Pan-Prediction of MHC-II Restricted Epitopes Across Species via an Alphafold-based Quantification Scheme

Wang, S.; Kong, L.; Hu, D.; Zheng, L.; Fei, C.; Du, L.; Tang, Z.; Xu, S.; Yang, H.; Zhang, N.

doi:10.1101/2024.10.11.617946

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bioRxiv · 10.1101/2024.10.11.617946

Pan-Prediction of MHC-II Restricted Epitopes Across Species via an Alphafold-based Quantification Scheme

Wang, S.·Kong, L.·Hu, D.·Zheng, L.·Fei, C.·Du, L.·Tang, Z.·Xu, S.·Yang, H.·Zhang, N.

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Abstract

Predicting MHC-II restricted epitopes across species used to be challenging, but Alphafold (AF) may provide a structure-based pan-prediction solution. In this study, we established the new tool AF-pred with a clear standard for quantitative prediction results. Compared to the sequence-based tools heavily trained with human ligandome, AF-pred does not show advantage in predicting the binding patterns of human HLA-II but has far better performance in predicting binding patterns of other animals MHC-II. Using recently resolved bat MHC-II structures, we analyzed AF-preds prediction capability, logic and limitation. In addition, we also explored the impact of AF algorithm iterations on the prediction of MHC-II restricted epitopes. The results demonstrated that AF-pred is capable of cross-species prediction of MHC-II restricted epitopes and is conducive to the development of novel veterinary vaccines.

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Wang, S., Kong, L., Hu, D., Zheng, L., Fei, C., Du, L., Tang, Z., Xu, S., Yang, H., Zhang, N.. 2024-10-15. Pan-Prediction of MHC-II Restricted Epitopes Across Species via an Alphafold-based Quantification Scheme. https://doi.org/10.1101/2024.10.11.617946

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