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ebi-pdbe-comp_intx_comp_intx_hetcode_8fee3085

Read-only

Retrieve aggregated protein-ligand interaction counts across all PDB structures for a given hetcode, showing ligand-atom contacts with specific amino-acid residues grouped by interaction type.

Instructions

Returns aggregated interaction counts for protein-ligand interactions, derived from all PDB structures containing the given chemical component. The response reports how frequently a ligand atom interacts with specific amino-acid residues across the PDB, grouped by interaction type.

Input Schema

NameRequiredDescriptionDefault
hetcodeYesHetcode for the compound title: Hetcode description: Hetcode for the compound

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv2.0.1

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, so the safety profile is covered. The description adds real value by explaining that counts are aggregated across all PDB structures and grouped by interaction type, but it says nothing about response size, pagination, or whether the aggregation scope can be narrowed.

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?

Two tightly written sentences with no filler, and the core purpose is front-loaded ahead of the description of the returned data. Nothing is repeated and nothing is wasted.

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?

Because there is no output schema, the description must convey the return shape, and it does so reasonably well by describing per-residue frequencies grouped by interaction type. What remains missing is the aggregation granularity, e.g., whether counts are global per PDB or normalized, which matters for interpreting results.

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?

With one parameter at 100% schema description coverage, the schema already documents the required 'hetcode'. The description only adds that a hetcode identifies a 'chemical component', which clarifies the concept but gives no format or lookup details (e.g., where to obtain a valid hetcode).

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 states a specific verb and resource ('Returns aggregated interaction counts for protein-ligand interactions') and names the scoping input ('derived from all PDB structures containing the given chemical component'). It is clear what the tool returns, but it never distinguishes itself from siblings such as ebi-pdbe-ligand-interactions or ebi-pdbe-comp_in_comp_in_hetcode, which an agent could easily confuse with it.

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 choose this tool over the many hetcode-based siblings (ligand_sum, comp_in, comp_intx_proteins), nor any stated prerequisites. The agent must infer selection purely from the resource named in the purpose sentence.

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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