  During the past decade, with the significant progress of computational power
as well as ever-rising data availability, deep learning techniques became
increasingly popular due to their excellent performance on computer vision
problems. The size of the Protein Data Bank has increased more than 15 fold
since 1999, which enabled the expansion of models that aim at predicting
enzymatic function via their amino acid composition. Amino acid sequence
however is less conserved in nature than protein structure and therefore
considered a less reliable predictor of protein function. This paper presents
EnzyNet, a novel 3D-convolutional neural networks classifier that predicts the
Enzyme Commission number of enzymes based only on their voxel-based spatial
structure. The spatial distribution of biochemical properties was also examined
as complementary information. The 2-layer architecture was investigated on a
large dataset of 63,558 enzymes from the Protein Data Bank and achieved an
accuracy of 78.4% by exploiting only the binary representation of the protein
shape. Code and datasets are available at https://github.com/shervinea/enzynet.
