E3bind: An end-to-end equivariant network for protein-ligand docking

Y Zhang, H Cai, C Shi, B Zhong, J Tang - arXiv preprint arXiv:2210.06069, 2022 - arxiv.org
In silico prediction of the ligand binding pose to a given protein target is a crucial but
challenging task in drug discovery. This work focuses on blind flexible selfdocking, where …

Fabind: Fast and accurate protein-ligand binding

Q Pei, K Gao, L Wu, J Zhu, Y Xia… - Advances in …, 2024 - proceedings.neurips.cc
Modeling the interaction between proteins and ligands and accurately predicting their
binding structures is a critical yet challenging task in drug discovery. Recent advancements …

GAABind: a geometry-aware attention-based network for accurate protein–ligand binding pose and binding affinity prediction

H Tan, Z Wang, G Hu - Briefings in Bioinformatics, 2024 - academic.oup.com
Protein–ligand interactions are increasingly profiled at high-throughput, playing a vital role
in lead compound discovery and drug optimization. Accurate prediction of binding pose and …

Equivariant flexible modeling of the protein–ligand binding pose with geometric deep learning

T Dong, Z Yang, J Zhou, CYC Chen - Journal of Chemical Theory …, 2023 - ACS Publications
Flexible modeling of the protein–ligand complex structure is a fundamental challenge for in
silico drug development. Recent studies have improved commonly used docking tools by …

Guiding conventional protein–ligand docking software with convolutional neural networks

H Jiang, M Fan, J Wang, A Sarma… - Journal of chemical …, 2020 - ACS Publications
The high-performance computational techniques have brought significant benefits for drug
discovery efforts in recent decades. One of the most challenging problems in drug discovery …

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 …

Diffdock: Diffusion steps, twists, and turns for molecular docking

G Corso, H Stärk, B Jing, R Barzilay… - arXiv preprint arXiv …, 2022 - arxiv.org
Predicting the binding structure of a small molecule ligand to a protein--a task known as
molecular docking--is critical to drug design. Recent deep learning methods that treat …

CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training

H Cai, C Shen, T Jian, X Zhang, T Chen, X Han… - Chemical …, 2024 - pubs.rsc.org
The expertise accumulated in deep neural network-based structure prediction has been
widely transferred to the field of protein–ligand binding pose prediction, thus leading to the …

Deep learning model for flexible and efficient protein-ligand docking

M Masters, AH Mahmoud, Y Wei… - … Machine Learning for Drug …, 2022 - openreview.net
Protein-ligand docking is an essential tool in structure-based drug design with applications
ranging from virtual high-throughput screening to pose prediction for lead optimization. Most …

Deep scoring neural network replacing the scoring function components to improve the performance of structure-based molecular docking

L Yang, G Yang, X Chen, Q Yang, X Yao… - ACS chemical …, 2021 - ACS Publications
Accurate prediction of protein–ligand interactions can greatly promote drug development.
Recently, a number of deep-learning-based methods have been proposed to predict protein …