protein-tools-mcp

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pdb_by_id

Get PDB entry information by 4-character ID: checks local PDB/mmCIF files for validation, sequence, and metal sites, and fetches RCSB metadata when an API key is set.

Instructions

Get info about a PDB entry by its 4-character PDB ID.

Checks if a local PDB/mmCIF file exists for the ID, and if so returns local structure info (validation, sequence, metal sites). Also fetches RCSB metadata if an API key is set (premium tool).

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": "pdb_by_id"
  }
}

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

B3.2/5.0

Behavior3/5

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

With no annotations, the description carries the full burden. It usefully discloses the local-file check, what is returned (validation, sequence, metal sites), and the premium/API-key gating. However it omits the effect of the 'refresh' flag, caching behavior, and what happens when neither a local file nor an API key is available.

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

Conciseness4/5

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

Front-loaded with the core purpose, then supporting detail in two short follow-on sentences. No filler, though the line-broken formatting is slightly awkward.

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

Completeness3/5

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 not be spelled out, and the description appropriately highlights the main categories anyway. But with no annotations and an undocumented 'refresh' parameter, the definition is only adequately complete for an agent to call it reliably.

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

Parameters2/5

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 conveys the 4-character format for pdb_id, but the 'refresh' parameter is entirely undocumented in both schema and description, leaving a real gap for a 2-param tool.

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+resource: 'Get info about a PDB entry by its 4-character PDB ID,' and clarifies it works on local files plus optional RCSB metadata. This is clear, though it does not explicitly differentiate itself from overlapping siblings like rcsb_entry or validate_pdb.

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?

The description implies when behavior kicks in (local file present, API key set) but gives no explicit when-to-use guidance or named alternatives versus rcsb_entry, validate_pdb, or structure_stats. Usage is inferable rather than stated.

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