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ebi-pdbe-doms_ent_doms_id_entity_id_17aad3ce

Read-only

Retrieve sequence and structural domain annotations for a PDB entity, including CATH, SCOP, Pfam and InterPro boundaries, identifiers, names, and best chain metadata.

Instructions

Returns sequence and structural domain annotations for a specified PDB Entity ID, including domain boundaries, identifiers, and names from CATH, SCOP 1.75, Pfam and InterPro domain resources, along with metadata such as the entity’s Best Chain ID.

Input 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. Addedv2.0.1

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 useful content-level detail (domain boundaries, identifiers, names, Best Chain metadata) but says nothing about response shape, per-chain aggregation, or behavior when no domains are annotated. Note the annotations themselves set idempotentHint=false for what reads as a pure lookup, which the description does not clarify.

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?

It is a single front-loaded sentence that leads with the action and resource, then enumerates sources and metadata. The trailed enumeration is long but each clause adds informational value; there is no filler or restatement of the title.

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

Completeness3/5

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 burden of explaining returns, and it does list the returned categories. However, for a task that merges four domain databases plus chain metadata, it omits how the results are structured, whether all chains or only the best chain are reported, and what an empty result looks like.

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 are already documented in structured form. The description only says 'specified PDB Entity ID' and adds no meaning beyond the schema — no explanation of how pdb_id scopes entity_id or that entity_id is a numeric molecule number. Baseline 3 applies when the schema does the work.

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 uses a concrete verb+resource ("Returns sequence and structural domain annotations for a specified PDB Entity ID") and enumerates the contributing sources (CATH, SCOP 1.75, Pfam, InterPro) plus the Best Chain ID metadata. That makes the tool's scope far more specific than vague siblings, though it never explicitly contrasts itself with neighboring entity-level tools like sec_struct or annot.

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 when-to-use guidance, no exclusions, and no mention of alternatives. An agent must infer from the word 'domain' whether to call this versus sec_struct, annot, or bind_sites, and nothing tells it that pdb_id and entity_id must be a valid pair or where entity_id comes from.

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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