Endogenous intracellular allosteric modulators of GPCRs remain largely unexplored, with limited binding and phenotype data available. This gap arises from the lack of robust computational methods for unbiased cavity identification, cavity-specific li...
Journal of computer-aided molecular design
Dec 3, 2025
The identification of protein target classes is a key step in drug discovery, as it enables prioritization of screening campaigns and supports target-based drug repurpose. In this study, we developed a deep-learning pipeline based on a multilayer per...
The Journal of clinical investigation
Oct 15, 2025
Hypoxia in the tumor microenvironment promotes lymphatic metastasis, yet the role of cancer-associated fibroblasts (CAFs) in this process remains insufficiently elucidated in colorectal cancer (CRC). In this study, we developed a large language model...
Journal of chemical information and modeling
Oct 13, 2025
β-Arrestins (βarr1 and βarr2) are key transducers of G protein-coupled receptor (GPCR) signaling, orchestrating both shared and isoform-specific intracellular pathways. Phosphorylation of the receptor C-terminal tail by GPCR kinases encodes regulator...
The health risks associated with excessive sodium intake have prompted an exploration of natural salt substitutes. This study was oriented to explore the salty peptides from enzymatic and fermented products of wheat gluten (WG) with different degrees...
Journal of chemical theory and computation
Sep 16, 2025
Biased allosteric modulators (BAMs) offer a promising avenue for developing safer and more selective therapeutics for G protein-coupled receptors (GPCRs). However, their molecular mechanisms remain unclear due to the complex combination of biased and...
Journal of chemical theory and computation
Jul 14, 2025
In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables the ranking of reaction coordinates according to their impact on protein properties. By leveraging machine learnin...
BACKGROUND: The activation of free fatty acid receptor 4 (FFAR4) enhances insulin sensitivity and glucose uptake while mitigating inflammation. It is a promising therapeutic approach for managing type 2 diabetes mellitus (T2DM).
Journal of molecular graphics & modelling
Jun 3, 2025
Experimental structures solved through cryo-electron microscopy have recently been published for GPR101, a G protein-coupled receptor (GPCR) implicated in the genetic condition X-linked acrogigantism (X-LAG). Here, we compared these experimental stru...
In this study, we identified and screened nine novel umami peptides derived from yellowfin tuna (Thunnus albacares) utilizing peptidomics combined with various machine learning based umami screening methodologies, including UMPred-FRL, TPDM, Umami-MR...
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