AbMAP: Antibody Mutagenesis-Augmented Processing

This repository is a work in progress.

Protein language model customized for antibodies.

Commands:

Augment

Given a sequence, generate a foundational PLM embedding augmented with in-silico mutagenesis and CDR isolation.

Train

Given a dataset of labeled pairs of sequences and their augmented embeddings, train the AbMAP model on downstream prediction tasks.

Embed

Given fasta sequences and a pre-trained AbMAP model, generate their AbMAP embeddings (fixed or variable).

Reference

[1] Madeira, Fábio, et al. "Search and sequence analysis tools services from EMBL-EBI in 2022." Nucleic acids research 50.W1 (2022): W276-W279. (Transeq)