Network-based prediction of drug combinations

F Cheng, IA Kovács, AL Barabási - Nature communications, 2019 - nature.com
Drug combinations, offering increased therapeutic efficacy and reduced toxicity, play an
important role in treating multiple complex diseases. Yet, our ability to identify and validate …

Accelerating high-throughput virtual screening through molecular pool-based active learning

DE Graff, EI Shakhnovich, CW Coley - Chemical science, 2021 - pubs.rsc.org
Structure-based virtual screening is an important tool in early stage drug discovery that
scores the interactions between a target protein and candidate ligands. As virtual libraries …

Nanoconfinement enabled non-covalently decorated MXene membranes for ion-sieving

Y Kang, T Hu, Y Wang, K He, Z Wang, Y Hora… - Nature …, 2023 - nature.com
Covalent modification is commonly used to tune the channel size and functionality of 2D
membranes. However, common synthesis strategies used to produce such modifications are …

Deep learning for molecular design—a review of the state of the art

DC Elton, Z Boukouvalas, MD Fuge… - … Systems Design & …, 2019 - pubs.rsc.org
In the space of only a few years, deep generative modeling has revolutionized how we think
of artificial creativity, yielding autonomous systems which produce original images, music …

Generating 3D molecules conditional on receptor binding sites with deep generative models

M Ragoza, T Masuda, DR Koes - Chemical science, 2022 - pubs.rsc.org
The goal of structure-based drug discovery is to find small molecules that bind to a given
target protein. Deep learning has been used to generate drug-like molecules with certain …

3d equivariant diffusion for target-aware molecule generation and affinity prediction

J Guan, WW Qian, X Peng, Y Su, J Peng… - arXiv preprint arXiv …, 2023 - arxiv.org
Rich data and powerful machine learning models allow us to design drugs for a specific
protein target\textit {in silico}. Recently, the inclusion of 3D structures during targeted drug …

Generating 3d molecules for target protein binding

M Liu, Y Luo, K Uchino, K Maruhashi, S Ji - arXiv preprint arXiv …, 2022 - arxiv.org
A fundamental problem in drug discovery is to design molecules that bind to specific
proteins. To tackle this problem using machine learning methods, here we propose a novel …

Mordred: a molecular descriptor calculator

H Moriwaki, YS Tian, N Kawashita, T Takagi - Journal of cheminformatics, 2018 - Springer
Molecular descriptors are widely employed to present molecular characteristics in
cheminformatics. Various molecular-descriptor-calculation software programs have been …

Inhibitors of bacterial H2S biogenesis targeting antibiotic resistance and tolerance

K Shatalin, A Nuthanakanti, A Kaushik, D Shishov… - Science, 2021 - science.org
Emergent resistance to all clinical antibiotics calls for the next generation of therapeutics.
Here we report an effective antimicrobial strategy targeting the bacterial hydrogen sulfide …

Structure-based drug design with equivariant diffusion models

A Schneuing, Y Du, C Harris, A Jamasb… - arXiv preprint arXiv …, 2022 - arxiv.org
Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with
high affinity and specificity to pre-determined protein targets. In this paper, we formulate …