science.pdb.sequence

SERVERApibase SOURCEapibase-mcp-client

Medium RISK CLASS

Category Write

Parameters 41 required

Recommended Rate-limitedsee the rule below

Registry record Grade F, identity unverified Pull the record →

This record as markdown: /tools/io-github-whiteknightonhorse-apibase/science.pdb.sequence.md

WHAT IT DOES

What science.pdb.sequence does on Apibase

AI agents use science.pdb.sequence to create or update resources in Apibase, usually the action step of a workflow, after the agent has gathered context. Every call changes real data in your Apibase environment.

Parameter	Type	Required	Description
`limit`	integer	—	Maximum number of results (1-50). Default: 10
`sequence`	string	Yes	Protein amino acid sequence in one-letter code (e.g. "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH" — first 50 residues of human hemoglobin alpha)
`evalue_cutoff`	number	—	Maximum E-value threshold for BLAST significance. Default: 0.1
`identity_cutoff`	number	—	Minimum sequence identity (0.1-1.0). Default: 0.9 (90% identical)

Parameters from the server's own tool schema.

RISK

Why science.pdb.sequence is rated Medium

An AI agent can call science.pdb.sequence faster than any human can review: one bad instruction and it creates or modifies resources in Apibase by the hundred, each call as confident as the last.

Attacks that exploit this kind of access

RECOMMENDED RULE

The rule that runs science.pdb.sequence 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.sequence, this is the rule to start with:

science.pdb.sequence Rate-limited

science.pdb.sequence stays usable, but capped: an agent stuck in a loop can't make hundreds of changes a minute. Everything else on the server is denied unless you say otherwise.

View as policy code

policy.json

{
  "version": "1",
  "default": "deny",
  "tools": {
    "science.pdb.sequence": {
      "limits": [
        {
          "counter": "science.pdb.sequence_rate",
          "window": "minute",
          "max": 30,
          "scope": "grant"
        }
      ]
    }
  }
}

LIMIT THIS TOOL → Instant setup, no code required.

The button opens the PolicyLayer dashboard: create your workspace, connect Apibase, apply this rule, and every science.pdb.sequence call is checked against it from then on.

FAQ

Questions about science.pdb.sequence

What does the science.pdb.sequence tool do? +

Search protein structures by amino acid sequence similarity (BLAST). Input a protein sequence and find all PDB structures with matching chains. Configure identity cutoff (e.g. 90%) and E-value threshold. Returns PDB entity IDs ranked by similarity score. Essential for homology modeling and structure prediction (RCSB PDB). It is categorised as a Write tool in the Apibase MCP Server, which means it can create or modify data. Consider rate limits to prevent runaway writes.

What parameters does science.pdb.sequence accept? +

science.pdb.sequence accepts 4 parameters: limit, sequence, evalue_cutoff, identity_cutoff. Required: sequence. The full parameter table on this page comes from the server's own tool schema.

How do I enforce a policy on science.pdb.sequence? +

Register the Apibase MCP server in PolicyLayer and add a rule for science.pdb.sequence: 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.

What risk level is science.pdb.sequence? +

science.pdb.sequence is a Write tool with medium risk. Write tools should be rate-limited to prevent accidental bulk modifications.

Can I rate-limit science.pdb.sequence? +

Yes. Add a rate_limit block to the science.pdb.sequence 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.

How do I block science.pdb.sequence completely? +

Set action: deny in the PolicyLayer policy for science.pdb.sequence. 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.

What MCP server provides science.pdb.sequence? +

science.pdb.sequence 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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