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AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

get_coverage_info

Retrieve sequence coverage details for AlphaFold protein structure predictions using a UniProt accession ID.

Instructions

Get information about sequence coverage in the AlphaFold prediction

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": "get_coverage_info"
  }
}

Input Schema

NameRequiredDescriptionDefault
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?

No annotations are provided, so the description carries full burden for behavioral disclosure. It states what the tool does but doesn't describe output format, error conditions, rate limits, or whether it's a read-only operation. For a tool with no annotations, this leaves significant behavioral gaps.

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, focused sentence with no wasted words. It's appropriately sized for a simple tool with one parameter and gets straight to the point without unnecessary elaboration.

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 no annotations and no output schema, the description is insufficiently complete. It doesn't explain what 'sequence coverage information' includes, the format of returned data, or how this differs from other information-retrieval tools in the sibling set. The agent would need to guess about the tool's behavior and output.

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%, with the single parameter 'uniprotId' documented as 'UniProt accession'. The description doesn't add any parameter-specific information beyond what the schema provides, so it meets the baseline for high schema coverage.

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 ('Get information') and resource ('sequence coverage in the AlphaFold prediction'), providing a specific purpose. However, it doesn't explicitly differentiate from sibling tools like 'get_confidence_scores' or 'get_prediction_metadata' that also retrieve AlphaFold-related information, which prevents 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?

No guidance is provided on when to use this tool versus alternatives. The description doesn't mention prerequisites, context, or exclusions, leaving the agent to infer usage from the tool name alone among many similar-sounding siblings.

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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