Machine learning-enabled retrobiosynthesis of molecules

T Yu, AG Boob, MJ Volk, X Liu, H Cui, H Zhao - Nature Catalysis, 2023 - nature.com
Retrobiosynthesis provides an effective and sustainable approach to producing functional
molecules. The past few decades have witnessed a rapid expansion of biosynthetic …

[HTML][HTML] Artificial intelligence in pharmaceutical technology and drug delivery design

LK Vora, AD Gholap, K Jetha, RRS Thakur, HK Solanki… - Pharmaceutics, 2023 - mdpi.com
Artificial intelligence (AI) has emerged as a powerful tool that harnesses anthropomorphic
knowledge and provides expedited solutions to complex challenges. Remarkable …

Diffusion models in bioinformatics and computational biology

Z Guo, J Liu, Y Wang, M Chen, D Wang, D Xu… - Nature reviews …, 2024 - nature.com
Denoising diffusion models embody a type of generative artificial intelligence that can be
applied in computer vision, natural language processing and bioinformatics. In this Review …

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

A Dhakal, R Gyawali, L Wang, J Cheng - Scientific Data, 2023 - nature.com
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of
biological macromolecular complexes. Picking single-protein particles from cryo-EM …

In silico methods for identification of potential active sites of therapeutic targets

J Liao, Q Wang, F Wu, Z Huang - Molecules, 2022 - mdpi.com
Target identification is an important step in drug discovery, and computer-aided drug target
identification methods are attracting more attention compared with traditional drug target …

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function

Z Wang, L Zheng, S Wang, M Lin, Z Wang… - Briefings in …, 2023 - academic.oup.com
The recently reported machine learning-or deep learning-based scoring functions (SFs)
have shown exciting performance in predicting protein–ligand binding affinities with fruitful …

A survey on adversarial attacks for malware analysis

K Aryal, M Gupta, M Abdelsalam - arXiv preprint arXiv:2111.08223, 2021 - arxiv.org
Machine learning has witnessed tremendous growth in its adoption and advancement in the
last decade. The evolution of machine learning from traditional algorithms to modern deep …

Deep learning-based bioactive therapeutic peptide generation and screening

H Zhang, KM Saravanan, Y Wei, Y Jiao… - Journal of Chemical …, 2023 - ACS Publications
Many bioactive peptides demonstrated therapeutic effects over complicated diseases, such
as antiviral, antibacterial, anticancer, etc. It is possible to generate a large number of …

NHGNN-DTA: a node-adaptive hybrid graph neural network for interpretable drug–target binding affinity prediction

H He, G Chen, CYC Chen - Bioinformatics, 2023 - academic.oup.com
Motivation Large-scale prediction of drug–target affinity (DTA) plays an important role in
drug discovery. In recent years, machine learning algorithms have made great progress in …

Molecular docking in organic, inorganic, and hybrid systems: A tutorial review

M Mohanty, PS Mohanty - Monatshefte für Chemie-Chemical Monthly, 2023 - Springer
Molecular docking simulation is a very popular and well-established computational
approach and has been extensively used to understand molecular interactions between a …