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 …
outlined.•The commonly used datasets and computational tools for kinase profiling …
Cracking the black box of deep sequence-based protein–protein interaction prediction
Identifying protein–protein interactions (PPIs) is crucial for deciphering biological pathways.
Numerous prediction methods have been developed as cheap alternatives to biological …
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 …
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
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 …
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
Biomolecular nuclear magnetic resonance (NMR) spectroscopy and artificial intelligence
(AI) have a burgeoning synergy. Deep learning-based structural predictors have forever …
(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
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 …
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 …
cause of death worldwide. However, our current understanding of the human diet is still …
Proper network randomization is key to assessing social balance
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 …
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
Given the prolonged timelines and high costs associated with traditional approaches,
accelerating drug development is crucial. Computational methods, particularly drug-target …
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
With the emergence of next‐generation nucleotide sequencing and mass spectrometry‐
based proteomics and metabolomics tools, we have comprehensive and scalable methods …
based proteomics and metabolomics tools, we have comprehensive and scalable methods …