Fast and accurate protein structure search with Foldseek
describe the conformation between the backbone fragments. In addition, we encode the sequence distance with the two featuresLearning the 3Di states using a vector quantized variational autoencoder
The 10-dimensional descriptors were discretized into an alphabet of 20 states using a vector quantized variational autoencoder -means, VQ-VAE is a nonlinear approach that can optimize decision surfaces for each of its states. In contrast to the standard VQ-VAE, we trained the VQ-VAE not as a simple generative model but, rather, to learn states that are maximally conserved in evolution.
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