Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation
Fig 4
Latent Space Analysis and Interpolation.
(A) Linear interpolation between two randomly selected embeddings. The starting and ending structures are 1TQB(H) and 5JW4(H) respectively. The backbones are unaltered, full-atom model outputs. Structures are colored by residue index in reverse rainbow order. (B) Centroid energy profiles of the structures from panel A after constrained refinement. (C) Higher frequency overlays of 80 sequential structures in the unrefined interpolation trajectory. The roman numerals correspond to the blue labels in panel A. A lighter shade of blue indicates an earlier structure while the darker shade indicates a later structure. Structure transitions are smooth and follow a near-continuous trajectory. (D) The top panel shows a tSNE dimensionality reduction of the embedding means of the 4154 non-redundant structures in the training set. Colorings correspond to k-means clusters (k = 40) of the post-tSNE data, and ten structures from three clusters are visualized to the right. The bottom panel depicts a principal components reduction of the latent space, showing five sampled data points per non-redundant structure.