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interpro-mcp-server

Find proteins by domain

interpro_find_proteins_by_domain
Read-onlyIdempotent

Find UniProt proteins carrying an InterPro or member signature. Defaults to reviewed human proteins; reviewedOnly=false includes reviewed and unreviewed proteins in the chosen taxon. Optional isFragment filters fragment annotations; false does not prove a complete canonical sequence.

Input Schema

NameRequiredDescriptionDefault
limitNoPositive integer page size; values above 50 are clamped to 50 with a notice; defaults to 20.
cursorNoOpaque nextCursor with unchanged target, taxonId, reviewedOnly, and isFragment selection; limit may change.
taxonIdNoPositive NCBI taxonomy identifier of at most 10 digits; defaults to human 9606.9606
accessionYesInterPro or member-database entry accession, such as IPR011615 or PF00870; no URL syntax.
isFragmentNoSelect fragment annotations: true for fragments, false for proteins not annotated as fragments; omit to include both. False does not establish sequence completeness.
reviewedOnlyNoDefaults to reviewed proteins; false includes reviewed and unreviewed proteins.
sourceDatabaseNoEntry database slug, inferred from standard accession prefixes when omitted.

Output Schema

NameRequiredDescriptionDefault
capNoEffective page size after clamping.
pageNoPage coverage and continuation.
errorNoPresent when the call failed. Absent on success.
queryNoApplied canonical target and selection, including defaults.
shownNoSelected records returned.
noticeNoInterpretation or recovery guidance.
proteinsNoComplete upstream protein result records.
sourceUrlNoOfficial API source URL.
truncatedNoMore records remain.
totalCountNoUpstream total matching records.
effectiveQueryNoApplied selection as JSON.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.7/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, idempotentHint, and openWorldHint, so safety is covered. The description adds real behavioral context beyond that: the default taxon/review status, and the important caveat that isFragment=false does not prove a complete canonical sequence. Pagination and clamping behavior are left to the schema.

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?

Three front-loaded, dense sentences with no filler; the default scope is stated first. Minor redundancy with the isFragment schema description keeps it from a 5.

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 an output schema, full schema coverage, and annotations present, the description need only cover intent and defaults, which it does. The only gap is that it does not route the agent to the complement sibling tools.

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 schema already documents all seven parameters thoroughly, making 3 the baseline. The description restates the reviewedOnly and isFragment semantics rather than adding syntax or format detail beyond the schema.

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 and resource: 'Find UniProt proteins carrying an InterPro or member signature.' This clearly sets the domain-to-protein direction, which implicitly differentiates it from the reverse-direction sibling interpro_get_protein_domains, but no sibling is named.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It establishes the default operating scope ('Defaults to reviewed human proteins') and explains the reviewedOnly=false alternative, which gives useful usage context. However, it never states when to prefer this over interpro_get_entry or interpro_get_protein_domains, nor any exclusion conditions.

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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