Antifold

Overview

The antifold tool designs antibody sequences using the inverse folding method. It can help with CDR sequence recovery.

Inputs

• File path to local pdb to upload

• Heavy and light chain identifiers

• Number of sequences per target chain

• Sampling temperature

• List of regions to sample from

• File path to store the returned FASTA content

Outputs

• A FASTA file containing the sample ID, global score, heavy and light chains, mutations and temperature

• Highlights of the changes made

• How many antibody sequences were generated

• What this output is suitable for

Description

Antifold uses an inverse folding method from structure to sequence antibody design. The parameters provided are passed to an EMLy, and then to an antibody endpoint that generates the new structure.

Paper Notes

Antifold is an antibody-specific inverse folding model, that improves on CDR sequence recovery, with CDRs with designed sequences showing high affinity to their solved counterparts. For each residue position, Antifold outputs residue probabilities, number of designed sequences for a selected region, and structural tolerences for mutation without altering the backbone structure. Protein inverse folding models can be trained not to alter the antibody backbone structure by predicting the sequence given structure.