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AlphaFold MCP Server

AlphaFold MCP Server

by Augmented-Nature
OverviewSchemaSourceRelated ServersDiscussionsAdmin
JavaScript
Remote

batch_download

Download multiple protein structure files in bulk (PDB or CIF formats) using UniProt IDs, streamlining access to AlphaFold MCP Server data for efficient research workflows.

Instructions

Download multiple structure files

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": "batch_download"
  }
}

Input Schema

NameRequiredDescriptionDefault
formatNoFile format (default: pdb)
uniprotIdsYesArray of UniProt accessions (max 20)

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 full burden. It states 'download' but doesn't disclose behavioral traits like authentication needs, rate limits, file size constraints, or what happens on failure. This is inadequate for a mutation tool with zero annotation coverage.

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 with zero waste. It is appropriately sized and front-loaded, directly stating the tool's purpose without unnecessary elaboration.

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, no output schema, and a mutation tool (download implies write operation), the description is incomplete. It lacks critical context like return values, error handling, or operational constraints, making it insufficient for safe agent 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 fully documents parameters (format with enum, uniprotIds with constraints). The description adds no meaning beyond what the schema provides, such as explaining 'structure files' in context of UniProt IDs or format implications.

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 'Download multiple structure files' clearly states the action (download) and resource (structure files), with 'multiple' indicating batch capability. It distinguishes from sibling 'download_structure' by implying batch vs. single operations, though not explicitly named.

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?

No explicit guidance on when to use this tool versus alternatives like 'download_structure' or 'get_structure'. The description implies batch downloading but lacks context on prerequisites, limitations, or comparison with siblings.

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

Deploy Server

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