Skip to main content
Glama
Sign In
AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

search_structures

Find AlphaFold protein structures by entering a protein or gene name. Filter results by organism and limit the number of outputs for targeted searches.

Instructions

Search for available AlphaFold structures by protein name or gene

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": {
      "query": "<query>"
    },
    "name": "search_structures"
  }
}

Input Schema

NameRequiredDescriptionDefault
organismNoFilter by organism (optional)
queryYesSearch term (protein name, gene name, etc.)
sizeNoNumber of results (1-100, default: 25)

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. While it mentions 'search' and 'available AlphaFold structures', it doesn't describe what 'available' means, whether results are paginated, what format they return, or any rate limits or authentication requirements. For a search tool with no annotation coverage, 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, efficient sentence that clearly states the tool's purpose without unnecessary words. It's appropriately sized and front-loaded with the essential information.

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 a search tool with no annotations and no output schema, the description is insufficient. It doesn't explain what the search returns (e.g., structure IDs, metadata), how results are ordered, or any limitations. With 3 parameters and many sibling tools, more context is needed for effective 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 all three parameters thoroughly. The description adds minimal value beyond the schema by mentioning 'protein name or gene' as search terms, which aligns with the query parameter description. Baseline 3 is appropriate when the schema does the heavy lifting.

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: 'Search for available AlphaFold structures by protein name or gene'. It specifies the verb ('Search'), resource ('AlphaFold structures'), and search criteria ('protein name or gene'). However, it doesn't explicitly differentiate from sibling tools like 'find_similar_structures' or 'list_by_organism', which also involve structure retrieval.

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 many sibling tools for structure retrieval (e.g., 'find_similar_structures', 'list_by_organism', 'get_structure'), there's no indication of when this search-based approach is preferred or what its limitations might be.

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

Deploy Server

Other Tools

Related Tools