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AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

compare_structures

Compare multiple AlphaFold protein structures by inputting UniProt IDs to analyze and identify structural differences. Supports 2 to 10 IDs for detailed comparison.

Instructions

Compare multiple AlphaFold structures for analysis

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": {
      "uniprotIds": "<uniprotIds>"
    },
    "name": "compare_structures"
  }
}

Input Schema

NameRequiredDescriptionDefault
uniprotIdsYesArray of UniProt accessions to compare (2-10)

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 compares structures 'for analysis', but lacks details on what the comparison entails (e.g., alignment metrics, visual output, or data format), whether it's read-only or has side effects, or any rate limits. This leaves significant gaps in understanding how the tool behaves.

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 wasted words. It is appropriately sized and front-loaded, 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 complexity of comparing protein structures and the lack of annotations and output schema, the description is incomplete. It doesn't explain what 'analysis' involves, the format or content of results, or any behavioral traits, making it inadequate for a tool that likely returns detailed comparison data.

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, fully documenting the 'uniprotIds' parameter with its array type and constraints (2-10 items). The description adds no additional parameter semantics beyond what the schema provides, so it meets the baseline score 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 ('Compare') and resource ('multiple AlphaFold structures'), providing a specific purpose. However, it doesn't explicitly differentiate from sibling tools like 'find_similar_structures' or 'validate_structure_quality', which might involve comparison aspects, 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 offers no guidance on when to use this tool versus alternatives. It doesn't mention prerequisites, context, or exclusions, leaving the agent to infer usage from the name alone, which is insufficient for effective tool selection.

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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