uniprot_mappingsPDBe (EBI): SIFTS cross-database mapping of a PDB structure to UniProt — for each UniProt accession, the matching chains and residue range. Curated cross-database mappings unique to EBI. Keyless. Pass a 4-char PDB id like "1cbs".
| Name | Required | Description | Default |
|---|---|---|---|
| pdb_id | Yes | A 4-char PDB id, e.g. "1cbs". |
Changes observed during successful MCP inspections.
Input schema / examplesAdded value: +[
+ {
+ "pdb_id": "1cbs"
+ },
+ {
+ "pdb_id": "3hbb"
+ }
+]Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare the tool as read-only, idempotent, and non-destructive. The description adds valuable behavioral context: it is keyless (no authentication needed), sourced from EBI, and returns specific data (chains and residue range). No contradiction with annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences and front-loaded with the main purpose. The first sentence is dense but conveys all essential information without waste. Minor verbosity is acceptable.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a simple one-parameter tool with rich annotations, the description fully covers the source, output format, keyless access, and example. No output schema exists, but the description explains return values sufficiently.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The input schema has 100% coverage for the single parameter (pdb_id), with a clear description and example. The description reinforces the 4-char format and example, adding no new semantics beyond the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool performs SIFTS cross-database mapping from PDB to UniProt, specifying the source (PDBe/EBI), output details (matching chains and residue range), and a concrete example. It distinguishes from siblings by emphasizing 'curated cross-database mappings unique to EBI.'
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides clear context (mapping PDB to UniProt) and implies authoritative curation, but does not explicitly state when not to use this tool or mention alternative tools for similar mappings. No exclusion criteria are given.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Add one secure layer between your agents and this server.