Rapid identification of potential inhibitors of SARS‐CoV‐2 main protease by deep docking of 1.3 billion compounds

AT Ton, F Gentile, M Hsing, F Ban… - Molecular …, 2020 - Wiley Online Library
Abstract The recently emerged 2019 Novel Coronavirus (SARS‐CoV‐2) and associated
COVID‐19 disease cause serious or even fatal respiratory tract infection and yet no …

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 …

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 …

Transfer learning for drug discovery

C Cai, S Wang, Y Xu, W Zhang, K Tang… - Journal of Medicinal …, 2020 - ACS Publications
The data sets available to train models for in silico drug discovery efforts are often small.
Indeed, the sparse availability of labeled data is a major barrier to artificial-intelligence …

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

J Tubiana, D Schneidman-Duhovny, HJ Wolfson - Nature Methods, 2022 - nature.com
Predicting the functional sites of a protein from its structure, such as the binding sites of small
molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two …

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 …

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 …

Artificial intelligence and machine learning‐aided drug discovery in central nervous system diseases: State‐of‐the‐arts and future directions

S Vatansever, A Schlessinger, D Wacker… - Medicinal research …, 2021 - Wiley Online Library
Neurological disorders significantly outnumber diseases in other therapeutic areas.
However, developing drugs for central nervous system (CNS) disorders remains the most …

Generating 3D molecules conditional on receptor binding sites with deep generative models

M Ragoza, T Masuda, DR Koes - Chemical science, 2022 - pubs.rsc.org
The goal of structure-based drug discovery is to find small molecules that bind to a given
target protein. Deep learning has been used to generate drug-like molecules with certain …

Machine learning on graphs: A model and comprehensive taxonomy

I Chami, S Abu-El-Haija, B Perozzi, C Ré… - Journal of Machine …, 2022 - jmlr.org
There has been a surge of recent interest in graph representation learning (GRL). GRL
methods have generally fallen into three main categories, based on the availability of …