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...
| Authors | Lin Ha, Chen Zhou, Haozheng Luo et al. |
|---|---|
| Primary category | q-bio.QM |
| Published | 19 October 2026 |
| Last updated at source | 19 October 2026 |
Recent changes
- 21 Oct 2026 Description: 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 → 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
- 21 Oct 2026 Topics added q-bio.QM, cs.LG removed hf-daily-papers, tcr-pmhc binding prediction, structure-based framework, docked complex, co-folded complex, contact surface, se(3)-invariant residue graphs, shared coordinate frame, relative pose
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