Lin Ha

TCR–pMHC binding prediction no longer has to start from a docked complex. Structure-based predictors co-fold the pair and read binding off the interface, so placement error changes which residues and contacts reach the model. EMBER folds each molecule as an unbound monomer, encodes both as rigid-motion-invariant residue graphs, and compares them through bidirectional attention over CDR3 and peptide residues. Across four folding tools and five epitope-disjoint folds it leads every metric, with 26% to 85% higher cross-tool ranking agreement than structure-based baselines.

TCR–pMHC binding prediction no longer has to start from a docked complex. Structure-based predictors co-fold the pair and read binding off the interface, so placement error changes which residues and contacts reach the model. EMBER folds each molecule as an unbound monomer, encodes both as rigid-motion-invariant residue graphs, and compares them through bidirectional attention over CDR3 and peptide residues. Across four folding tools and five epitope-disjoint folds it leads every metric, with 26% to 85% higher cross-tool ranking agreement than structure-based baselines.