Computational approaches streamlining drug discovery

AV Sadybekov, V Katritch - Nature, 2023 - nature.com
Computer-aided drug discovery has been around for decades, although the past few years
have seen a tectonic shift towards embracing computational technologies in both academia …

Leveraging artificial intelligence in the fight against infectious diseases

F Wong, C de la Fuente-Nunez, JJ Collins - Science, 2023 - science.org
Despite advances in molecular biology, genetics, computation, and medicinal chemistry,
infectious disease remains an ominous threat to public health. Addressing the challenges …

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 …

Clustering predicted structures at the scale of the known protein universe

I Barrio-Hernandez, J Yeo, J Jänes, M Mirdita… - Nature, 2023 - nature.com
Proteins are key to all cellular processes and their structure is important in understanding
their function and evolution. Sequence-based predictions of protein structures have …

Discovery of a structural class of antibiotics with explainable deep learning

F Wong, EJ Zheng, JA Valeri, NM Donghia… - Nature, 2024 - nature.com
The discovery of novel structural classes of antibiotics is urgently needed to address the
ongoing antibiotic resistance crisis,,,,,,,–. Deep learning approaches have aided in exploring …

AlphaFold2 and its applications in the fields of biology and medicine

Z Yang, X Zeng, Y Zhao, R Chen - Signal Transduction and Targeted …, 2023 - nature.com
Abstract AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind
that can predict three-dimensional (3D) structures of proteins from amino acid sequences …

[HTML][HTML] Before and after AlphaFold2: An overview of protein structure prediction

LMF Bertoline, AN Lima, JE Krieger… - Frontiers in …, 2023 - frontiersin.org
Three-dimensional protein structure is directly correlated with its function and its
determination is critical to understanding biological processes and addressing human …

Discovering small-molecule senolytics with deep neural networks

F Wong, S Omori, NM Donghia, EJ Zheng, JJ Collins - Nature Aging, 2023 - nature.com
The accumulation of senescent cells is associated with aging, inflammation and cellular
dysfunction. Senolytic drugs can alleviate age-related comorbidities by selectively killing …

[PDF][PDF] How good are AlphaFold models for docking-based virtual screening?

V Scardino, JI Di Filippo, CN Cavasotto - Iscience, 2023 - cell.com
A crucial component in structure-based drug discovery is the availability of high-quality three-
dimensional structures of the protein target. Whenever experimental structures were not …

How accurately can one predict drug binding modes using AlphaFold models?

M Karelina, JJ Noh, RO Dror - Elife, 2023 - elifesciences.org
Computational prediction of protein structure has been pursued intensely for decades,
motivated largely by the goal of using structural models for drug discovery. Recently …