Molecular activity prediction using graph convolutional deep neural network considering distance on a molecular graph
This is an incremental improvement for virtual screening in drug discovery, potentially aiding in finding pharmacologically active compounds.
The authors tackled the problem of predicting molecular activity by improving a graph convolutional neural network to better align graph distances with 3D coordinate distances, resulting in slightly better performance than the baseline weave module.
Machine learning is often used in virtual screening to find compounds that are pharmacologically active on a target protein. The weave module is a type of graph convolutional deep neural network that uses not only features focusing on atoms alone (atom features) but also features focusing on atom pairs (pair features); thus, it can consider information of nonadjacent atoms. However, the correlation between the distance on the graph and the three-dimensional coordinate distance is uncertain. In this paper, we propose three improvements for modifying the weave module. First, the distances between ring atoms on the graph were modified to bring the distances on the graph closer to the coordinate distance. Second, different weight matrices were used depending on the distance on the graph in the convolution layers of the pair features. Finally, a weighted sum, by distance, was used when converting pair features to atom features. The experimental results show that the performance of the proposed method is slightly better than that of the weave module, and the improvement in the distance representation might be useful for compound activity prediction.