SPPIDER-seq: Sequence-based partner-aware predictor of protein-protein interaction sites (opens in new tab)

Motivation: Sequence-based protein-protein interaction (PPI) site predictors typically analyze proteins in isolation, neglecting partner-specific context that is critical for interface specificity, particularly in transient and disordered interactions. Results: We introduce SPPIDER-seq, a partner-aware PPI site prediction framework that combines pretrained ESM-2 embeddings with a cross-attention architecture to enable residue-level conditioning on interacting partners. We curated non-redundan...