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.
You have an antibody sequence and you want to know which residues touch the antigen — the paratope — so you can engineer around them. Paragraph predicts it from sequence: paste the sequence, set the chain type, submit, and read the paratope residues and their probabilities off the result card.
Predict a paratope
Provide sequences
Paste one or more antibody variable-region sequences (up to 20 per job). Name them if you want the labels carried through.
Set the chain type
Choose H for heavy chains or L for light. Keep the default imgt numbering scheme — chothia is rejected with an error, not silently applied — and set the probability threshold that decides which residues count as paratope.
Submit and wait
Paragraph runs as an asynchronous GPU job on Modal — it folds each antibody before predicting, so allow more time than the CPU tools. A result card appears on the canvas when the job finishes.
Read the paratope
The card shows the predicted paratope residues, each residue's probability and region, the count of paratope residues, and the mean paratope probability.
In chat
Describe the antibody and ask for the binding residues — the model routes to Paragraph and chains a redesign tool when your prompt asks to engineer the loop.
What to do next
- Protect the paratope during humanization — keep BioPhi's
biophi_humanizebinding-residue preservation on (the default) so it doesn't rewrite the residues Paragraph flagged. - Cross-check humanness — compare the paratope against Humatch's flagged positions.
- Number the sequence — run ANARCI if you need canonical position labels.
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Paragraph outputs and interpretation
Paratope residues, per-residue probabilities, and regions from Paragraph.
How Paragraph results compare to the bench
What a Paragraph paratope has been shown to agree with experimentally, why a contact is not a binding hot spot, and what the fixed reference chain changes.