protein-tools-mcp

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rcsb_entry

Fetch RCSB PDB entry metadata—title, experimental method, resolution, and deposit date—by PDB ID. Requires an API key and a 24-hour disk cache; set refresh to force a live lookup.

Instructions

Fetch RCSB PDB entry metadata: title, experimental method, resolution, deposit date. Premium tool (API key required). Disk-cached for 24 h; refresh=True forces a live fetch.

Tool call template

Replace each placeholder with a value matching the input schema. Only required parameters are included; add optional parameters as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {
      "pdb_id": "<pdb_id>"
    },
    "name": "rcsb_entry"
  }
}

Input Schema

Name	Required	Description	Default
`pdb_id`	Yes
`refresh`	No

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A3.8/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden and does well: it discloses the API-key requirement (a real auth constraint), a 24 h disk cache, and the refresh override to bypass it. It stops short of error/throttling or failure behavior, but the key operational traits are present.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three short sentences, front-loaded with purpose and followed by the two operational facts (auth, caching) in priority order. Every sentence earns its place with no filler.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values need no explanation, and the description covers the auth and caching behavior an agent needs to call it correctly. The only real gap is that it never positions the tool against its many PDB/entry siblings.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It explains refresh meaningfully ('forces a live fetch'), but pdb_id is left entirely to inference and there is no format guidance for it. Partial compensation only.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb ('Fetch') and resource ('RCSB PDB entry metadata') and enumerates the returned fields (title, method, resolution, deposit date), so an agent knows exactly what it gets. It does not, however, distinguish itself from sibling tools like pdb_by_id, which an agent could plausibly confuse it with.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Usage is only implied: the description signals a premium/authenticated tool and explains that refresh=True forces a live fetch, which is a usable hint. But it never says when to choose this over alternatives such as pdb_by_id, uniprot_entry, or the caching tools, and gives no exclusions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.