[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 …

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 …

[HTML][HTML] Artificial intelligence in pharmaceutical sciences

M Lu, J Yin, Q Zhu, G Lin, M Mou, F Liu, Z Pan, N You… - Engineering, 2023 - Elsevier
Drug discovery and development affects various aspects of human health and dramatically
impacts the pharmaceutical market. However, investments in a new drug often go …

Conserved sites and recognition mechanisms of T1R1 and T2R14 receptors revealed by ensemble docking and molecular descriptors and fingerprints combined with …

Z Cui, N Zhang, T Zhou, X Zhou, H Meng… - Journal of Agricultural …, 2023 - ACS Publications
Taste peptides, as an important component of protein-rich foodstuffs, potentiate the nutrition
and taste of food. Thereinto, umami-and bitter-taste peptides have been ex tensively …

A generalized protein–ligand scoring framework with balanced scoring, docking, ranking and screening powers

C Shen, X Zhang, CY Hsieh, Y Deng, D Wang, L Xu… - Chemical …, 2023 - pubs.rsc.org
Applying machine learning algorithms to protein–ligand scoring functions has aroused
widespread attention in recent years due to the high predictive accuracy and affordable …

Integrated molecular modeling and machine learning for drug design

S Xia, E Chen, Y Zhang - Journal of Chemical Theory and …, 2023 - ACS Publications
Modern therapeutic development often involves several stages that are interconnected, and
multiple iterations are usually required to bring a new drug to the market. Computational …

Systematic improvement of the performance of machine learning scoring functions by incorporating features of protein-bound water molecules

X Qu, L Dong, J Zhang, Y Si… - Journal of Chemical …, 2022 - ACS Publications
Water molecules at the ligand–protein interfaces play crucial roles in the binding of the
ligands, but the behavior of protein-bound water is largely ignored in many currently used …

Open-source machine learning in computational chemistry

A Hagg, KN Kirschner - Journal of Chemical Information and …, 2023 - ACS Publications
The field of computational chemistry has seen a significant increase in the integration of
machine learning concepts and algorithms. In this Perspective, we surveyed 179 open …

Template‐guided method for protein–ligand complex structure prediction: Application to CASP15 protein–ligand studies

X Xu, R Duan, X Zou - Proteins: Structure, Function, and …, 2023 - Wiley Online Library
Abstract Critical Assessment of Structure Prediction 15 (CASP15) added a new category of
ligand prediction to promote the development of protein/RNA‐ligand modeling methods …