protein-tools-mcp

Overview Schema Source Related Servers Discussions Admin

uniprot_entry

Fetch UniProtKB protein details—name, organism, function, length, sequence, and metal-binding annotations—by accession; API key required, with 24 h cache or forced live refresh.

Instructions

Fetch a UniProtKB entry: protein name, organism, function, length, sequence, and metal-binding annotations. Premium tool (API key required). Results are disk-cached for 24 h; refresh=True forces a live fetch.

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": {
      "accession": "<accession>"
    },
    "name": "uniprot_entry"
  }
}

Input Schema

Name	Required	Description	Default
`refresh`	No
`accession`	Yes

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Oct 20, 2026

TDQS

A3.6/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description carries full burden and it does well: it discloses the auth requirement (API key), the caching behavior (24 h disk cache), and the force-refresh semantics. It omits rate limits and error/failure behavior, keeping it short of a 5.

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?

Three tight sentences: purpose first, then auth, then caching/refresh. Every sentence earns its place and nothing is redundant.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

An output schema exists, so return values needn't be enumerated and the tool avoids that. The essential calling constraints (auth, cache, refresh) are present; only the accession format detail is missing.

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 0%, so the description must compensate. It meaningfully explains the non-obvious `refresh` parameter ('forces a live fetch'), but the required `accession` parameter gets no format or validity guidance beyond its name, leaving a real gap.

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?

States a specific verb ('Fetch') and resource ('UniProtKB entry') and enumerates the returned fields (protein name, organism, function, length, sequence, metal-binding annotations). It's clearly distinct from siblings like rcsb_entry or pdb_by_id by resource, though it doesn't explicitly name the alternative it contrasts with.

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?

There is no guidance on when to use this tool versus alternatives such as rcsb_entry or sequence_from_pdb. The only contextual cue is 'Premium tool (API key required)', which informs cost/auth but not selection.

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