Skip to main content
Glama
Sign In
AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

list_by_organism

Retrieve AlphaFold protein structures for a specific organism by entering its name. Specify the number of results to efficiently access relevant data.

Instructions

List all available structures for a specific 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": "list_by_organism"
  }
}

Input Schema

NameRequiredDescriptionDefault
organismYesOrganism name (e.g., "Homo sapiens", "Escherichia coli")
sizeNoNumber of results (1-100, default: 50)

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 it 'lists all available structures' but doesn't clarify what 'available' means (e.g., public vs. restricted), whether it's a read-only operation, if there are rate limits, or the format of the output. This is inadequate for a tool with potential complexity.

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 front-loads the core purpose ('List all available structures for a specific organism'). There is no wasted text, making it highly concise and well-structured for quick understanding.

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 incomplete. It doesn't explain what 'structures' entail (e.g., protein models, datasets), the return format, or any behavioral traits like pagination or errors. For a tool in a scientific context with many siblings, more detail is needed to ensure proper 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 'size') thoroughly. The description adds no additional meaning beyond implying organism filtering, which is already clear from the schema. Baseline 3 is appropriate as 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 verb 'list' and the resource 'structures', specifying it's for a 'specific organism'. It distinguishes from siblings like 'search_structures' or 'get_structure' by focusing on organism-based listing. However, it doesn't explicitly differentiate from 'get_organism_stats', which might overlap in scope.

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 like 'search_structures' or 'get_organism_stats'. It lacks context on prerequisites, exclusions, or comparative use cases, leaving the agent to infer usage from the name alone.

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