Hepatitis C virus (HCV) causes an infectious disease that manifests itself as liver inflammation, cirrhosis, and can lead to the development of liver cancer. Its NS3/4A serine protease is a potent target for drug design and development since it is responsible for cleavage of the scissile peptide bonds in the polyprotein important for the HCV life cycle. Herein, the ligand-target interactions an...

Combining Lipinski's rule with the docking and steered molecular dynamics simulations and using the PubChem data base of about 1.4 million compounds, we have obtained DNA dyes Hoechst 34580 and Hoechst 33342 as top-leads for the Alzheimer's disease. The binding properties of these ligands to amyloid beta (Aβ) fibril were thoroughly studied by in silico and in vitro experiments. Hoechst 34580 an...

The human–computer interaction (HCI) design of educational technologies influences cognitive behaviour, so it is imperative to assess how different HCI strategies support intended behaviour. We developed a neuroscience-inspired game that trains children's use “stopping-and-thinking” (S&T)—an inhibitory control-related behaviour—in the context counterintuitive science problems. tested effica...

the effect of geometry and material of the micro/nano particle on contact mechanic for manipulation was studied in this work based on atomic force microscopy. hertz contact model simulation for eph biological micro particle with spherical, cylindrical, and circular crowned roller shape was used to investigate the effect of geometry on contact simulation process in manipulation. then, to validat...

Hybrid simulations of molecular systems, which combine all-atom (AA) with simplified (or coarse grain, CG) representations, propose an advantageous alternative to gain atomistic details on relevant regions while getting profit from the speedup of treating a bigger part of the system at the CG level. Here we present a reduced set of parameters derived to treat a hybrid interface in DNA simulatio...

The pathways of proton abstraction (PA), a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive...