Predicting protein-ligand binding structure using E (n) Equivariant graph neural networks

A Dhakal, R Gyawali, J Cheng - bioRxiv, 2023 - biorxiv.org
Drug design is a costly and time-consuming process, often taking more than 12 years and
costing up to billions of dollars. The COVID-19 pandemic has signified the urgent need for …

VN-EGNN: E (3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification

F Sestak, L Schneckenreiter, J Brandstetter… - arXiv preprint arXiv …, 2024 - arxiv.org
Being able to identify regions within or around proteins, to which ligands can potentially
bind, is an essential step to develop new drugs. Binding site identification methods can now …

Predicting protein-ligand binding affinity with equivariant line graph network

Y Yi, X Wan, K Zhao, L Ou-Yang, P Zhao - arXiv preprint arXiv:2210.16098, 2022 - arxiv.org
Binding affinity prediction of three-dimensional (3D) protein ligand complexes is critical for
drug repositioning and virtual drug screening. Existing approaches transform a 3D protein …

Equipocket: an e (3)-equivariant geometric graph neural network for ligand binding site prediction

Y Zhang, W Huang, Z Wei, Y Yuan, Z Ding - arXiv preprint arXiv …, 2023 - arxiv.org
Predicting the binding sites of the target proteins plays a fundamental role in drug discovery.
Most existing deep-learning methods consider a protein as a 3D image by spatially …

Equivariant Line Graph Neural Network for Protein-Ligand Binding Affinity Prediction

Y Yi, X Wan, K Zhao, L Ou-Yang… - IEEE Journal of …, 2024 - ieeexplore.ieee.org
Binding affinity prediction of three-dimensional (3D) protein-ligand complexes is critical for
drug repositioning and virtual drug screening. Existing approaches usually transform a 3D …

CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity

J Wu, H Chen, M Cheng, H Xiong - BMC bioinformatics, 2023 - Springer
Accurately predicting the binding affinity between proteins and ligands is crucial for drug
discovery. Recent advances in graph neural networks (GNNs) have made significant …

Edge-gated graph neural network for predicting protein-ligand binding affinities

Q Jiao, Z Qiu, Y Wang, C Chen… - 2021 IEEE international …, 2021 - ieeexplore.ieee.org
Predicting Protein-ligand binding affinities using Deep Learning can significantly shorten the
drug development cycle. Recently, Graph neural network models have been developed, and …

Geometric interaction graph neural network for predicting protein–ligand binding affinities from 3d structures (gign)

Z Yang, W Zhong, Q Lv, T Dong… - The journal of physical …, 2023 - ACS Publications
Predicting protein–ligand binding affinities (PLAs) is a core problem in drug discovery.
Recent advances have shown great potential in applying machine learning (ML) for PLA …

Learning characteristics of graph neural networks predicting protein–ligand affinities

A Mastropietro, G Pasculli, J Bajorath - Nature Machine Intelligence, 2023 - nature.com
In drug design, compound potency prediction is a popular machine learning application.
Graph neural networks (GNNs) predict ligand affinity from graph representations of protein …

Giant: Protein-ligand binding affinity prediction via geometry-aware interactive graph neural network

S Li, J Zhou, T Xu, L Huang, F Wang… - … on Knowledge and …, 2023 - ieeexplore.ieee.org
Drug discovery often relies on the successful prediction of protein-ligand binding affinity.
Recent advances have shown great promise in applying graph neural networks (GNNs) for …