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Jean — Molecular Biology & Genomics

graft_antibody_cdrs

Read-only

Humanize an antibody variable domain by CDR grafting: find the closest human germline V and J, merge them into an acceptor framework, and put the parental CDRs onto it.

Input Schema

NameRequiredDescriptionDefault
topNograft onto the n-th closest germline instead of the closest (0-based).
jGeneNouse this human J germline instead of the closest one.
vGeneNouse this human V germline instead of the closest one (a family, gene or allele: IGHV1, IGHV1-18, IGHV1-18*01).
_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.
domainNowhich variable domain to graft when the sequence holds several (0-based, in sequence order).
proteinYesthe protein sequence (one-letter amino acids); the variable domains in it are found and numbered first.
_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.
cdrDefinitionNowhich CDR definition decides what is grafted from the parental antibody. Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), north (North).imgt
rankByFrameworksNorank germlines on framework identity alone, ignoring the CDRs.
backmutateVernierNokeep the parental residues at the Kabat Vernier positions, the framework residues that support the CDR loops.

Output Schema

NameRequiredDescriptionDefault
graftedYesthe grafted variable domain sequence
germlineYesthe V and J alleles the frameworks came from
identityYespercent identity of the grafted domain to the parental one
candidatesYesthe closest human V and J germlines, best first

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • addedOutput schema / properties / identity / x-unit
      Added value: +"%"
  2. First observed

TDQS

A3.5/5.0
Behavior3/5

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

Annotations already establish readOnlyHint=true, non-destructive, and closed-world, so safety is covered. The description adds real behavioral value by spelling out the algorithmic steps (germline search, framework merge, CDR transfer). It stops short of disclosing edge-case behavior: what happens if no suitable germline is found, whether the result is returned as a new sequence or a report, or how the graft differs per cdrDefinition.

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?

One tight sentence with the core action front-loaded and the workflow steps following in logical order. No filler or repetition. It could be marginally stronger by adding a single clause distinguishing it from the humanize_antibody sibling.

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?

For a 10-parameter, nested-schema tool with an output schema, the description supplies the conceptual model an agent needs to pick and configure it. Nothing critical is absent because parameters and returns are covered elsewhere. The main gap is sibling differentiation rather than missing mechanics.

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 every parameter including top, vGene, jGene, domain, cdrDefinition, rankByFrameworks, and backmutateVernier is already documented in the schema. The description's phrase 'closest human germline V and J' implicitly explains the default behavior that vGene/jGene/top override, but adds no new syntax or constraint detail beyond the schema.

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

Purpose4/5

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

The description names a specific verb and resource ('Humanize an antibody variable domain by CDR grafting') and enumerates the mechanism: find closest human germline V and J, merge into acceptor framework, graft parental CDRs. That is much more informative than the name alone. It does not, however, distinguish itself from the sibling humanize_antibody, which likely covers a broader or overlapping humanization strategy.

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 grafting workflow implies when to use it (when a humanization must be done by CDR transfer onto a human framework), but there is no explicit when-to-use statement and no mention of alternatives such as humanize_antibody. The agent must infer the choice from the sibling's 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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