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jean — Molecular Biology & Genomics

humanize_antibody

Read-only

Humanize an antibody variable domain with Sapiens, the antibody language model behind BioPhi: score every position against human repertoires, take the highest-scoring residue in the frameworks, and keep the parental CDRs (and optionally the Kabat Vernier zone). Reports every mutation, and what the model would change next. Validated against the published PyTorch model on every chain of ANARCI's PDB benchmark.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
_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 humanize 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.
iterationsNoSapiens passes, each re-scoring the previous output (BioPhi's default 1).
humanizeCdrsNohumanize the CDRs too instead of grafting the parental ones back (raises the risk of losing binding).
cdrDefinitionNowhich CDR definition marks the residues kept from the parental antibody. Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), north (North).imgt
backmutateVernierNoalso keep the parental residues at the Kabat Vernier positions, which support the CDR loops.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
identityYespercent identity of the humanized domain to the parental one
humanizedYesthe humanized variable domain sequence
mutationsYeseach change: 0-based index in the domain, IMGT position, region, parental and humanized residue, and the model's probability for each
mutationCountYesnumber of positions changed

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.8/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnlyHint, destructiveHint false, openWorldHint false). The description adds real behavioral context: iterations re-score prior output, humanizing CDRs 'raises the risk of losing binding', and it reports every mutation plus what the model would change next. It stops short of 5 only by not describing rate limits or output structure beyond the mutations note.

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 the core action and method, then supporting detail. It is dense but every clause is informative; the final validation sentence adds trust context rather than filler.

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 complex 8-parameter tool with an output schema and nested _subject object, the description covers method, risk trade-offs, and iteration behavior. Return values need not be explained since an output schema exists; the definition is nearly complete.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters4/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so the baseline is 3. The description meaningfully cross-references parameters, tying 'keep the parental CDRs' to humanizeCdrs and 'optionally the Kabat Vernier zone' to backmutateVernier, making their purpose interpretable in the algorithm's terms.

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?

States a specific verb (humanize) and resource (antibody variable domain) and details the mechanism: score positions against human repertoires, take highest-scoring framework residue, keep parental CDRs. This is well beyond a tautology. It does not, however, explicitly distinguish itself from the sibling graft_antibody_cdrs, so it falls short of a 5.

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 workflow is described and options imply different scenarios (grafting parental CDRs is implied, humanizeCdrs is flagged as riskier), but there is no explicit when-to-use/when-not-to-use statement or named alternative. Usage must be inferred from the mechanism.

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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