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io.github.rcsb/rcsb-mcp

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by rcsb

rcsb_find_interpro_domains

Read-onlyIdempotent

Resolve protein domain, family, or fold names to InterPro accessions for precise PDB searches, replacing keyword guessing with structured identifiers.

Instructions

Resolve a free-text protein domain, family, or fold (e.g. SH2 domain, immunoglobulin fold, zinc finger, beta-barrel, WD40 repeat, kinase domain) to InterPro entries, for precise InterPro-based PDB searches instead of keyword guessing.

Use this whenever a request references a protein DOMAIN, FAMILY, or fold — "structures containing / with a ", "-containing proteins", "members of the family". Resolve the phrase to an InterPro accession (IPRxxxxxx) here, then search by it — see the resolver guidance in the server instructions for the attribute path and lineage semantics.

Args: query: Free-text domain/family name, e.g. "SH2 domain", "immunoglobulin". entry_type: Optional InterPro type filter. Omit to return all types. limit: Max entries to return. with_pdb_counts: If true (default), annotate each entry with pdb_entry_count (PDB entries carrying it).

Returns: {query, entry_type, count, entries:[{id, name, type, pdb_entry_count?}]}.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
limitNo
queryYes
entry_typeNo
with_pdb_countsNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior4/5

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

Annotations already convey read-only, idempotent, and non-destructive behavior. The description adds context about its role as a resolver (returning InterPro entries) and the optional pdb_entry_count annotation. It does not dwell on auth or rate limits, which is acceptable given the strong 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?

The description is well-structured: a clear purpose statement, usage context, parameter definitions, and return shape. Every sentence contributes; no filler. The pointer to server instructions is concise and relevant.

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 moderate complexity, the description covers purpose, usage timing, parameters, and return format. It also references the resolver guidance for attribute path and lineage semantics, ensuring the agent knows how to proceed. The presence of an output schema further reduces the need to describe return values in detail.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Input schema coverage is 0%, but the description's Args section fully compensates by defining each parameter: query as 'Free-text domain/family name', entry_type as 'Optional InterPro type filter', limit as 'Max entries', and with_pdb_counts as 'annotate each entry with pdb_entry_count'. This adds value beyond the schema's bare types/defaults.

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 explicitly states the tool 'Resolve a free-text protein domain, family, or fold ... to InterPro entries', with specific examples (SH2 domain, zinc finger). It clearly differentiates itself from sibling resolver tools like rcsb_find_go_terms and rcsb_find_enzyme_classes by focusing on protein domains/families/folds.

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

Usage Guidelines5/5

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

The description gives explicit when-to-use guidance: 'Use this whenever a request references a protein DOMAIN, FAMILY, or fold', with concrete phrasings. It also contrasts with keyword guessing and points to resolver guidance in server instructions for precise search integration.

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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