.search
Search 220K+ macromolecular 3D structures in the Protein Data Bank by keyword, protein name, organism, or author. Returns PDB IDs with relevance scores. The canonical database for structural biology, X-ray crystallography, cryo-EM, and NMR structures (RCSB PDB). It is categorised as a Read tool in the Apibase MCP Server, which means it retrieves data without modifying state.
science.pdb.search accepts 2 parameters: limit, query. Required: query. The full parameter table on this page comes from the server's own tool schema.
Register the Apibase MCP server in PolicyLayer and add a rule for science.pdb.search: 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 Apibase. Nothing to install.
science.pdb.search 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 science.pdb.search 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 science.pdb.search. 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.
science.pdb.search is provided by the Apibase MCP server (apibase-mcp-client). PolicyLayer sits as a proxy in front of this server to enforce policies before tool calls reach the server.
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