Deep learning in drug discovery: an integrative review and future challenges

H Askr, E Elgeldawi, H Aboul Ella… - Artificial Intelligence …, 2023 - Springer
Recently, using artificial intelligence (AI) in drug discovery has received much attention
since it significantly shortens the time and cost of developing new drugs. Deep learning (DL) …

Key topics in molecular docking for drug design

PHM Torres, ACR Sodero, P Jofily… - International journal of …, 2019 - mdpi.com
Molecular docking has been widely employed as a fast and inexpensive technique in the
past decades, both in academic and industrial settings. Although this discipline has now had …

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 …

Equibind: Geometric deep learning for drug binding structure prediction

H Stärk, O Ganea, L Pattanaik… - International …, 2022 - proceedings.mlr.press
Predicting how a drug-like molecule binds to a specific protein target is a core problem in
drug discovery. An extremely fast computational binding method would enable key …

AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings

J Eberhardt, D Santos-Martins… - Journal of chemical …, 2021 - ACS Publications
AutoDock Vina is arguably one of the fastest and most widely used open-source programs
for molecular docking. However, compared to other programs in the AutoDock Suite, it lacks …

Tankbind: Trigonometry-aware neural networks for drug-protein binding structure prediction

W Lu, Q Wu, J Zhang, J Rao, C Li… - Advances in neural …, 2022 - proceedings.neurips.cc
Illuminating interactions between proteins and small drug molecules is a long-standing
challenge in the field of drug discovery. Despite the importance of understanding these …

GNINA 1.0: molecular docking with deep learning

AT McNutt, P Francoeur, R Aggarwal, T Masuda… - Journal of …, 2021 - Springer
Molecular docking computationally predicts the conformation of a small molecule when
binding to a receptor. Scoring functions are a vital piece of any molecular docking pipeline …

An open-source drug discovery platform enables ultra-large virtual screens

C Gorgulla, A Boeszoermenyi, ZF Wang, PD Fischer… - Nature, 2020 - nature.com
On average, an approved drug currently costs US $2–3 billion and takes more than 10 years
to develop. In part, this is due to expensive and time-consuming wet-laboratory experiments …

Structure-based de novo drug design using 3D deep generative models

Y Li, J Pei, L Lai - Chemical science, 2021 - pubs.rsc.org
Deep generative models are attracting much attention in the field of de novo molecule
design. Compared to traditional methods, deep generative models can be trained in a fully …

Therapeutics data commons: Machine learning datasets and tasks for drug discovery and development

K Huang, T Fu, W Gao, Y Zhao, Y Roohani… - arXiv preprint arXiv …, 2021 - arxiv.org
Therapeutics machine learning is an emerging field with incredible opportunities for
innovatiaon and impact. However, advancement in this field requires formulation of …