Investigation of the bindings of a class of inhibitors with GSK3β kinase using thermodynamic integration MD simulation and kinase assay.

GSK3β kinase is a noteworthy target for discovery of the drugs that will be used to treat several diseases. In the effort to identify a new inhibitor lead compound, we utilized thermodynamic integration (TI)-molecular dynamics (MD) simulation and kinase assay to investigate the bindings between GSK3β kinase and five compounds that were analogous to a known inhibitor with an available crystal structure. TI-MD simulations of the first two compounds (analogs 1 and 2) were used for calibration.

Identifying GSK-3β kinase inhibitors of Alzheimer's disease: Virtual screening, enzyme, and cell assays.

Glycogen synthase kinase 3β (GSK-3β) is widely known as a critical target protein for treating Alzheimer's disease (AD). We utilized virtual screening to search databases for compounds with the potential to be used in drugs targeting GSK-3β kinase, and kinase as well as cell assays to investigate top-scored, selected compounds. Virtual screening of >1.

Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation.

Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influenced by the presence or absence of the peptide tag in p38 kinase. This possible effect of protein length on the binding affinity of a ligand-which is seldom addressed in the literature-is important because, even when two labs claim to have performed experiments with the same protein, they may actually have studied variants of the same protein with different lengths because they applied different protein expression conditions/procedures. Thus, if we wanted to compare ligand binding affinities measured in the two labs, it would be necessary to account for any variation in ligand binding affinity with protein length.

Using thermodynamic integration MD simulation to compute relative protein-ligand binding free energy of a GSK3β kinase inhibitor and its analogs.

Thermodynamic integration molecular dynamics simulation was used to investigate how TI-MD simulation preforms in reproducing relative protein-ligand binding free energy of a pair of analogous GSK3β kinase inhibitors of available experimental data (see Fig. 1), and to predict the affinity for other analogs. The computation for the pair gave a ΔΔG of 1.

Filtration of dust particulates with a moving granular bed filter.

The goal of this study was to evaluate the performance of a moving granular bed filter designed for cold test to filter coal particulates. A series of experiments were carried out at room temperature to demonstrate the collection efficiency of this method of filtration technology (i.e.

Development of a reliable assay protocol for identification of diseases (RAPID)-bioactive amplification with probing (BAP) for detection of Newcastle disease virus.

Due to appearance of new genotypes of Newcastle disease virus (NDV) with no cross-protection and with vaccine strains, some outbreaks have been reported in Taiwan that caused significant damage to the poultry industry. A reliable assay protocol, (RAPID)-bioactive amplification with probing (BAP), for detection of NDV that uses a nested PCR and magnetic bead-based probe to increase sensitivity and specificity, was developed. Primers and probes were designed based on the conserved region of the F protein-encoding gene sequences of all NDV Taiwan isolates.

Magnetic viscosity and microstructure of GePt/FePt films.

We found various GePt/FePt microstructures at different post-annealing temperatures. The Ge(2)Pt(3) compound was formed when the annealing temperature was 800 °C and the particle-like structure was able to relax the growth stress between Ge(2)Pt(3) and quartz. After deposition of FePt film, a discontinuous L1(0) FePt layer was formed when it was post-annealed at 400 °C.