AI in drug discovery and its clinical relevance

R Qureshi, M Irfan, TM Gondal, S Khan, J Wu, MU Hadi… - Heliyon, 2023 - cell.com
The COVID-19 pandemic has emphasized the need for novel drug discovery process.
However, the journey from conceptualizing a drug to its eventual implementation in clinical …

Machine-learning methods for ligand–protein molecular docking

K Crampon, A Giorkallos, M Deldossi, S Baud… - Drug discovery today, 2022 - Elsevier
Artificial intelligence (AI) is often presented as a new Industrial Revolution. Many domains
use AI, including molecular simulation for drug discovery. In this review, we provide an …

Efficient and accurate large library ligand docking with KarmaDock

X Zhang, O Zhang, C Shen, W Qu, S Chen… - Nature Computational …, 2023 - nature.com
Ligand docking is one of the core technologies in structure-based virtual screening for drug
discovery. However, conventional docking tools and existing deep learning tools may suffer …

Physics-inspired structural representations for molecules and materials

F Musil, A Grisafi, AP Bartók, C Ortner… - Chemical …, 2021 - ACS Publications
The first step in the construction of a regression model or a data-driven analysis, aiming to
predict or elucidate the relationship between the atomic-scale structure of matter and its …

Boosting protein–ligand binding pose prediction and virtual screening based on residue–atom distance likelihood potential and graph transformer

C Shen, X Zhang, Y Deng, J Gao, D Wang… - Journal of Medicinal …, 2022 - ACS Publications
The past few years have witnessed enormous progress toward applying machine learning
approaches to the development of protein–ligand scoring functions. However, the robust …

InteractionGraphNet: a novel and efficient deep graph representation learning framework for accurate protein–ligand interaction predictions

D Jiang, CY Hsieh, Z Wu, Y Kang, J Wang… - Journal of medicinal …, 2021 - ACS Publications
Accurate quantification of protein–ligand interactions remains a key challenge to structure-
based drug design. However, traditional machine learning (ML)-based methods based on …

A practical guide to machine-learning scoring for structure-based virtual screening

VK Tran-Nguyen, M Junaid, S Simeon, PJ Ballester - Nature Protocols, 2023 - nature.com
Abstract Structure-based virtual screening (SBVS) via docking has been used to discover
active molecules for a range of therapeutic targets. Chemical and protein data sets that …

A survey on deep learning in medicine: Why, how and when?

F Piccialli, V Di Somma, F Giampaolo, S Cuomo… - Information …, 2021 - Elsevier
New technologies are transforming medicine, and this revolution starts with data. Health
data, clinical images, genome sequences, data on prescribed therapies and results …

[HTML][HTML] Protein–ligand docking in the machine-learning era

C Yang, EA Chen, Y Zhang - Molecules, 2022 - mdpi.com
Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …

Advancing ligand docking through deep learning: challenges and prospects in virtual screening

X Zhang, C Shen, H Zhang, Y Kang… - Accounts of chemical …, 2024 - ACS Publications
Conspectus Molecular docking, also termed ligand docking (LD), is a pivotal element of
structure-based virtual screening (SBVS) used to predict the binding conformations and …