graft_antibody_cdrs
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
| Name | Required | Description | Default |
|---|---|---|---|
| top | No | graft onto the n-th closest germline instead of the closest (0-based). | |
| jGene | No | use this human J germline instead of the closest one. | |
| vGene | No | use this human V germline instead of the closest one (a family, gene or allele: IGHV1, IGHV1-18, IGHV1-18*01). | |
| _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 graft 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. | |
| cdrDefinition | No | which CDR definition decides what is grafted from the parental antibody. Values: imgt (IMGT), kabat (Kabat), chothia (Chothia), north (North). | imgt |
| rankByFrameworks | No | rank germlines on framework identity alone, ignoring the CDRs. | |
| backmutateVernier | No | keep the parental residues at the Kabat Vernier positions, the framework residues that support the CDR loops. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| grafted | Yes | the grafted variable domain sequence | |
| germline | Yes | the V and J alleles the frameworks came from | |
| identity | Yes | percent identity of the grafted domain to the parental one | |
| candidates | Yes | the closest human V and J germlines, best first |