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ebi-pdbe-seq_cescie_id_5a830e8e

Read-only

Retrieve residue-level sequence conservation data for a specified PDB entry and entity ID, including per-residue scores and amino-acid probability distributions.

Instructions

Returns residue-level sequence conservation data for a specified PDB entry ID and PDB entity ID, including per-residue conservation scores and amino-acid probability distributions.

Input Schema

NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
entity_idYesEntity id (molecule number in mmcif-speak). type: string pattern: ^[0-9]+$ title: Entity Id description: Entity id (molecule number in mmcif-speak).

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

B3.2/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description adds useful behavioral content beyond that by disclosing the shape of the result (residue-level scores plus probability distributions), but it says nothing about response size, pagination, or what happens when an entity has no conservation data — notable given idempotentHint=false on an otherwise read-only operation.

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?

A single front-loaded sentence with no filler, stating the resource first and the returned contents second. It is slightly redundant with the tool's own annotation title, which repeats the same text verbatim, but the sentence itself earns its place.

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?

For a two-parameter read-only lookup with full schema coverage and no output schema, the description covers what is returned and at what granularity. What remains missing is whether results are per-chain, whether an empty result is possible, and the response encoding, which an agent would have to discover by calling it.

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 both parameters are already documented in the schema, including the 4-character PDB code constraint and the numeric entity ID pattern. The description merely restates that both are required; it adds no format or validation detail beyond the schema, so the baseline of 3 applies.

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 names a specific verb ('Returns') and a specific resource ('residue-level sequence conservation data') scoped to a PDB entry and entity, and it lists the payload contents (per-residue conservation scores, amino-acid probability distributions). It does not distinguish this from the many sibling per-entity tools (sec_struct, var, doms, bind_sites), all of which also take a PDB ID plus entity ID, so an agent cannot rule out alternatives from the text alone.

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 prerequisites, and no named alternative. The only signal is implicit in the parameter names — that this applies to one entity of one entry — which an agent must infer.

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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