SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders.

ABSTRACT: Protein-protein interactions (PPIs) are critical for biological processes and predicting the sites of these interactions is useful for both computational and experimental applications. We present a Structure-agnostic Language Transformer and Peptide Prioritization (SaLT&PepPr) pipeline to predict interaction interfaces from a protein sequence alone for the subsequent generation of peptidic binding motifs. Our model fine-tunes the ESM-2 protein language model (pLM) with a per-position prediction task to identify PPI sites using data from the PDB, and prioritizes motifs which are most likely to be involved within inter-chain binding. By only using amino acid sequence as input, our model is competitive with structural homology-based methods, but exhibits reduced performance compared with deep

SUBMITTER: Brixi G 

PROVIDER: S-EPMC10598214 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature