Humanize antibody sequences and evaluate humanness scores for therapeutic development. Learn more
Input
BioPhi webserver overview
BioPhi 1.0.11 humanizes antibody variable domains with Sapiens, evaluates sequence humanness with OASis, performs CDR grafting, and applies explicit Designer mutations. Results include a structured table and the native FASTA, CSV, XLSX, and alignment files produced by the selected mode.
For mode selection, input preparation, scientific background, interpretation, and validation, see how to use BioPhi online.
Pricing
BioPhi uses a 10-credit base charge plus 10 credits per FASTA record. A standard paired VH/VL run therefore costs 30 credits:
| Input | FASTA records | Credits | Calculation |
|---|---|---|---|
| One VH/VL antibody | 2 | 30 | 10 + (2 x 10) |
| One unpaired chain | 1 | 20 | 10 + (1 x 10) |
The exact quote is shown before submission. The examples above apply to FASTA input; review the displayed quote for PDB or RCSB inputs, which BioPhi parses into recognized antibody chains during the run.
Inputs
| Input mode | Accepted data | Limits | Notes |
|---|---|---|---|
| Fast Sapiens modes | Separate protein FASTA inputs for Heavy chain (VH) and Light chain (VL) | Up to one sequence in each field; at least one chain is required; 10 MiB per upload | Used by Sapiens, Both, positional scores, and mean score. Heavy chains support up to 144 residues; the BioPhi light-chain model supports up to 128 residues. |
| Parser-backed modes | Protein or coding-DNA FASTA (.fasta, .fa, .faa, .fna), PDB, or RCSB PDB fetch | One submitted input or file; up to 10 MiB | Used by OASis, complete Sapiens report, CDR grafting, and Designer. A FASTA can contain one chain or one paired VH/VL antibody. BioPhi parses the source-native input. |
Use complete antibody variable domains. The default interface accepts one VH, one VL, or a VH/VL pair. When both are present, ProteinIQ assigns matching BioPhi identifiers automatically, so the submitted FASTA headers do not need to match. Parser-backed modes retain one source-native input field. If that file contains both chains, use the same base identifier with _VH and _VL, or _HC and _LC, suffixes.
Fast protein modes accept the 20 standard amino acids, X, and a terminal *. They reject alignment gaps, DNA-like input, unrecognized variable domains, and sequences beyond the Sapiens model capacity.
Settings
Core setting
| Parameter | Type | Default | Description |
|---|---|---|---|
Processing mode | enum | Both (Humanization + Scoring) | Selects one of the eight workflows listed below. |
| Mode | Accepted input | Result |
|---|---|---|
Sapiens (Humanization) | Protein FASTA | Final humanized sequence for each recognized chain |
OASis (Humanness Scoring) | Protein or coding-DNA FASTA, PDB | Humanness and germline report without sequence modification |
Both (Humanization + Scoring) | Protein FASTA | Sapiens sequence plus parental and final OASis metrics |
Sapiens positional scores | Protein FASTA | BioPhi score matrix for all 20 amino acids at each position |
Sapiens mean score | Protein FASTA | One mean Sapiens score per chain |
Sapiens complete report | Protein or coding-DNA FASTA, PDB | Native Sapiens alignment, FASTA, and workbook |
CDR grafting | Protein or coding-DNA FASTA, PDB | CDRs grafted onto selected human V germlines |
Designer mutations | One protein or coding-DNA FASTA, or one PDB input | Explicit chain-numbered substitutions |
Advanced settings
| Parameter | Type | Default | Description |
|---|---|---|---|
Humanization iterations | integer, 1 or greater | 1 | Number of successive Sapiens passes. Available in Sapiens, Both, and complete-report modes. |
Numbering scheme | enum: Kabat, Chothia, IMGT, AHo | Kabat | Antibody numbering scheme passed to BioPhi. |
CDR definition | enum: Kabat, Chothia, IMGT, North | Kabat | Defines the CDR boundaries used by BioPhi. |
Humanize CDRs | boolean | Off | Allows Sapiens to modify CDR residues. Available in Sapiens, Both, and complete-report modes. |
VHH / nanobody input | boolean | Off | Declares a heavy-chain-only single-domain input and adds a VHH-specific interpretation warning. It does not change BioPhi's scientific model. |
Prevalence threshold | enum: Loose, Relaxed, Medium, Strict | Relaxed | Requires an OASis 9-mer to occur in at least 1%, 10%, 50%, or 90% of human subjects. Available in OASis, Both, CDR grafting, and Designer modes. |
Heavy-chain V germline | string | auto | Human heavy V family or gene for CDR grafting, such as IGHV3 or IGHV3-23. auto selects BioPhi's closest germline. |
Light-chain V germline | string | auto | Human kappa or lambda V family or gene for CDR grafting, such as IGKV1 or IGLV2. auto selects BioPhi's closest germline. |
Backmutate Vernier residues | boolean | On | Preserves parental Vernier residues during CDR grafting. |
Run final Sapiens pass | boolean | Off | Applies one Sapiens pass after CDR grafting. |
Designer mutations | text | empty, required in Designer mode | Chain-numbered substitutions such as H35:Y, L46:W, or H100A:F, separated by commas or new lines. |
Outputs
| Output | Format | Modes | Contents |
|---|---|---|---|
| Chain results | Interactive | Both | Chain-specific OASis summary, parental and humanized sequences, and BioPhi's residue-level evidence table |
| Structured data | Spreadsheet | All | Mode-specific chain rows, identifiers, scores, mutations, germline annotations, sequences, and lengths |
| Humanized sequences | FASTA | Sapiens, Both, complete report, CDR grafting, Designer | Final recognized variable-domain sequences |
| OASis workbook | XLSX | OASis, Both | Native chain, peptide, humanness, and germline report |
| Parental OASis workbook | XLSX | Both | OASis report for the submitted sequences before humanization |
| Positional scores | CSV | Sapiens positional scores | Per-position scores for all 20 amino acids |
| Mean scores | CSV | Sapiens mean score | One mean Sapiens score per input chain |
| Humanization alignments | TXT | Complete report, CDR grafting, Designer | Numbered parental and final sequence alignments |
| Sapiens workbook | XLSX | Complete report | BioPhi's complete native Sapiens report |
| Humanization workbook | XLSX | CDR grafting, Designer | BioPhi's native CDR-grafting or mutation report |
| Normalized input | FASTA | All | Protein variable domains used for result interpretation |
The Files view also includes results.csv and every native file returned by the selected mode. Files remain downloadable and supported native outputs can be routed into workflows.
Result fields
| Field | Meaning |
|---|---|
Sequence ID and Chain type | Recognized input identifier and VH or VL class |
Parental sequence retained (%) | Numbered sequence identity between the parental and final chain |
OASis identity (%) | Percentage of evaluated 9-mers that meet the selected subject-prevalence threshold |
OASis percentile (%) | Position of the OASis identity within BioPhi's therapeutic-antibody reference distribution |
Parental OASis identity (%) and Parental OASis percentile (%) | The corresponding values before humanization |
Mutations and Mutation details | Count and chain-numbered substitutions between parental and final chains |
V germline, J germline, and Germline % | BioPhi germline assignments and germline content |
Non-human peptides | OASis 9-mers that do not meet the selected prevalence threshold |
Humanized sequence and Length | Final amino-acid sequence and residue count |
OASis values are repertoire-based humanness evidence. They are not clinical immunogenicity predictions or universal pass/fail thresholds.
A heavy-chain-only job is treated as an unpaired VH unless VHH / nanobody input is enabled. BioPhi is not VHH-specific, so declared VHH results include a warning to review framework mutations and validate single-domain solubility and function independently.
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