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var_ent_var_id_entity_id_777d29d4

Read-only

Fetch UniProt sequence-variation annotations for a specific PDB entity, remapped to residue positions, including variant types, alternative sequences, evidence, and structural impact.

Instructions

Returns UniProt sequence-variation annotations for a specified PDB Entity ID, remapped to the entity’s residue positions. The response includes each mapped UniProt accession and its variant features, such as variant type, alternative sequence, position, associated evidence, cross-references, clinical or functional annotations, and any available structural-impact metadata.

Input Schema

TableJSON 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. Addedv1.1.10

TDQS

A3.5/5.0
Behavior4/5

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

Annotations declare readOnlyHint=true and destructiveHint=false, so safety is covered. The description adds genuinely useful behavioral context about the response payload (variant type, alternative sequence, evidence, cross-references, clinical/functional hits, structural-impact metadata), which compensates for the absence of an output schema. No auth, rate-limit, or edge-case caveats are given.

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 core purpose before enumerating response contents. The second sentence is a long list but every element maps to actual returned data, so there is little waste.

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 rightly spends its budget describing the return payload, and read-only semantics are covered by annotations. An agent has enough to decide and call correctly, though it lacks guidance on picking this over the UniProt-accession variant 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?

With 100% schema description coverage, the schema already documents both pdb_id and entity_id, including the numeric pattern for entity_id. The description adds nothing about parameter format, valid ranges, or index semantics beyond the schema, so the baseline 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 states a specific verb ('Returns'), a concrete resource ('UniProt sequence-variation annotations'), and the scoping mechanism ('for a specified PDB Entity ID, remapped to the entity's residue positions'). This is far more informative than a tautology and implies the entity-based nature that separates it from accession-keyed siblings. It stops short of naming a sibling tool explicitly, so it is clear but not fully differentiated.

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 description never says when an agent should reach for this tool versus alternatives such as unip_var_unip_var (UniProt accession keyed) or annot_ent. Usage can only be inferred from the required PDB entity inputs, and there are no stated prerequisites or exclusions.

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