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Conditional Generation of Paired Antibody Chain Sequences through Encoder-Decoder Language Model

2023-01-06 23:34:52
Simon K.S. Chu, Kathy Y. Wei

Abstract

Protein language models (LMs) have been successful in sequence, structural and functional predictions. However, currently, protein LMs are limited to encoder- or decoder-only architectures for single sequences while many biological contexts involve protein-protein interactions. Here, we introduce pAbT5, which models antibody chain pairing as forward- and back-translations using a T5-based architecture. We show that pAbT5 accurately reflects chain pairing through sequence generation and mispairing as unsupervised and supervised classifications. Our protein LM generates variable-length sequences and its next-word prediction probability agrees with position-specific scoring matrix from sequence alignment. Like other works in protein LM, pAbT5 performs state-of-the-art unsupervised prediction on experimental measurements. To the best of our knowledge, pAbT5 is the first encoder-decoder protein LM for protein-protein interactions.

Abstract (translated)

URL

https://arxiv.org/abs/2301.02748

PDF

https://arxiv.org/pdf/2301.02748.pdf


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