Fig. 1

Local box sampling and extraction. a For each structure in the training and test structure sets, we placed a 3D grid with 10 Å spacing to sample positions in the protein for local box extraction. The teal spheres represent the sampled grid positions. (For illustration purpose, a grid size of 25 Å instead of 10 Å is shown here). b For each sampled position, the nearest atom (pink sphere) to the sampled position (teal sphere) is first identified. c The amino acid which this atom belongs to is then assigned as the central amino acid. The selected amino acids are highlighted in red and the atoms are shown as dotted spheres. d A local box of 20 Å is then defined around the central amino acid, centering on the Cβ. For each amino acid microenvironment, a local box is extracted around the amino acid using the following procedure: e Backbone atoms of the center amino acid is first used to calculate the orthogonal axes for box extraction. f A 20 Å box is extracted around the Cβ atom of the center amino acid using the defined orientation. g Side-chain atoms of the center amino acid are removed. The extracted box is then labeled with the removed amino acid side-chain type