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by PDBeurope

ebi-pdbe-get_ai_summary

Read-only

Retrieve a pre-generated AI summary for a four-character PDB entry to get an entry overview with summary sections and abstract key points, preserving inline reference markers.

Instructions

Retrieve the pre-generated AI summary for a four-character PDB entry. Use this for an entry overview instead of writing a new summary. Returns the available summary sections and abstract key points, preserving inline reference markers and listing their PDBe source URLs and fields. A summary may not exist for every entry.

Input Schema

NameRequiredDescriptionDefault
pdb_idYesFour-character PDB entry ID, for example 1rio.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

A3.9/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnly, openWorld, non-destructive), so the description's job is to add context — and it does: it discloses that content is pre-generated, that sections and abstract key points are returned, that inline reference markers are preserved, and that supporting PDBe source URLs and fields are listed. The important failure mode ("may not exist for every entry") is stated up front. It does not say what the miss looks like (empty result vs. error), leaving one behavioral gap.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Three sentences, front-loaded with purpose, then usage, then return shape. The middle sentence is slightly dense (sections, abstract points, references, URLs, fields), but every clause carries information an agent needs. No filler or repetition of the tool name.

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?

With no output schema, the description properly compensates by describing what comes back: summary sections, an abstract, and linked source fields. The existence caveat handles the main failure mode. Only minor gaps remain (size of the payload, whether sections are always all present).

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?

There is only one parameter and the schema documents it fully at 100% coverage, including the 4-character pattern and an example. The description's "four-character PDB entry" is consistent with the schema but adds nothing new. Baseline 3 is appropriate when schema coverage is complete.

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 opens with a specific verb and resource: "Retrieve the pre-generated AI summary for a four-character PDB entry." That is unambiguous and implicitly separates it from the UniProt-keyed LLM summary sibling (llm_unip_sum_...) by scoping to a 4-character PDB ID. It stops short of naming any sibling explicitly, so it does not earn a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

"Use this for an entry overview instead of writing a new summary" gives a clear selection rule: prefer this tool over synthesizing an overview yourself. The caveat that a summary may not exist for every entry tells the agent what to expect on a miss. However, no sibling tool is named as an alternative (e.g. the UniProt-keyed summary tool), and there is no explicit when-not guidance.

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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