Skip to main content
Glama
PDBeurope

PDBe MCP Servers

Official
by PDBeurope
OverviewSchemaSourceRelated ServersDiscussionsAdmin
Python
Remote

unip_map_ent_unip_map_id_entity_id_ce7aaa0c

Read-only

Map a PDB entity to UniProt using a PDB ID and entity ID; get matched accessions, residue-level alignment ranges, and Best Chain ID metadata.

Instructions

Returns UniProt mappings for a specific PDB Entity ID, including matched UniProt accessions, residue-level alignment ranges, and metadata identifying the corresponding Best Chain ID for the mapping.

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

B3.4/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and idempotentHint=false, covering the safety profile. The description adds useful return-content detail but does not disclose additional behavioral traits such as error cases, rate limits, or what happens when no mapping exists.

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?

A single front-loaded sentence with no wasted words. It efficiently states the return scope and key output fields.

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?

Given no output schema, the description usefully explains the return values: matched UniProt accessions, residue-level alignment ranges, and Best Chain ID metadata. It is nearly complete for a read-only lookup tool, though it could mention behavior when no mapping is found or whether multiple mappings are returned.

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. The description mentions the PDB Entity ID scope but adds no syntax, format, or constraint details beyond what the schema provides.

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 verb and resource: returns UniProt mappings for a PDB Entity ID, with details on matched accessions, alignment ranges, and Best Chain ID. This clearly differentiates it from simple accession-based UniProt tools, but it does not explicitly name or compare against any sibling tool.

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 gives no guidance on when to use this tool versus the many other UniProt-related siblings. It only says what it returns, with no conditions, exclusions, or alternatives.

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

Deploy Server

Other Tools