Molecular distance matrix prediction based on graph convolutional networks

Abstract: Molecular structure has important applications in many fields. For example, some studies show that molecular spatial information can be used to achieve better prediction results when predicting molecular properties. However, traditional molecular geometry calculations, such as density functional theory (DFT), are time-consuming. In view of this, we propose a model based on graph convolutional networks to predict the pairwise distance between atoms, also called distance matrix prediction of the molecule(DMGCN). In order to indicate the effect of DMGCN model, the model is compared with the model DeeperGCN-DAGNN and the method of calculating molecular conformation in RDKit. Results show that the MAE of DMGCN is smaller than DeeperGCN-DAGNN and RDKit. In addition, the distances predicted by the DMGCN model and the distances calculated by the QM9 dataset are used to predict the molecular properties, thus showing the effectiveness of the distance predicted by the DMGCN model.