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interpro-mcp-server

Map protein domains

interpro_get_protein_domains
Read-onlyIdempotent

Retrieve InterPro and member-signature matches on a canonical UniProt protein, preserving every location and discontinuous fragment. Optionally retain matches covering a residue and include extra predicted features. Large maps arrive in segments of whole matches that fit the response budget: the first segment carries the protein metadata, requested extra features follow the last match, and coverage.nextCursor continues until hasMore is false.

Input Schema

NameRequiredDescriptionDefault
cursorNoOpaque coverage.nextCursor with unchanged accession, residuePosition, and includeExtraFeatures.
accessionYesCanonical six- or ten-character UniProt accession, without an isoform suffix.
residuePositionNoResidue position, 1-based and inclusive; must not exceed protein length.
includeExtraFeaturesNoInclude complete extra predicted features, returned after the last match; defaults to false.

Output Schema

NameRequiredDescriptionDefault
capNoMost match records one call reads; a segment can stop sooner at the response byte budget.
urlNoCanonical protein website URL.
errorNoPresent when the call failed. Absent on success.
shownNoSelected match records in this segment.
noticeNoInterpretation, continuation, or recovery guidance.
matchesNoWhole selected match records in this segment, sorted by earliest coordinate then accession; a match is never split across segments.
proteinNoComplete upstream protein metadata on the first segment, the call without cursor; continuation segments omit it.
coverageNoWhere this segment sits in the protein map: every match, then requested extra features.
accessionNoCanonical UniProt accession.
selectionNoApplied residue and extra-feature selection.
sourceUrlNoOfficial protein API source URL.
truncatedNoMore segments remain.
totalCountNoUpstream total matching records.
extraFeaturesNoWhole selected extra features in this segment, in feature-key order; {} when none are selected. Omitted when not requested or when this segment ends before the features that follow the last match.
effectiveQueryNoApplied selection as JSON.

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior5/5

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

Goes well beyond the readOnly/openWorld/idempotent annotations by disclosing segmentation behavior: results are returned as whole-match segments within a response budget, the first segment carries protein metadata, extra features follow the last match, and coverage.nextCursor is followed until hasMore is false. It also states that all locations and discontinuous fragments are preserved, which tells the agent not to expect collapsed coordinates.

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 sentences, front-loaded with the core operation and tail-loaded with pagination mechanics. The final sentence is dense and long but every clause conveys distinct information an agent needs; nothing is redundant.

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

Completeness5/5

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

Given an output schema exists, the description does not need to document return values, and it covers the one thing the schema cannot: how large results are segmented and how to continue. Combined with complete parameter coverage and safety annotations, an agent has everything needed to invoke and iterate correctly.

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 all four parameters are already documented in structured fields. The description reinforces the residue-filter meaning and restates includeExtraFeatures placement, but adds no syntax or constraint detail beyond the schema, so the baseline holds.

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 ('Retrieve InterPro and member-signature matches on a canonical UniProt protein') with the direction of the mapping made explicit, which distinguishes it from the reverse-direction sibling interpro_find_proteins_by_domain. It does not name that sibling directly, so the differentiation is inferential rather than stated.

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?

Use conditions are only implied through optional behaviors ('retain matches covering a residue', 'include extra predicted features'). No sibling is named as an alternative and there is no explicit when-not guidance, though the required-accession framing makes the entry point reasonably obvious.

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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