Summary
The latent space of ESMFold is discontinuous (1,2). However, it can be smoothened by compression using a VAE.
Figures
Ref (2)
See also
1.
del Alamo D, Jeliazkov JR, Truan D, Karpiak JD. Conformational sampling and interpolation using language-based protein folding neural networks. openRxiv; 2023. Available from: https://doi.org/10.1101/2023.12.16.571997
2.
Lu AX, Yan W, Yang KK, Gligorijevic V, Cho K, Abbeel P, et al. Tokenized and continuous embedding compressions of protein sequence and structure. Patterns. 2025;6(6):101289. Available from: https://doi.org/10.1016/j.patter.2025.101289