Lim, Ryu, Park, Choe, Ham, Kim (2019) Predicting Drug-Target Interaction Using a Novel Graph Neural Network with 3D Structure-Embedded Graph Representation Journal of chemical information and modeling ()

Abstract

We propose a novel deep learning approach for predicting drug-target interaction using a graph neural network. We introduce a distance-aware graph attention algorithm to differentiate various types of intermolecular interactions. Furthermore, we extract the graph feature of intermolecular interactions directly from the 3D structural information on the protein-ligand binding pose. Thus, the model can learn key features for accurate predictions of drug-target interaction rather than just memorize certain patterns of ligand molecules. As a result, our model shows better performance than docking and other deep learning methods for both virtual screening (AUROC of 0.968 for the DUD-E test set) and pose prediction (AUROC of 0.935 for the PDBbind test set). In addition, it can reproduce the natural population distribution of active molecules and inactive molecules.

Links

http://www.ncbi.nlm.nih.gov/pubmed/31443612
http://dx.doi.org/10.1021/acs.jcim.9b00387

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