Protein Structure from Scientific Research

Visualizations of AMBRA1-SOX12 modeling are presented. E3-substrate pairs were folded together withAlphaFold-Multimer, and interacting substrate peptides are highlighted. Line plots of pLDDT values across the substrate protein are visualized in the context of a folded substrate monomer (red) or the substrate co-folded with the COMET-nominated E3 (blue). Finally, the log2-scaled ratio (monomer/complex) of pLDDT values at each residue is plotted, with peaks indicating regions of elevated pLDDT values in the complex prediction relative to the monomer. Note that scales for log2ratios are different in each panel, i.e., adjusted for each plot to maximize contrast.

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