Biochemistry Archive MCP Server

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get_structures

Retrieve experimental protein structures for a UniProt accession, ranked by resolution, and optionally filter to ligand-bound structures to exclude apo forms.

Instructions

Experimental structures for a UniProt accession, best-resolved first. Set require_ligand to exclude apo structures.

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": {
      "uniprot_accession": "<uniprot_accession>"
    },
    "name": "get_structures"
  }
}

Input Schema

Name	Required	Description
`limit`	No
`require_ligand`	No	Only structures with a bound small molecule
`uniprot_accession`	Yes	UniProt accession, e.g. 'P00533'

Output Schema

Name	Required	Description	Default
No arguments

Schema Changelog

Changes observed during successful MCP inspections.

First observedv0.1.0Nov 5, 2026

TDQS

B3.3/5.0

Behavior3/5

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

With no annotations supplied, the description carries the behavioral burden and does disclose two useful traits: results are ordered 'best-resolved first' and only experimental structures are covered (implying predicted models are excluded). It says nothing about result volume, whether the list can be empty, or rate/availability limits, so the safety and cost profile remains partly opaque.

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?

Two sentences with no filler, and the scope statement is front-loaded before the optional filter hint. Every clause carries information an agent can act on.

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

Completeness3/5

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

The tool is simple (3 params, no nesting) and an output schema exists, so return values need not be described. However, the description omits the key routing decision against the closely named sibling get_structure and never clarifies what 'experimental' excludes, leaving a meaningful gap for a tool whose name is nearly identical to a sibling.

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 coverage is 67%, and the one parameter the schema documents (require_ligand) is re-expressed in the description with added domain meaning: 'exclude apo structures' translates the boolean into the structural-biology outcome. The limit parameter is only constrained by the schema (1-50, default 10) and gets no explanation of ordering interaction in the description, so the added value is moderate rather than substantial.

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 resource (experimental structures) scoped to a specific key (a UniProt accession) with an implied retrieval verb, which is enough for an agent to know what it returns. It implicitly separates from the singular sibling get_structure by scoping to an accession rather than a structure ID, but it never names that sibling explicitly.

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 only conditional guidance is parameter-level ('Set require_ligand to exclude apo structures'), not tool-level. There is no statement of when to call get_structures versus get_structure, find_target, or find_ligands, and no prerequisites such as whether the accession must be reviewed or whether AlphaFold models are returned.

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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