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AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

get_organism_stats

Retrieve AlphaFold coverage statistics for a specific organism to analyze protein structure prediction data. Input the organism name for detailed insights.

Instructions

Get statistics about AlphaFold coverage for an organism

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": {
      "organism": "<organism>"
    },
    "name": "get_organism_stats"
  }
}

Input Schema

NameRequiredDescriptionDefault
organismYesOrganism name

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 the full burden of behavioral disclosure. It mentions 'Get statistics' but doesn't specify what kind of statistics, whether it's a read-only operation, if there are rate limits, or how results are returned. This leaves significant gaps for an agent to understand the tool's behavior beyond basic purpose.

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 directly states the tool's purpose without any unnecessary words. It's front-loaded and appropriately sized for its function, making it easy to parse quickly.

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 lack of annotations and output schema, the description is insufficiently complete. It doesn't explain what statistics are returned, how they're formatted, or any behavioral traits like error handling. For a tool with no structured metadata, more detail is needed to fully guide an agent.

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?

The input schema has 100% description coverage, with the 'organism' parameter clearly documented as 'Organism name'. The description doesn't add any extra meaning beyond this, such as format examples or constraints, so it meets the baseline for adequate but minimal parameter information.

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 verb ('Get statistics') and resource ('AlphaFold coverage for an organism'), making the purpose understandable. However, it doesn't explicitly differentiate from sibling tools like 'get_coverage_info' or 'list_by_organism', which might have overlapping functionality, so it doesn't reach the highest 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. With siblings like 'get_coverage_info' and 'list_by_organism' that might relate to organism data, there's no indication of specific contexts, exclusions, or comparisons to help an agent choose appropriately.

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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