Journal of the American Chemical Society
Nov 23, 2025
The HIV-1 envelope glycoprotein (Env) trimer (gp120/gp41) forms the key functional envelope spike and is the target of neutralizing antibodies. The glycoprotein gp41 component mediates the fusion of viral and host cell membranes. The membrane-interac...
Journal of chemical information and modeling
Nov 18, 2025
Understanding molecular flexibility and dynamics across different structural ensembles is essential for interpreting the behavior of complex biological systems. Here, we introduce eRMSF, a fast and user-friendly Python package built with MDAKit from ...
Conformational changes essential for protein function involve transitions through multiple short-lived, high-energy states within the complex free energy landscape. While existing methods, such as Markov State Models and non-Markovian approaches buil...
Journal of controlled release : official journal of the Controlled Release Society
Nov 17, 2025
Long-acting injectables (LAIs) represent promising drug delivery platforms for chronic diseases management, but their clinical translation remains constrained by extremely long trial-and-error experiments (8-10 years), limited mechanism insights, and...
Dioxin-like pollutants, especially 2,3,7,8-Tetrachlorodibenzo-p-dioxin, are recognized human carcinogens. Retrospective studies suggest a link between dioxins and soft tissue sarcomas, including liposarcoma, but mechanisms remain unclear. This study ...
Journal of chemical information and modeling
Nov 13, 2025
Heterobifunctional degraders, a class of targeted protein degraders (TPDs), often occupy beyond-rule-of-five (bRo5) chemical space, where traditional passive permeability models─calibrated on drug-like molecules or peptides and based on topological d...
Journal of chemical information and modeling
Nov 12, 2025
Dispersion-corrected density functional theory (DFT-D) is widely employed to model large molecular systems at an affordable computational cost and to develop machine-learning interatomic potentials (MLIPs), enabling reliable molecular dynamics (MD) s...
Anhydroicaritin (AHI), a chemically characterized prenylated flavonoid, exhibits strong and selective cytotoxicity against estrogen receptor-positive (ER+) breast cancer cells. In this study, we aimed to elucidate its molecular and cellular toxicolog...
Per- and polyfluoroalkyl substances (PFAS) are over 14 000 synthetic compounds with exceptional environmental persistence. Used extensively in industrial and consumer applications, PFAS resist degradation and accumulate in environmental media and liv...
Journal of chemical information and modeling
Nov 11, 2025
Molecular dynamics (MD) simulations are currently widely used to study large-scale displacement cascades based on massive simulation trajectories. However, when the irradiation process involves the complex chemical reactions, effectively analyzing an...
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