EMBER: Predicting TCR–pMHC Binding Without a Docked Complex

We propose **EMBER**, a structure-based framework for TCR–pMHC binding prediction that eliminates the need for a predicted docked complex, and with it the placement error that dominates such predictions. Traditional structure-based predictors utilize the co-folded complex structure of the receptor and the antigen and interpret binding from its contact surface. Consequently, every downstream feature inherits any deviation the structure-prediction tool introduced. Methodologically, EMBER folds the TCR and pMHC independently, encodes them as SE(3)-invariant residue graphs, and compares their learned representations without constructing a shared coordinate frame. A relative pose is therefore not an input of the model, so placement error cannot propagate into the prediction. Computationally, EMBER preprocesses $\mathcal{O}(N+M)$ monomer folds where a complex-based predictor needs $\mathcal{O}(NM)$ operations. Experimentally, under epitope-disjoint evaluation with six retrained baselines, EMBER is first on every metric under all four folding tools, by**0.9 to 14.4%** in micro-AUROC, **18.5 to 25.3%** in micro-AUPRC and **10.6 to 24.1%** in MCC${}^{\ast }$. Its ranking is also up to **85%** more stable across folding tools.