Artificial intelligence methods in kinase target profiling: Advances and challenges

S Gu, H Liu, L Liu, T Hou, Y Kang - Drug Discovery Today, 2023 - Elsevier
Highlights•The ML-based and DL-based approaches for profiling kinase targets are
outlined.•The commonly used datasets and computational tools for kinase profiling …

Cracking the black box of deep sequence-based protein–protein interaction prediction

J Bernett, DB Blumenthal, M List - Briefings in Bioinformatics, 2024 - academic.oup.com
Identifying protein–protein interactions (PPIs) is crucial for deciphering biological pathways.
Numerous prediction methods have been developed as cheap alternatives to biological …

[HTML][HTML] ZeroBind: a protein-specific zero-shot predictor with subgraph matching for drug-target interactions

Y Wang, Y Xia, J Yan, Y Yuan, HB Shen… - Nature …, 2023 - nature.com
Existing drug-target interaction (DTI) prediction methods generally fail to generalize well to
novel (unseen) proteins and drugs. In this study, we propose a protein-specific meta …

[HTML][HTML] PMF-CPI: assessing drug selectivity with a pretrained multi-functional model for compound–protein interactions

N Song, R Dong, Y Pu, E Wang, J Xu, F Guo - Journal of Cheminformatics, 2023 - Springer
Compound–protein interactions (CPI) play significant roles in drug development. To avoid
side effects, it is also crucial to evaluate drug selectivity when binding to different targets …

[HTML][HTML] Biomolecular NMR spectroscopy in the era of artificial intelligence

VK Shukla, GT Heller, DF Hansen - Structure, 2023 - cell.com
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence
(AI) have a burgeoning synergy. Deep learning-based structural predictors have forever …

[HTML][HTML] A robust drug–target interaction prediction framework with capsule network and transfer learning

Y Huang, HY Huang, Y Chen, YCD Lin, L Yao… - International Journal of …, 2023 - mdpi.com
Drug–target interactions (DTIs) are considered a crucial component of drug design and drug
discovery. To date, many computational methods were developed for drug–target …

Molecular interaction networks and cardiovascular disease risk: the role of food bioactive small molecules

F Nasirian, G Menichetti - Arteriosclerosis, thrombosis, and …, 2023 - Am Heart Assoc
Diet is a well-known modifiable risk factor for cardiovascular diseases, which are the leading
cause of death worldwide. However, our current understanding of the human diet is still …

Proper network randomization is key to assessing social balance

B Hao, IA Kovács - Science Advances, 2024 - science.org
Social ties, either positive or negative, lead to signed network patterns, the subject of
balance theory. For example, strong balance introduces cycles with even numbers of …

[HTML][HTML] Towards explainable interaction prediction: Embedding biological hierarchies into hyperbolic interaction space

D Pogány, P Antal - Plos one, 2024 - journals.plos.org
Given the prolonged timelines and high costs associated with traditional approaches,
accelerating drug development is crucial. Computational methods, particularly drug-target …

Decoding the molecular interplay in the central dogma: An overview of mass spectrometry‐based methods to investigate protein‐metabolite interactions

P Stincone, A Naimi, AJ Saviola, R Reher… - …, 2023 - Wiley Online Library
With the emergence of next‐generation nucleotide sequencing and mass spectrometry‐
based proteomics and metabolomics tools, we have comprehensive and scalable methods …