Chunyan Li1,2, Jianmin Wang3, Zhangming Niu4, Junfeng Yao1, Xiangxiang Zeng3. 1. School of Informatics, Xiamen University, Xiamen 361005, China. 2. Yunnan Minzu University, Kunming 650500, China. 3. College of Computer Science and Electronic Engineering, Hunan University, Changsha 410205, China. 4. MindRank AI ltd., Hangzhou, Zhejiang 311113, China.
Abstract
MOTIVATION: Geometry-based properties and characteristics of drug molecules play an important role in drug development for virtual screening in computational chemistry. The 3D characteristics of molecules largely determine the properties of the drug and the binding characteristics of the target. However, most of the previous studies focused on 1D or 2D molecular descriptors while ignoring the 3D topological structure, thereby degrading the performance of molecule-related prediction. Because it is very time-consuming to use dynamics to simulate molecular 3D conformer, we aim to use machine learning to represent 3D molecules by using the generated 3D molecular coordinates from the 2D structure. RESULTS: We proposed Drug3D-Net, a novel deep neural network architecture based on the spatial geometric structure of molecules for predicting molecular properties. It is grid-based 3D convolutional neural network with spatial-temporal gated attention module, which can extract the geometric features for molecular prediction tasks in the process of convolution. The effectiveness of Drug3D-Net is verified on the public molecular datasets. Compared with other deep learning methods, Drug3D-Net shows superior performance in predicting molecular properties and biochemical activities. AVAILABILITY AND IMPLEMENTATION: https://github.com/anny0316/Drug3D-Net. SUPPLEMENTARY DATA: Supplementary data are available online at https://academic.oup.com/bib.
MOTIVATION: Geometry-based properties and characteristics of drug molecules play an important role in drug development for virtual screening in computational chemistry. The 3D characteristics of molecules largely determine the properties of the drug and the binding characteristics of the target. However, most of the previous studies focused on 1D or 2D molecular descriptors while ignoring the 3D topological structure, thereby degrading the performance of molecule-related prediction. Because it is very time-consuming to use dynamics to simulate molecular 3D conformer, we aim to use machine learning to represent 3D molecules by using the generated 3D molecular coordinates from the 2D structure. RESULTS: We proposed Drug3D-Net, a novel deep neural network architecture based on the spatial geometric structure of molecules for predicting molecular properties. It is grid-based 3D convolutional neural network with spatial-temporal gated attention module, which can extract the geometric features for molecular prediction tasks in the process of convolution. The effectiveness of Drug3D-Net is verified on the public molecular datasets. Compared with other deep learning methods, Drug3D-Net shows superior performance in predicting molecular properties and biochemical activities. AVAILABILITY AND IMPLEMENTATION: https://github.com/anny0316/Drug3D-Net. SUPPLEMENTARY DATA: Supplementary data are available online at https://academic.oup.com/bib.