Paragraph outputs and interpretation
Paratope residues, per-residue probabilities, and regions from Paragraph.
Paragraph returns, per sequence, the list of predicted paratope residues, a per-residue table of position, amino acid, probability, and region, and summary counts including the mean paratope probability. Read the per-residue probabilities, not just the paratope/not-paratope call: a residue at 0.9 is a firmer "don't touch this" than one at 0.51, which matters when you're deciding which positions to hold fixed during humanization.
Per-sequence result
| Field | Type | What it tells you |
|---|---|---|
sequence_name | string | The name you gave the sequence. |
chain_type | string | The chain reported (H or L). |
residue_predictions | list | Per-residue predictions (see below). |
paratope_residues | string[] | Residues predicted to be part of the paratope. |
paratope_sequence | string | null | The paratope residues concatenated. |
num_paratope_residues | int | Count of predicted paratope residues. |
mean_paratope_probability | float | null | Mean probability across the paratope residues. |
Per-residue prediction
Each entry in residue_predictions:
| Field | Type | What it tells you |
|---|---|---|
position | string | Numbered position (e.g. "31"). |
residue | string | Amino-acid one-letter code. |
probability | float | Paratope probability (0–1). |
is_paratope | bool | Whether it cleared the threshold. |
region | string | null | Region annotation (CDR-H1, FR-H2, …). |
Job-level summary
| Field | Type | Meaning |
|---|---|---|
failed_sequences | string[] | Sequences Paragraph could not predict. |
success_count | int | Sequences predicted successfully. |
fail_count | int | Sequences that failed. |
threshold_used | float | Probability threshold applied. |
Reading the result card
The Paragraph result renders on the canvas as an antibody paratope card, surfacing the binding-residue count and the per-residue probabilities so you can see the paratope at a glance.
What to do next
- Before running
biophi_humanize, check whether its paratope overlaps the framework — if it's clean, keep binding-residue preservation on (the default) rather than naming positions, since the tool only exposes an on/off toggle. - Compare the paratope against Humatch's flagged low-humanness positions to avoid a conflict.
- Use the region annotations to target a specific CDR loop for redesign.
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Paragraph inputs and parameters
Up to 20 sequences and the probability threshold that decides which residues are paratope — plus why only imgt works, since a chothia request is rejected.
Paragraph quickstart
Paste a sequence and set the chain type; Paragraph folds the antibody first, then returns paratope residues with a probability and region for each.