Characterizing and validating which mutations influence development of cancer is challenging. Artificial intelligence (AI) has delivered significant advances in protein structure prediction, but its utility for identifying cancer drivers is less expl...
Liver cancer, particularly hepatocellular carcinoma (HCC), remains a significant health burden with poor survival rates due to late diagnosis and limited treatment options. Sorafenib, a multi-kinase inhibitor, is the standard first-line therapy for a...
Antioxidant peptides derived from dietary proteins positively impact human health due to their high activity and safety. In this study, a database of 76,343 peptides was constructed via in silico hydrolysis of 29 dietary proteins. A novel antioxidant...
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here...
Journal of chemical information and modeling
Dec 1, 2023
Protein-protein interactions (PPIs) are essential for various biological processes and diseases. However, most existing computational methods for identifying PPI modulators require either target structure or reference modulators, which restricts thei...
Doxorubicin-induced cardiomyopathy (DIC) brings tough clinical challenges as well as continued demand in developing agents for adjuvant cardioprotective therapies. Here, a zebrafish phenotypic screening with deep-learning assisted multiplex cardiac f...
Chemical communications (Cambridge, England)
May 30, 2023
We combined a library of medium-sized molecules with iterative screening using multiple machine learning algorithms that were ligand-based, which resulted in a large increase of the hit rate against a protein-protein interaction target. This was demo...
International journal of molecular sciences
May 28, 2021
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and th...
Protein-protein interactions (PPIs) are prospective but challenging targets for drug discovery, because screening using traditional small-molecule libraries often fails to identify hits. Recently, we developed a PPI-oriented library comprising 12,593...
Journal of the American Chemical Society
Mar 8, 2021
Macrocycles, including macrocyclic peptides, have shown promise for targeting challenging protein-protein interactions (PPIs). One PPI of high interest is between Kelch-like ECH-Associated Protein-1 (KEAP1) and Nuclear Factor (Erythroid-derived 2)-li...
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