Structure-based drug design with equivariant diffusion models

A Schneuing, C Harris, Y Du, K Didi… - Nature Computational …, 2024 - nature.com
Abstract Structure-based drug design (SBDD) aims to design small-molecule ligands that
bind with high affinity and specificity to pre-determined protein targets. Generative SBDD …

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 …

3D molecular generation models expand chemical space exploration in drug design

YT Xiang, GY Huang, XX Shi, GF Hao, GF Yang - Drug Discovery Today, 2024 - Elsevier
Drug discovery is essential in human diseases but faces challenges because of the vast
chemical space. Molecular generation models have become powerful tools to accelerate …

Active sparse Bayesian committee machine potential for isothermal–isobaric molecular dynamics simulations

SY Willow, DG Kim, R Sundheep… - Physical Chemistry …, 2024 - pubs.rsc.org
Recent advancements in machine learning potentials (MLPs) have significantly impacted
the fields of chemistry, physics, and biology by enabling large-scale first-principles …

Generalized protein pocket generation with prior-informed flow matching

Z Zhang, M Zitnik, Q Liu - arXiv preprint arXiv:2409.19520, 2024 - arxiv.org
Designing ligand-binding proteins, such as enzymes and biosensors, is essential in
bioengineering and protein biology. One critical step in this process involves designing …

Isosteric 3D Bicyclo [1.1. 1] Pentane (BCP) Core-Based Lipids for mRNA Delivery and CRISPR/Cas Gene Editing

S Wu, Y Yang, X Lian, F Zhang, C Hu… - Journal of the …, 2024 - ACS Publications
Lipid nanoparticles (LNPs) are an essential component of messenger RNA (mRNA)
vaccines and genome editing therapeutics. Ionizable amino lipids, which play the most …

Exploring the alignment landscape: Llms and geometric deep models in protein representation

D Shu, B Duan, K Guo, K Zhou, J Tang… - arXiv preprint arXiv …, 2024 - arxiv.org
Latent representation alignment has become a foundational technique for constructing
multimodal large language models (MLLM) by mapping embeddings from different …

Generative flows on synthetic pathway for drug design

S Seo, M Kim, T Shen, M Ester, J Park, S Ahn… - arXiv preprint arXiv …, 2024 - arxiv.org
Generative models in drug discovery have recently gained attention as efficient alternatives
to brute-force virtual screening. However, most existing models do not account for …

TamGen: drug design with target-aware molecule generation through a chemical language model

K Wu, Y Xia, P Deng, R Liu, Y Zhang, H Guo… - Nature …, 2024 - nature.com
Generative drug design facilitates the creation of compounds effective against pathogenic
target proteins. This opens up the potential to discover novel compounds within the vast …

A Machine Learning-Guided Approach to Navigate the Substrate Activity Scope of Galactose Oxidase: Application in the Conversion of Pharmaceutically Relevant …

S Supekar, DWP Tay, WL Yeo, KWE Tam, YS Koo… - ACS …, 2024 - ACS Publications
Biocatalysis is increasingly being adopted in industry for producing important chemicals in a
selective and efficient manner. Engineering an enzyme can often confer it with an altered …