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ebi-pdbe-mol_cbliicis_id_c117dabc

Read-only

Retrieve interactions for a bound ligand in a PDB entry by specifying the PDB ID, chain ID, and residue number.

Instructions

This call provides interactions for a bound ligand found in the entry.

Input Schema

NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
seq_idYesResidue number (in PDB-style residue addressing scheme). title: Seq Id description: Residue number (in PDB-style residue addressing scheme).
chain_idYesPDB chain id. title: Chain Id description: PDB chain id.
preserve_caseNoPreserve the case of the chain identifier

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

TDQS

C2.5/5.0
Behavior2/5

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

Annotations already declare readOnlyHint=true, destructiveHint=false, and idempotentHint=false, but the description adds no behavioral context beyond the safety profile. It does not say what kinds of interactions are returned, how the ligand is identified, or what the response looks like.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness3/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The definition is a single sentence with little wasted wording, but "This call provides" is filler and the sentence is under-specified rather than front-loaded with useful detail. It is concise but not particularly informative.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a four-parameter query tool with no output schema, the description is too thin: it does not explain interaction types, return format, or how the required pdb_id/chain_id/seq_id identify the bound ligand. An agent could attempt a call, but would lack context to interpret or trust the result.

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 the input schema already documents pdb_id, chain_id, seq_id, and preserve_case. The description adds no parameter meaning beyond that baseline, which is acceptable when the schema is fully covered but provides no extra value.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states that the tool provides interactions for a bound ligand in an entry, which gives a general resource and action. However, "interactions" is vague, the verb is generic, and it does not distinguish this tool from sibling tools such as ebi-pdbe-ligand-interactions or the comp_intx tools.

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 guidance on when to use this tool versus alternatives, nor any prerequisites or exclusions. An agent must infer its role entirely from the vague description and the tool name.

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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