Predicting drug–protein interaction using quasi-visual question answering system

Identifying novel drug–protein interactions is crucial for drug discovery. For this purpose, many machine learning-based methods have been developed based on drug descriptors and one-dimensional protein sequences. However, protein sequences cannot accurately reflect the interactions in three-dimensional space. However, direct input of three-dimensional structure is of low efficiency due to the sparse three-dimensional matrix, and is also prevented by the limited number of co-crystal structures available for training. Here we propose an end-to-end deep learning framework to predict the interactions by representing proteins with a two-dimensional distance map from monomer structures (Image) and drugs with molecular linear notation (String), following the visual question answering mode. For efficient training of the system, we introduce a dynamic attentive convolutional neural network to learn fixed-size representations from the variable-length distance maps and a self-attentional sequential model to automatically extract semantic features from the linear notations.