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...
G-protein-coupled receptors (GPCRs) are pivotal in cellular signal transduction and serve as key drug targets. Among them, the β-adrenergic receptors (βAR and βAR) regulate cardiovascular function and are activated by endogenous catecholamines, norep...
ConspectusThis Account discusses recent progress and challenges in binding free energy computations, focusing on two classes of enhanced sampling techniques: alchemical transformations and path-based methods. Binding free energy is a crucial metric i...
Journal of chemical information and modeling
Oct 9, 2025
In this work, we introduce an automated methodology for the efficient and relatively inexpensive exploration of large high-dimensional chemical spaces, with particular focus on number-of-atoms-conserving processes, such as in mechanochemical reaction...
Journal of chemical information and modeling
Oct 9, 2025
In molecular studies, the accurate parametrization of small molecules stands as an essential yet growing demand. Addressing this, we introduce ParametrizANI, a tool crafted explicitly for establishing detailed protocols for dihedral parametrization u...
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...
Finding process pathways in molecular simulations such as the unbinding paths of small molecule ligands from their binding sites at protein targets in a set of trajectories via unsupervised learning approaches requires the definition of a suitable si...
Having an accurate reaction coordinate (RC) is essential for reliable kinetic characterization of molecular processes, but there are few quantitative metrics to evaluate RC quality. In this study, we consider the dimensionless γ metric from the Expon...
Intrinsically disordered proteins and regions (IDRs) lack stable 3D structures, posing challenges for interaction prediction. We present SpatPPI, a geometric deep learning model tailored for IDPPI prediction. SpatPPI leverages structural cues from fo...
Journal of computer-aided molecular design
Oct 6, 2025
Protein pockets, or small cavities on the protein surface, are critical sites for enzymatic catalysis, molecular recognition, and drug binding. Accurately identifying these pockets is crucial for understanding protein function and designing therapeut...
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