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). 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
| 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 |