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 …

Challenges and advances in clinical applications of mesenchymal stromal cells

T Zhou, Z Yuan, J Weng, D Pei, X Du, C He… - Journal of hematology & …, 2021 - Springer
Mesenchymal stromal cells (MSCs), also known as mesenchymal stem cells, have been
intensely investigated for clinical applications within the last decades. However, the majority …

Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

F Wong, A Krishnan, EJ Zheng, H Stärk… - Molecular systems …, 2022 - embopress.org
Efficient identification of drug mechanisms of action remains a challenge. Computational
docking approaches have been widely used to predict drug binding targets; yet, such …

Accelerating antibiotic discovery through artificial intelligence

MCR Melo, JRMA Maasch… - Communications …, 2021 - nature.com
By targeting invasive organisms, antibiotics insert themselves into the ancient struggle of the
host-pathogen evolutionary arms race. As pathogens evolve tactics for evading antibiotics …

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 …

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 …

New machine learning and physics-based scoring functions for drug discovery

IA Guedes, AMS Barreto, D Marinho, E Krempser… - Scientific reports, 2021 - nature.com
Scoring functions are essential for modern in silico drug discovery. However, the accurate
prediction of binding affinity by scoring functions remains a challenging task. The …

[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 …

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 …

[HTML][HTML] Enhancing preclinical drug discovery with artificial intelligence

RSK Vijayan, J Kihlberg, JB Cross, V Poongavanam - Drug discovery today, 2022 - Elsevier
Artificial intelligence (AI) is becoming an integral part of drug discovery. It has the potential to
deliver across the drug discovery and development value chain, starting from target …