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jean — Molecular Biology & Genomics

antibody_liabilities

Read-only

Scan antibody and TCR variable domains for sequence liabilities (Asn deamidation, Asp isomerization, N-glycosylation sequons, Asp-Pro cleavage, Met and Trp oxidation, unpaired or missing conserved cysteines), each placed in its IMGT region so CDR hits can be told from framework ones. Every motif is cited to its source.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
rulesNowhich liabilities to report (default: all).
_filesNoThe 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.
cdrOnlyNoreport only liabilities that start inside a CDR.
proteinYesthe protein sequence (one-letter amino acids).
_subjectNoThe 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.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
countYesnumber of liabilities reported
cdrCountYesnumber of reported liabilities inside a CDR
liabilitiesYeseach hit: rule, motif, 0-based start and end, IMGT positions, region, whether in a CDR, source

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A4/5.0
Behavior4/5

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

Annotations already establish readOnlyHint=true, destructiveHint=false and openWorldHint=false, so the safety profile is covered. The description adds real behavioral context beyond that: hits are annotated with their IMGT region so CDR vs framework can be distinguished, and every motif is cited to a source. It does not discuss limits, performance, or failure modes, but the annotated baseline keeps the bar modest.

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?

Two sentences with zero filler: purpose plus the enumerated checks up front, then the region-placement and citation behavior. Every clause carries information an agent can act on.

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?

An output schema exists, so return-value explanation is not required, and the description covers what is scanned, the liability taxonomy, and the region/citation behavior. It could be more explicit that the input must be a variable-domain sequence for IMGT placement to be meaningful, which is the only notable 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 description coverage is 100%, so the schema already documents all five parameters, including the rules enum values and cdrOnly semantics. The description's enumeration of liability classes corroborates the rules enum and the IMGT-region framing explains why CDR filtering matters, but it adds no syntax or format detail beyond the schema. Baseline 3 is appropriate.

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 ('Scan') and resource ('antibody and TCR variable domains') and enumerates the exact liability classes it reports. An agent can distinguish this from neighbors like protein_properties, number_antibody, or antibody_molecule without opening any schema.

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?

The domain restriction to antibody/TCR variable domains implies when the tool applies, but there is no explicit when-to-use versus alternatives and no stated prerequisites or exclusions. Usage is inferable rather than spelled out.

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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