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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.

Input 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

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

A3.9/5.0
Behavior4/5

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

Annotations already declare a safe read-only, closed-world operation, so the description needs to add analytical substance rather than safety detail. It does: it lists the exact liability motifs detected and discloses that every hit is mapped to an IMGT region, which tells the agent the output is region-annotated rather than a flat position list.

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?

A single front-loaded sentence with a parenthetical enumeration; dense but every clause carries information. The long parenthesis makes it slightly harder to scan than a short purpose sentence followed by detail.

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 and full parameter documentation, the description only needs to convey what is scanned and how hits are contextualized, which it does. Minor gaps remain around whether numbering is done automatically and whether non-antibody sequences are rejected.

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 rules, cdrOnly, protein and file/subject parameters are already documented in the schema. The description only hints at cdrOnly behavior via 'CDR hits can be told from framework ones' and adds no format or syntax detail 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 and resource ('Scan antibody and TCR variable domains for sequence liabilities') and enumerates the liability classes covered, so an agent can distinguish it from generic protein property or manufacturability tools without opening the 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 scope (antibody/TCR variable domains only) is implied by the wording, but there is no explicit when-to-use guidance or naming of alternatives such as check_manufacturability, protein_properties, or the other antibody_* siblings.

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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