interpro-mcp-server

Search InterPro entries

interpro_search_entries

Read-onlyIdempotent

Search InterPro entries or member signatures by text or entry type. GO filters require sourceDatabase interpro; integratedInto selects member signatures for an InterPro accession. Results are cursor-paged; use interpro_get_entry for full metadata.

Tool call template

This tool declares no required parameters. Add optional parameters from the input schema as needed.

{
  "id": 1,
  "jsonrpc": "2.0",
  "method": "tools/call",
  "params": {
    "arguments": {},
    "name": "interpro_search_entries"
  }
}

Input Schema

Name	Required	Description	Default
`limit`	No	Positive integer page size; values above 100 are clamped to 100 with a notice; defaults to 20.
`query`	No	Text to search; omit all filters to browse the database.
`cursor`	No	Opaque nextCursor from this tool with unchanged filters; limit may change.
`goTerm`	No	GO annotation identifier such as GO:0003677; requires sourceDatabase interpro and cannot combine with goCategory.
`entryType`	No	Entry annotation type.
`goCategory`	No	GO category: P biological process, F molecular function, C cellular component; requires sourceDatabase interpro and cannot combine with goTerm.
`integratedInto`	No	Integrating InterPro accession; requires a member sourceDatabase.
`sourceDatabase`	No	Database to search; defaults to interpro.	interpro

Output Schema

Name	Required	Description
`cap`	No	Effective page size after clamping.
`page`	No	Continuation and upstream total.
`error`	No	Present when the call failed. Absent on success.
`query`	No	Applied canonical filters.
`shown`	No	Records returned in this page.
`notice`	No	Interpretation or recovery guidance.
`entries`	No	Complete entry summaries from this page.
`sourceUrl`	No	Official API source URL.
`truncated`	No	More records remain.
`totalCount`	No	Upstream total matching records.
`effectiveQuery`	No	Applied filters as JSON.

Schema Changelog

Changes observed during successful MCP inspections.

Changed4 schema fields changedOct 24, 2026

changedInput schema / properties / goCategory / description

Previous value: -"GO category: P biological process, F molecular function, C cellular component; requires sourceDatabase interpro."New value: +"GO category: P biological process, F molecular function, C cellular component; requires sourceDatabase interpro and cannot combine with goTerm."

changedInput schema / properties / goTerm / description

Previous value: -"GO annotation identifier such as GO:0003677; requires sourceDatabase interpro."New value: +"GO annotation identifier such as GO:0003677; requires sourceDatabase interpro and cannot combine with goCategory."

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `go_filters_require_interpro`: goTerm or goCategory is supplied for a member sourceDatabase. `database_mismatch`: Integration filtering is requested on the integrating database. `invalid_cursor`: Cursor decoding or scope fails, or upstream rejects continuation. `entry_withdrawn`: InterPro answers the search with HTTP 410, reporting a withdrawn record. `upstream_shape_invalid`: Upstream JSON, structure, or continuation is incompatible. `upstream_response_too_large`: An upstream response exceeds 4 MiB. `upstream_rejected`: InterPro returns an unhandled redirect or client rejection. `upstream_unavailable`: InterPro has a network or server failure; HTTP 501 is not retryable. `upstream_timeout`: InterPro returns HTTP 408/504 or an attempt exceeds its deadline. `upstream_rate_limited`: InterPro returns HTTP 429. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `incompatible_go_filters`: Both goTerm and goCategory are supplied. `go_filters_require_interpro`: goTerm or goCategory is supplied for a member sourceDatabase. `database_mismatch`: Integration filtering is requested on the integrating database. `invalid_cursor`: Cursor decoding or scope fails, or upstream rejects continuation. `entry_withdrawn`: InterPro answers the search with HTTP 410, reporting a withdrawn record. `upstream_shape_invalid`: Upstream JSON, structure, or continuation is incompatible. `upstream_response_too_large`: An upstream response exceeds 4 MiB. `upstream_rejected`: InterPro returns an unhandled redirect or client rejection. `upstream_unavailable`: InterPro has a network or server failure; HTTP 501 is not retryable. `upstream_timeout`: InterPro returns HTTP 408/504 or an attempt exceeds its deadline. `upstream_rate_limited`: InterPro returns HTTP 429. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "go_filters_require_interpro",
-  "database_mismatch",
-  "invalid_cursor",
-  "entry_withdrawn",
-  "upstream_shape_invalid",
-  "upstream_response_too_large",
-  "upstream_rejected",
-  "upstream_unavailable",
-  "upstream_timeout",
-  "upstream_rate_limited"
-]New value: +[
+  "incompatible_go_filters",
+  "go_filters_require_interpro",
+  "database_mismatch",
+  "invalid_cursor",
+  "entry_withdrawn",
+  "upstream_shape_invalid",
+  "upstream_response_too_large",
+  "upstream_rejected",
+  "upstream_unavailable",
+  "upstream_timeout",
+  "upstream_rate_limited"
+]

First observedOct 24, 2026

TDQS

A4.3/5.0

Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, so the safety profile is covered. The description adds useful behavioral context about cursor-based paging and filter prerequisites, without contradicting annotations.

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?

It is three tightly written sentences with the core search purpose front-loaded. No sentence is wasted, and pagination and the metadata alternative are placed after the primary scope.

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 the rich input schema, output schema, and annotations, the description covers what an agent needs: search scope, key filter constraints, pagination behavior, and the handoff to interpro_get_entry. Remaining details such as defaults and limit clamping are already handled by the schema.

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 coverage is 100%, so the schema already documents the parameters and their constraints in detail. The description restates the main cross-parameter rules for GO filters and integratedInto, but adds only limited meaning beyond the structured schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb and resource: search InterPro entries or member signatures by text or entry type. It also distinguishes this from interpro_get_entry by assigning full metadata retrieval there.

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

Usage Guidelines4/5

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

It gives explicit conditions for GO filters and integratedInto, notes cursor paging, and directs agents to interpro_get_entry for full metadata. It does not explicitly compare against other search-oriented siblings such as interpro_find_proteins_by_domain.

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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