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ebi-pdbe-best_soubsu_acc_11b902cf

Read-only

Retrieve PDB structures mapped to a UniProt accession, ranked by quality score, with chain, resolution, method, coverage, and alignment details for structural analysis.

Instructions

Provides a ranked list of PDB structures mapped to the given UniProt accession based on an internal quality score (based on data quality, model quality and resolution ). Each structure entry includes the experimental method, taxonomic origin, resolution, PDB ID and chain, entity and assembly identifiers, observed UniProt alignment segments, model residue ranges, and computed coverage of the UniProt sequence.

Input Schema

NameRequiredDescriptionDefault
uniprot_accessionYesUniProt accession. title: Uniprot Accession description: UniProt accession.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

A3.5/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false and idempotentHint=false, so safety is covered. The description adds substantive context beyond that: the ranking basis (data quality, model quality, resolution) and the full shape of each returned entry, which is real behavioral value. It could still note that rankings may shift over time (consistent with idempotentHint=false) and where results are truncated.

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?

Two sentences, front-loaded with the operation and ranking rationale, followed by the field inventory. The second sentence is a dense enumeration, but every listed field genuinely helps the agent understand the payload since no output schema exists.

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 carries the burden of describing the return and does so thoroughly (method, taxonomy, resolution, IDs, alignment segments, coverage). For a one-parameter lookup tool this is nearly complete; only result count, ordering direction, and pagination behavior are unstated.

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 a single parameter and schema description coverage is 100%, so the schema fully documents 'uniprot_accession'. The description only re-states that the accession is the mapping key and adds no format, validation, or alternative-input detail, making the baseline 3 correct.

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 gives a specific verb+resource: a ranked list of PDB structures mapped to a UniProt accession, ranked by a named internal quality score. An agent knows precisely what it returns, though it never distinguishes itself from close siblings such as best_nosoubnosu_acc or unip_map, so differentiation is left to inference.

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 explicit when-to-use guidance, no stated prerequisites, and no mention of alternatives. The phrase 'mapped to the given UniProt accession' implies the input context but leaves the agent to guess why it would pick this over best_nosoubnosu_acc or unip_map.

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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