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AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

download_structure

Retrieve AlphaFold protein structure files in PDB, CIF, or BCIF formats by providing a UniProt accession ID to streamline structural biology research.

Instructions

Download AlphaFold structure file in specified format

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": {
      "uniprotId": "<uniprotId>"
    },
    "name": "download_structure"
  }
}

Input Schema

NameRequiredDescriptionDefault
formatNoFile format (default: pdb)
uniprotIdYesUniProt accession

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observedv1.0.0

TDQS

C2.9/5.0
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It states the tool downloads a file but doesn't mention critical details like whether it requires authentication, has rate limits, what happens on errors, or if it's a read-only operation. This leaves significant gaps for an AI agent to understand how to use it safely and effectively.

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?

The description is a single, efficient sentence that front-loads the core purpose without any wasted words. It directly communicates what the tool does in a clear and structured manner.

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

Completeness2/5

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

Given the complexity of downloading files (which often involves authentication, error handling, and output details) and the lack of annotations and output schema, the description is incomplete. It doesn't address what the downloaded file contains, how it's delivered, or any prerequisites, making it inadequate for safe and informed use.

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 100%, so the schema already fully documents both parameters (uniprotId and format with enum values). The description adds no additional meaning beyond what's in the schema, such as explaining what an AlphaFold structure is or why these parameters are needed, resulting in the baseline score.

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?

The description clearly states the action ('Download') and resource ('AlphaFold structure file'), making the purpose immediately understandable. However, it doesn't differentiate this tool from sibling tools like 'batch_download' or 'get_structure', which appear to offer similar functionality, preventing a perfect score.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives like 'batch_download' or 'get_structure' from the sibling list. It mentions a format specification but doesn't explain why one might choose this tool over others for downloading structures.

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

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