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Fig. 6 | BMC Bioinformatics

Fig. 6

From: Deep clustering of protein folding simulations

Fig. 6

CVAE identifies partially folded states within the VHP simulations. a For the VHP simulations, we project the conformations onto the CVAE space spanned by the three latent dimensions (z1z3). Each conformation is painted by the RMSD to the native state with the color scale depicting the range of RMSD values between the folded and unfolded states. For the VHP simulations we consider any state with an RMSD of less than 5 Å as essentially folded (since these simulations are carried out at a higher temperature). To enable a better characterization of the VHP folding landscape, we project the conformations using t-SNE to identify conformational substates. Each conformation is painted with b the RMSD to the native state, and c the fraction of native contacts. The separation between the folded, unfolded and intermediate states can be understood by examining the conformational states labeled (i) - (v). d A simple histogram representation from the projected t-SNE space allows us to characterize the locations of the conformational states observed from this simulation. The labels provide a relative location of the various conformational states

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