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ebi-pdbe-complex_bmscbmsc_id_02b199bd

Read-only

Retrieve an aggregated small-molecule ligand summary for a PDB complex, including ligand names, functional annotations, and occurrence counts across entries, chains, and instances.

Instructions

Retrieve an aggregated summary of small-molecule ligands observed across different structural instances of a given macromolecular complex. The response includes ligand names, functional annotations (such as cofactor-like, drug-like, and reactant-like), and occurrence counts based on PDB entries, chains, and ligand instances.

Input Schema

NameRequiredDescriptionDefault
pdb_complex_idYesPDB Complex ID type: string title: Pdb Complex Id description: PDB Complex ID

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

A3.5/5.0
Behavior4/5

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 real value by disclosing the shape of the response: ligand names, functional annotation categories, and occurrence counts broken down by PDB entries, chains, and ligand instances, which is meaningful because no output schema exists. It does not explain the odd idempotentHint=false on a read-only aggregate, nor whether the aggregation spans all entries or a filtered subset.

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 purpose and followed by the return contents; there is no filler. Slightly more verbose than strictly needed, but every clause conveys substance.

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 single-parameter, read-only aggregation tool with no output schema, the description covers what is returned and in what dimensions, which is the main gap such tools usually leave. Missing pieces are minor: identifier format and whether 'occurrence counts' can be filtered or aggregated at different levels.

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?

There is only one parameter and the schema description coverage is 100%, so the baseline is 3. The description adds no syntax or format detail for 'pdb_complex_id' beyond what the schema already states, leaving the expected identifier format to inference.

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 gives a specific verb and resource: 'Retrieve an aggregated summary of small-molecule ligands observed across different structural instances of a given macromolecular complex.' It also spells out what the summary contains (ligand names, functional annotations, occurrence counts). It stops short of naming which sibling to use instead, e.g. 'ebi-pdbe-ligand_sum_comp_sum_hetcode' or 'ebi-pdbe-bound_molecules', so the agent must infer positioning among the many ligand-related siblings.

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 or when-not-to-use guidance, and no alternatives are named despite a crowded set of ligand-centric siblings. The scope phrase 'for a given macromolecular complex' implies context, but an agent cannot tell from this text whether to pick this over the ligand summary or bound molecules tools.

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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