The bacterial cell division protein FtsZ, a crucial GTPase, plays a vital role in the formation of the contractile Z-ring, which is essential for bacterial cytokinesis. Consequently, inhibiting FtsZ could prevent the formation of proto-filaments and ...
In humans, selective and promiscuous interactions between 46 secreted chemokine ligands and 23 cell surface chemokine receptors of the G-protein-coupled receptor (GPCR) family form a complex network to coordinate cell migration. While chemokines and ...
We present a comprehensive, quantitative model of the allosteric molecular mechanisms of selective cholesterol (CHL) uptake and delivery by the StarD4 protein - an intracellular cholesterol trafficking protein that facilitates the crucial non-vesicul...
Journal of molecular graphics & modelling
Apr 15, 2025
Ankyrins are proteins widely distributed in nature that mediate protein‒protein interactions. Owing to their outstanding stability and ability to recognize targets, ankyrins have been used as therapeutic and diagnostic tools in several diseases, incl...
Accurately identifying protein-DNA binding sites is essential for understanding the molecular mechanisms underlying biological processes, which in turn facilitates advancements in drug discovery and design. While biochemical experiments provide the m...
Journal of chemical information and modeling
Apr 8, 2025
Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we ...
Protein-ligand interactions are crucial in drug discovery. Accurately predicting protein-ligand binding affinity is essential for screening potential drugs. Graph neural networks have proven highly effective in modeling spatial relationships and thre...
Journal of chemical theory and computation
Apr 5, 2025
Directionality in molecular and biomolecular networks plays an important role in the accurate representation of the complex, dynamic, and asymmetrical nature of interactions present in protein-ligand binding, signal transduction, and biological pathw...
Farnesoid X receptor (FXR) is a key regulator of bile acid, lipid, and glucose homeostasis, making it a promising target for treating metabolic diseases. FXR antagonists have shown therapeutic potential in cholestasis, metabolic disorders, and certai...
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
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