Skip to main content
Glama
PDBe MCP Servers

PDBe MCP Servers

Official
by PDBeurope

ebi-pdbe-maps_maps_acc_cb64101d

Read-only

Retrieve SIFTS residue-level mappings between PDB chains and UniProt, Pfam, InterPro, CATH, SCOP, GO, Ensembl, and HMMER for an accession. Supports PDB-to-ID and ID-to-PDB queries with annotations.

Instructions

Provides unified SIFTS residue-level mappings between PDB protein chains (auth_asym_id or struct_asym_id) and all major sequence and domain resources, including UniProt, Pfam, InterPro, CATH, SCOP, GO, Ensembl, and HMMER. Supports both PDB-to-identifier and identifier-to-PDB queries, returning the mapped residue segments and associated annotations for each resource.

Input Schema

NameRequiredDescriptionDefault
accessionYesUniProt accession or 4-character PDB id code or Pfam domain accession or Interpro domain accession or CATH cathcode or SCOP sunid or GO accession. title: Accession description: UniProt accession or 4-character PDB id code or Pfam domain accession or Interpro domain accession or CATH cathcode or SCOP sunid or GO accession.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered. The description adds the return shape ('mapped residue segments and associated annotations for each resource'), which is useful, but says nothing about pagination, size limits, or behavior for unmapped residues.

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 dense sentences, front-loaded with the core mapping capability and the resource list. No filler, though the second sentence packs query directions and return values without much structural separation.

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 one parameter, full schema coverage, and no output schema, the description covers purpose, accepted inputs, and return content adequately. Only the absence of guidance on result volume and sibling differentiation leaves a modest gap.

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 coverage is 100% with a single required parameter, so the schema already enumerates accepted identifier types. The description adds little beyond that, and its mention of 'auth_asym_id or struct_asym_id' cannot be supplied through the one-parameter schema, which risks confusing the agent.

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 uses a specific verb and resource ('Provides unified SIFTS residue-level mappings between PDB protein chains... and all major sequence and domain resources') and enumerates the covered resources (UniProt, Pfam, InterPro, CATH, SCOP, GO, Ensembl, HMMER). It is clear what the tool returns, though it never names or contrasts with a sibling such as ebi-pdbe-unip_map_ent, which covers adjacent mapping ground.

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

Usage Guidelines3/5

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

It states both query directions are supported ('PDB-to-identifier and identifier-to-PDB'), which implies when the tool applies, but gives no explicit when-to-use/when-not guidance, no prerequisites, and no pointer to alternatives among the many mapping-oriented siblings.

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