LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks

Antoine Delaunay | Yunguan Fu | Nikolai Gorbushin | Robert McHardy | Bachir Djermani | Liviu Copoiu | Michael Rooney 1 | Maren Lang 2 | Andrey Tovchigrechko 1 | Ugur Sahin 2 | Karim Beguir | Nicolas Lopez Carranza

1 BioNTech US | 2 BioNTech DE



The peptide-major histocompatibility complex (pMHC) is a crucial protein in cell-mediated immune recognition and response. Accurate structure prediction is potentially beneficial for protein interaction prediction and therefore helps immunotherapy design. However, predicting these structures is challenging due to the sequential and structural variability. In addition, existing pre-trained models such as AlphaFold 2 require expensive computation thus inhibiting high throughput in silico peptide screening. In this study, we propose LightMHC: a lightweight model (2.2M parameters) equipped with attention mechanisms, graph neural networks, and convolutional neural networks. LightMHC predicts full-atom pMHC structures from amino-acid sequences alone, without template structures. The model achieved comparable or superior performance to AlphaFold 2 and ESMFold (93M and 15B parameters respectively), with five-fold acceleration (6.65 seconds/sample for LightMHC versus 36.82 seconds/sample for AlphaFold 2), potentially offering a valuable tool for immune protein structure prediction and immunotherapy design. The model and inference code have been released.