Fig. 2
From: 3D deep convolutional neural networks for amino acid environment similarity analysis
Local box featurization. a Local structure in each 20 Å box is first decomposed into Oxygen, Carbon, Nitrogen, and Sulfur channels. b Each atom type channel structure is divided into 3D 1-Å voxels, within which the presence of atom of the corresponding atom type is recorded. Within each channel, Gaussian filters are applied to the discrete counts to approximate the atom connectivity and electron delocalization. c The resulting numerical 3D matrices of each atom type channel are then stacked together as different input channels, resulting in a (4, 20, 20, 20) 4D–tensor, which will serve as an input example to our 3DCNN