jean — Molecular Biology & Genomics

lookup_residue_sites

Read-only

The individual catalytic, substrate-binding, metal-binding and interface residues a member database annotates INSIDE a domain, for a known protein. Takes a UniProt accession. This is what InterProScan itself does not return — its per-location site array comes back empty — so it is a separate lookup against InterPro, keyed to an entry whose sequence the residue numbers belong to.

Input Schema

TableJSON Schema

Name	Required	Description
`_files`	No	The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name.
`_subject`	No	The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several.
`accession`	Yes	UniProt accession, e.g. P00330. It must be the entry whose CURRENT sequence you mean: residues are numbered against it, so an accession for a protein that merely resembles yours puts a catalytic residue on the wrong amino acid.

Output Schema

TableJSON Schema

Name	Required	Description	Default
`signatures`	Yes	per member-database signature: its accession, the database, its name, and each named site with every annotated residue and 1-based position
`residueCount`	Yes	total annotated residues across every signature

Schema Changelog

Changes observed during successful MCP inspections.

First observedOct 20, 2026

TDQS

A4.1/5.0

Behavior4/5

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

Annotations cover the safety profile (readOnly, non-destructive, open-world). The description adds genuinely useful behavior: this is a live separate lookup against InterPro rather than a local computation, and it is keyed to a specific entry whose sequence the residue numbers belong to.

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?

Front-loaded with what is returned, followed by the input and the InterProScan gap. Three sentences are dense but each carries information; minor redundancy between the description and the accession schema blurb.

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 present, return-value explanation is not needed. Purpose, input, and the reason this exists as a separate tool are all covered, leaving only the absence of named sibling alternatives as a small gap.

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% and the accession parameter already carries the warning about current-sequence numbering. The description reinforces that the accession must be the entry the residue numbers belong to, but adds little syntax or meaning beyond the 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?

States a specific verb+resource (residue sites annotated by a member database inside a domain) and the input (a UniProt accession). The scoping is precise enough to separate it from domain-scanning siblings like scan_protein_domains or RPS-BLAST tools.

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?

Explains the condition for using it: it retrieves what InterProScan itself does not return, because its per-location site array comes back empty, so this is a separate InterPro lookup. Clear context, though it never names an alternative tool by name.

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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