Fig. 4: Automatic mapping of function prediction to sites on protein structures.
From: Structure-based protein function prediction using graph convolutional networks
a An example of the gradient-weighted class activation map for ‘Ca Ion Binding’ (right) mapped onto the 3D structure of rat α-parvalbumin (PDB Id: 1S3P), chain A (left), annotated with calcium ion binding. The two highest peaks in the grad-CAM activation profile correspond to calcium-binding residues. b ROC curves showing the overlap between grad-CAM activation profiles and binding sites, retrieved from the BioLiP database, computed for the PDB chains shown in panel (c). c Examples of other PDB chains annotated with DNA binding, GTP binding, and glutathione transferase activity. All residues are colored using a gradient color scheme matching the grad-CAM activity profile, with more salient residues highlighted in red and less salient residues highlighted in blue. No information about co-factors, active sites, or site-specificity was used during training of the model.
