A practical guide to large-scale docking

BJ Bender, S Gahbauer, A Luttens, J Lyu, CM Webb… - Nature protocols, 2021 - nature.com
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …

[HTML][HTML] Drug design by pharmacophore and virtual screening approach

D Giordano, C Biancaniello, MA Argenio, A Facchiano - Pharmaceuticals, 2022 - mdpi.com
Computer-aided drug discovery techniques reduce the time and the costs needed to
develop novel drugs. Their relevance becomes more and more evident with the needs due …

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 …

An artificial intelligence accelerated virtual screening platform for drug discovery

G Zhou, DV Rusnac, H Park, D Canzani… - Nature …, 2024 - nature.com
Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing
interest in the screening of multi-billion chemical compound libraries. However, the success …

Structure-based virtual screening: from classical to artificial intelligence

EHB Maia, LC Assis, TA De Oliveira… - Frontiers in …, 2020 - frontiersin.org
The drug development process is a major challenge in the pharmaceutical industry since it
takes a substantial amount of time and money to move through all the phases of develo** …

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 …

Concepts of artificial intelligence for computer-assisted drug discovery

X Yang, Y Wang, R Byrne, G Schneider… - Chemical …, 2019 - ACS Publications
Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides
opportunities for the discovery and development of innovative drugs. Various machine …

[HTML][HTML] New avenues in artificial-intelligence-assisted drug discovery

C Cerchia, A Lavecchia - Drug Discovery Today, 2023 - Elsevier
Over the past decade, the amount of biomedical data available has grown at unprecedented
rates. Increased automation technology and larger data volumes have encouraged the use …

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 …

[HTML][HTML] 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 …