humanize_antibody
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).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _files | No | The 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. | |
| domain | No | which variable domain to humanize when the sequence holds several (0-based, in sequence order). | |
| protein | Yes | the protein sequence (one-letter amino acids); the variable domains in it are found and numbered first. | |
| _subject | No | The 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. | |
| iterations | No | Sapiens passes, each re-scoring the previous output (BioPhi's default 1). | |
| humanizeCdrs | No | humanize the CDRs too instead of grafting the parental ones back (raises the risk of losing binding). | |
| cdrDefinition | No | which CDR definition marks the residues kept from the parental antibody. Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), north (North). | imgt |
| backmutateVernier | No | also keep the parental residues at the Kabat Vernier positions, which support the CDR loops. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| identity | Yes | percent identity of the humanized domain to the parental one | |
| humanized | Yes | the humanized variable domain sequence | |
| mutations | Yes | each change: 0-based index in the domain, IMGT position, region, parental and humanized residue, and the model's probability for each | |
| mutationCount | Yes | number of positions changed |