Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions.

ABSTRACT: The explosion of sequence data has allowed the rapid growth of protein language models (pLMs). pLMs have now been employed in many frameworks including variant-effect and peptide-specificity prediction. Traditionally, for protein-protein or peptide-protein interactions (PPIs), corresponding sequences are either co-embedded followed by post-hoc integration or the sequences are concatenated prior to embedding. Interestingly, no method utilizes a language representation of the interaction itself. We developed an interaction LM (iLM), which uses a novel language to represent interactions between protein/peptide sequences. Sliding Window Interaction Grammar (SWING) leverages differences in amino acid properties to generate an interaction vocabulary. This vocabulary is the input into a LM follow

SUBMITTER: Omelchenko AA 

PROVIDER: S-EPMC11092674 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature