Improved B-cell epitope prediction using AlphaFold2 modeling and inverse folding latent representations

Accurate computational identification of B-cell epitopes is crucial for the development of vaccines, therapies, and diagnostic tools. However, current structure-based prediction methods face limitations due to the dependency on experimentally solved structures. Here, we introduce a markedly improved B-cell epitope prediction tool that innovatively employs inverse folding structure representations and a positive-unlabelled learning strategy, and is explicitly adapted for both solved and predicted structures. Our tool demonstrates a considerable improvement in performance over existing methods, accurately predicting linear and conformational epitopes across multiple independent datasets. Most notably, it maintains high predictive performance across solved, relaxed and predicted structures, alleviating the need for experimental validation and extending the general applicability of accurate B-cell epitope prediction by more than 3 orders of magnitude.