---
title: BioPhi inputs and parameters
description: VH/VL sequences, mode, target humanness, and residues to preserve for BioPhi.
tags:
  - biophi
  - inputs
---

You provide a heavy-chain variable-region sequence (and optionally the light chain), and which BioPhi tool you call decides the mode: `biophi_humanness` only reads the sequence, while `biophi_humanize` and `biophi_graft` rewrite it. When you humanize with `biophi_humanize`, keeping binding-residue preservation on is your guardrail against breaking the binding site.

## Sequences

- `vh_sequence` (string) —
Heavy-chain variable-region amino acid sequence.

- `vl_sequence` (string) —
Light-chain variable-region amino acid sequence.

## Mode: which tool you call

- `tool` (string) —
`biophi_humanness` (score only), `biophi_humanize` (Sapiens deep-learning humanization), or `biophi_graft` (CDR grafting). Each calls the same backend with its mode fixed — there is no separate `mode` argument to set.

## Humanization controls

These apply to `biophi_humanize` and `biophi_graft`.

- `target_humanness` (float) —
Target humanness score to humanize toward (0.0–1.0). Accepted by both `biophi_humanize` and `biophi_graft`.

- `preserve_binding_residues` (bool) —
`biophi_humanize` only. Toggles whether known binding residues are held fixed during Sapiens humanization — it is an on/off switch, not a list of positions to name yourself. `biophi_graft` has no equivalent control.

## Classification

- `oasis_percentile_threshold` (float) —
OASis percentile threshold for the humanness classification (0.0–100.0). Accepted by `biophi_humanness` and `biophi_humanize`; `biophi_graft` doesn't take it.

## From a therapeutic name

All three tools also accept a `therapeutic_name` — name a known antibody and the platform resolves its VH/VL from Thera-SAbDab before scoring or humanizing.

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