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AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

find_similar_structures

Identify protein structures in AlphaFold similar to a reference UniProt ID. Filter results by organism to refine matches for precise structural analysis.

Instructions

Find AlphaFold structures similar to a given protein

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": "find_similar_structures"
  }
}

Input Schema

NameRequiredDescriptionDefault
organismNoFilter by organism (optional)
uniprotIdYesReference UniProt 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 the full burden of behavioral disclosure. It states the tool finds similar structures but does not explain what 'similar' means (e.g., by sequence, structure, or other metrics), how results are returned (e.g., list, scores), or any limitations like rate limits or authentication needs. This leaves significant gaps in understanding the tool's behavior.

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, clear sentence that efficiently conveys the core purpose without unnecessary words. It is front-loaded and wastes no space, making it highly concise and well-structured for quick comprehension.

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 finding similar protein structures, the lack of annotations, and no output schema, the description is insufficient. It does not cover what 'similar' entails, the format or scope of results, or any behavioral traits like performance or constraints, making it incomplete for effective tool 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 documents both parameters ('organism' and 'uniprotId') adequately. The description does not add any meaning beyond the schema, such as explaining the role of 'uniprotId' as the reference for similarity or providing examples. Thus, it meets the baseline but does not enhance parameter understanding.

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 tool's purpose with a specific verb ('Find') and resource ('AlphaFold structures similar to a given protein'), making it easy to understand what the tool does. However, it does not explicitly differentiate from sibling tools like 'search_structures' or 'compare_structures', which might have overlapping functionality, so it falls short of 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. With sibling tools like 'search_structures' and 'compare_structures' available, there is no indication of scenarios where this tool is preferred, prerequisites, or exclusions, leaving usage ambiguous.

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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