Skip to main content
Glama
PDBeurope

PDBe MCP Servers

Official
by PDBeurope

annot_ent_annot_id_entity_id_e5718131

Read-only

Fetch residue-level functional and biophysical annotations for a given PDB Entity ID, aggregating PDBe-KB scores, confidence metrics, and source URLs.

Instructions

Returns residue-level functional and biophysical annotations for a specified PDB Entity ID, aggregated from multiple PDBe-KB partner resources (e.g., SASA, hydrophobicity, disorder, flexibility, EM local resolution). Data returned includes annotation type, per-residue scores, confidence metrics, group labels, and the originating resource URL, as well as the Best Chain ID for the entity.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.
entity_idYesEntity id (molecule number in mmcif-speak). type: string pattern: ^[0-9]+$ title: Entity Id description: Entity id (molecule number in mmcif-speak).

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

B3.2/5.0
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 that data is aggregated from multiple PDBe-KB partner resources and enumerates return contents, which is useful context but does not add auth, rate-limit, or pagination behavior.

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 core purpose before the enumeration of returned fields. The parenthetical examples and return list are dense but each element conveys content; nothing is filler.

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 no output schema, the description carries the return-value burden and does so by listing annotation type, per-residue scores, confidence metrics, group labels, resource URL, and Best Chain ID. For a read-only tool this is nearly complete, missing only usage routing.

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 both parameters (pdb_id, entity_id) are already documented with format and pattern constraints. The description reiterates the PDB Entity ID but adds no syntax or constraint meaning beyond the schema, so the baseline 3 applies.

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?

States a specific verb (Returns) and resource (residue-level functional and biophysical annotations for a PDB Entity ID), and names the aggregation sources. The residue-level scope distinguishes it from sequence-level siblings, but it does not explicitly name an alternative to route the agent.

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?

The description explains what the tool returns but gives no when-to-use or when-not-to-use guidance, and never names a sibling alternative despite many adjacent per-entity tools (sec_struct, bind_sites, doms). Usage is only implied by the input being a PDB Entity ID.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.