Artificial intelligence for science in quantum, atomistic, and continuum systems

X Zhang, L Wang, J Helwig, Y Luo, C Fu, Y Xie… - arXiv preprint arXiv …, 2023 - arxiv.org
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural
sciences. Today, AI has started to advance natural sciences by improving, accelerating, and …

Artificial intelligence in drug development

K Zhang, X Yang, Y Wang, Y Yu, N Huang, G Li, X Li… - Nature Medicine, 2025 - nature.com
Drug development is a complex and time-consuming endeavor that traditionally relies on the
experience of drug developers and trial-and-error experimentation. The advent of artificial …

Toward generalizable structure‐based deep learning models for protein–ligand interaction prediction: Challenges and strategies

S Moon, W Zhung, WY Kim - Wiley Interdisciplinary Reviews …, 2024 - Wiley Online Library
Accurate and rapid prediction of protein–ligand interactions (PLIs) is the fundamental
challenge of drug discovery. Deep learning methods have been harnessed for this purpose …

Protein language models are performant in structure-free virtual screening

HYI Lam, JS Guan, XE Ong, R Pincket… - Briefings in …, 2024 - academic.oup.com
Hitherto virtual screening (VS) has been typically performed using a structure-based drug
design paradigm. Such methods typically require the use of molecular docking on high …

Data-augmented machine learning scoring functions for virtual screening of YTHDF1 m6A reader protein

M Junaid, B Wang, W Li - Computers in Biology and Medicine, 2024 - Elsevier
Abstract Machine learning is rapidly advancing the drug discovery process, significantly
enhancing speed and efficiency. Innovation in computer-aided drug design is primarily …

Small-Molecule Inhibitors of TIPE3 Protein Identified through Deep Learning Suppress Cancer Cell Growth In Vitro

X Chen, Z Lu, J Xiao, W Xia, Y Pan, H Xia, YH Chen… - Cells, 2024 - mdpi.com
Tumor necrosis factor-α-induced protein 8-like 3 (TNFAIP8L3 or TIPE3) functions as a
transfer protein for lipid second messengers. TIPE3 is highly upregulated in several human …

Combined Usage of Ligand-and Structure-based Virtual Screening in the Artificial Intelligence Era

J Dai, Z Zhou, Y Zhao, F Kong, Z Zhai, Z Zhu… - European Journal of …, 2024 - Elsevier
Drug design has always been pursuing techniques with time-and cost-benefits. Virtual
screening, generally classified as ligand-based (LBVS) and structure-based (SBVS) …

Enhancing Generalizability in Protein–Ligand Binding Affinity Prediction with Multimodal Contrastive Learning

D Luo, D Liu, X Qu, L Dong, B Wang - Journal of Chemical …, 2024 - ACS Publications
Improving the generalization ability of scoring functions remains a major challenge in protein–
ligand binding affinity prediction. Many machine learning methods are limited by their …

PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening

S Seo, WY Kim - Chemical Science, 2024 - pubs.rsc.org
As ultra-large-scale virtual screening becomes critical for early-stage drug discovery, highly
efficient screening methods are gaining prominence. Deep-learning-based approaches …

DeepBioisostere: Discovering Bioisosteres with Deep Learning for a Fine Control of Multiple Molecular Properties

H Kim, S Moon, W Zhung, J Lim, WY Kim - arXiv preprint arXiv:2403.02706, 2024 - arxiv.org
Optimizing molecules to improve their properties is a fundamental challenge in drug design.
For a fine-tuning of molecular properties without losing bio-activity validated in advance, the …