Indeed, we find a loss of distinctive clustering in AlphaFold2 embeddings when meanreduction is performed (Figure ). The ESM2 embeddings, however, preserve local kinase relationships in all cases. Additionally, we used a convolutional autoencoder (CAE) to process each embedding into a low-dimensional latent space to capture the relationships between kinases. This process yielded latent vectors sized 192 for AlphaFold2 and 1680 for ESM2, effectively preserving family-wise relationships within the latent space, as demonstrated in Figure .