Deep learning algorithms applied to computational chemistry

A Guzman-Pando, G Ramirez-Alonso… - Molecular Diversity, 2024 - Springer
Recently, there has been a significant increase in the use of deep learning techniques in the
molecular sciences, which have shown high performance on datasets and the ability to …

MGraphDTA: deep multiscale graph neural network for explainable drug–target binding affinity prediction

Z Yang, W Zhong, L Zhao, CYC Chen - Chemical science, 2022 - pubs.rsc.org
Predicting drug–target affinity (DTA) is beneficial for accelerating drug discovery. Graph
neural networks (GNNs) have been widely used in DTA prediction. However, existing …

Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey

T Kuang, P Liu, Z Ren - Big Data Mining and Analytics, 2024 - ieeexplore.ieee.org
The precise prediction of molecular properties is essential for advancements in drug
development, particularly in virtual screening and compound optimization. The recent …

The prediction of molecular toxicity based on BiGRU and GraphSAGE

J Liu, X Lei, Y Zhang, Y Pan - Computers in biology and medicine, 2023 - Elsevier
The prediction of molecules toxicity properties plays an crucial role in the realm of the drug
discovery, since it can swiftly screen out the expected drug moleculars. The conventional …

Beyond group additivity: Transfer learning for molecular thermochemistry prediction

Y Ureel, FH Vermeire, MK Sabbe… - Chemical Engineering …, 2023 - Elsevier
The accuracy of thermochemical prediction methods is strongly dependent on the size of the
set of training data. Group additivity is an interpretable modeling strategy that can be …

Physical pooling functions in graph neural networks for molecular property prediction

AM Schweidtmann, JG Rittig, JM Weber… - Computers & Chemical …, 2023 - Elsevier
Graph neural networks (GNNs) are emerging in chemical engineering for the end-to-end
learning of physicochemical properties based on molecular graphs. A key element of GNNs …

Deep learning to catalyze inverse molecular design

AS Alshehri, F You - Chemical Engineering Journal, 2022 - Elsevier
The discovery of superior molecular solutions through computational methods is critical for
innovative technologies and their role in addressing pressing resources, health, and …

Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism

Y Tian, X Wang, X Yao, H Liu… - Briefings in bioinformatics, 2023 - academic.oup.com
Graph neural networks based on deep learning methods have been extensively applied to
the molecular property prediction because of its powerful feature learning ability and good …

SSR-DTA: Substructure-aware multi-layer graph neural networks for drug–target binding affinity prediction

Y Liu, X Xia, Y Gong, B Song, X Zeng - Artificial Intelligence in Medicine, 2024 - Elsevier
Accurate prediction of drug–target binding affinity (DTA) is essential in the field of drug
discovery. Recently, scientists have been attempting to utilize artificial intelligence prediction …

Deep Learning with Geometry-Enhanced Molecular Representation for Augmentation of Large-Scale Docking-Based Virtual Screening

L Yu, X He, X Fang, L Liu, J Liu - Journal of Chemical Information …, 2023 - ACS Publications
Structure-based virtual screening has been a crucial tool in drug discovery for decades.
However, as the chemical space expands, the existing structure-based virtual screening …