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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. The classical humanization route, and the counterpart to humanize_antibody's language model. Reproduces abnumber 0.4.4 over every antibody chain of ANARCI's PDB benchmark.

Input Schema

TableJSON 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

TableJSON 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. First observed

TDQS

A4.1/5.0
Behavior4/5

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

Annotations already declare readOnlyHint, openWorldHint=false, and destructiveHint=false, so the safety profile is covered. The description adds real context beyond that: the exact grafting pipeline (find germlines, merge into acceptor, place parental CDRs) and a reproducibility claim against abnumber/ANARCI. It omits any note about input constraints or failure modes, keeping it from a 5.

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?

Three sentences, front-loaded with the core action before the sibling contrast and the reproducibility note. Every sentence carries weight, though the trailing ANARCI/abnumber benchmark claim is the most digressive element.

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, the description needn't explain return values, and annotations cover safety. It explains the method well for a 10-parameter tool, though it leaves the multi-domain behavior and germline-selection interaction to the schema, which is acceptable but not exhaustive.

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 parameters (top, vGene, jGene, cdrDefinition, rankByFrameworks, backmutateVernier, domain) are already fully documented. The description's mentions of closest germline V/J and grafting map onto these but add no syntax or default semantics beyond the schema, so the baseline 3 applies.

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 (humanize), resource (antibody variable domain), and method (CDR grafting), then spells out the internal steps. It explicitly names and contrasts with the sibling humanize_antibody, so an agent can distinguish the two without opening schemas.

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?

Frames itself as 'the classical humanization route' and the counterpart to humanize_antibody's language model, which gives clear context for choosing between the two. It stops short of an explicit when-to-use/when-not rule or naming conditions that favor one method.

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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