GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking

Protein–ligand docking is a useful tool for providing atomic-level understanding of protein functions in nature and design principles for artificial ligands or proteins with desired properties. The ability to identify the true binding pose of a ligand to a target protein among numerous possible candidate poses is an essential requirement for successful protein–ligand docking. Many previously developed docking scoring functions were trained to reproduce experimental binding affinities and were also used for scoring binding poses. However, in this study, we developed a new docking scoring function, called GalaxyDock BP2 Score, by directly training the scoring power of binding poses. This function is a hybrid of physics-based, empirical, and knowledge-based score terms that are balanced to strengthen the advantages of each component. The performance of the new scoring function exhibits significant improvement over existing scoring functions in decoy pose discrimination tests. In addition, when the score is used with the GalaxyDock2 protein–ligand docking program, it outperformed other state-of-the-art docking programs in docking tests on the Astex diverse set, the Cross2009 benchmark set, and the Astex non-native set. GalaxyDock BP2 Score and GalaxyDock2 with this score are freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.     

Proteomic Evaluation of Biomarkers to Determine the Postmortem Interval

Proteomics separates and analyzes proteins for investigation at the cellular level in regard to disease processing by analyzing the proteins’ expression, function, structure, post-translational modification, and protein–protein interaction. In general forensic investigations, the postmortem interval was evaluated by measuring changes in body temperature after death, along with forensic entomological knowledge. These investigations may be restrictive and subjective because of external factors. The objectives of this study are to sort biomarker candidates and develop a direct postmortem-interval characterization method using proteomics through analyzing and tracking down proteins in the deceased that change in accordance with the postmortem interval. The liver and heart tissues of rats were collected for protein extraction in the 24-h interval following death, and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis was conducted based on the isoelectric point and the molecular weight for separation. To validate protein spot changes on the gel, the stained electrophoresis gels were scanned and converted to digital images. Through image analysis, 14 liver proteins and 12 heart proteins were sorted and classified into four groups based on pattern changes. These proteins containing spots were extracted from the gel and analyzed by high-performance liquid chromatography with tandem mass spectrometry. Finally, 26 protein postmortem-interval relevant biomarker candidates were identified using software. Some of the proteins were muscle proteins while others were oxidation-related proteins. This study presents a new approach to the postmortem-interval research using proteomics and could be substituted for postmortem-interval evaluation.     

Charging and Release Mechanisms of Flexible Macromolecules in Droplets

We study systematically the charging and release mechanisms of a flexible macromolecule, modeled by poly(ethylene glycol) (PEG), in a droplet by using molecular dynamics simulations. We compare how PEG is solvated and charged by sodium Na⁺ ions in a droplet of water (H₂O), acetonitrile (MeCN), and their mixtures. Initially, we examine the location and the conformation of the macromolecule in a droplet bearing no net charge. It is revealed that the presence of charge carriers do not affect the location of PEG in aqueous and MeCN droplets compared with that in the neutral droplets, but the location of the macromolecule and the droplet size do affect the PEG conformation. PEG is charged on the surface of a sodiated aqueous droplet that is found close to the Rayleigh limit. Its charging is coupled to the extrusion mechanism, where PEG segments leave the droplet once they coordinate a Na⁺ ion or in a correlated motion with Na⁺ ions. In contrast, as PEG resides in the interior of a MeCN droplet, it is sodiated inside the droplet. The compact macro-ion transitions through partially unwound states to an extended conformation, a process occurring during the final stage of desolvation and in the presence of only a handful of MeCN molecules. For charged H₂O/MeCN droplets, the sodiation of PEG is determined by the H₂O component, reflecting its slower evaporation and preference over MeCN for solvating Na⁺ ions. We use the simulation data to construct an analytical model that suggests that the droplet surface electric field may play a role in the macro-ion–droplet interactions that lead to the extrusion of the macro-ion. This study provides the first evidence of the effect of the surface electric field by using atomistic simulations.

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Spatial statistical analysis of the effects of urban form indicators on road-traffic noise exposure of a city in South Korea

The purpose of this study is to present a statistical model which can predict the noise level of road-traffic in urban area. A spatial statistical model which can take into account spatial dependency on geographically neighboring areas is constructed from a noise map of a city in South Korea. A system of 250 m × 250 m grid cells is placed on the city of Cheongju, South Korea, and the noise level and urban form indicators are averaged over each cell. The population-weighted mean of the noise level is subsequently regressed on the average urban form by adopting the spatial autoregressive model (SAR) and the spatial error model (SEM), as well as an ordinary least squares (OLS) model. Direct and indirect impacts are analyzed for a valid interpretation of the spatial statistical models. Factors such as GSI, FSI, traffic volume, traffic speed, road area density, and the fraction of industrial area turn out to have significant impacts on the noise level.     

Fabrication of polycrystalline silicon films by Al‐induced crystallization of silicon‐rich oxide films

Polycrystalline silicon (poly‐Si) films were fabricated by aluminum (Al)‐induced crystallization of Si‐rich oxide (SiO_x) films. The fabrication was achieved by thermal annealing of SiO_x /Al bilayers below the eutectic temperature of the Al–Si alloy. The poly‐Si film resulting from SiO_1.45 exhibited good crystallinity with highly preferential (111) orientation, as deduced from Raman scattering, X‐ray diffraction, and transmission electron microscopy measurements. The poly‐Si film is probably formed by the Al‐induced layer exchange mechanism, which is mediated by Al oxide.     

Optimization of the sonication extraction method of Hibiscus tiliaceus L. flowers

The influence of several experimental parameters on the ultrasonic extraction of Hibiscus tiliaceus L. flowers were investigated: extraction time, solvent polarity, sample amount, solvent volume and sample particle size. It was concluded that the most influential variables were extraction time and solvent polarity. The optimized procedure employed 5 g of ground flowers, 150 mL of methanol and 140 min of extraction. The extracts were fractionated using preparative silica columns and the resulting fractions were analyzed by GC/MS. Some saturated hydrocarbons, fatty acids, fatty acid methyl esters, phytosterols, and vitamin E were identified in the plant extracts.     

Single-electron transistors fabricated with sidewall spacer patterning

We have implemented a sidewall spacer patterning method for novel dual-gate single-electron transistor (DGSET) and metal–oxide–semiconductor-based SET (MOSET) based on the uniform SOI wire, using conventional lithography and processing technology. A 30 nm wide silicon quantum wire is defined by a sidewall spacer patterning method, and depletion gates for two tunnel junctions of the DGSET are formed by the doped polycrystalline silicon sidewall. The fabricated DGSET and MOSET show clear single-electron tunneling phenomena at liquid nitrogen temperature and insensitivity of the Coulomb oscillation period to gate bias conditions. On the basis of the phase control capability of the sidewall depletion gates, we have proposed a complementary self-biasing method, which enables the SET/CMOS hybrid multi-valued logic (MVL) to operate perfectly well at high temperature, where the peak-to-valley current ratio of Coulomb oscillation severely decreases. The suggested scheme is evaluated by SPICE simulation with an analytical DGSET model, and it is confirmed that even DGSETs with a large Si island can be utilized efficiently in the multi-valued logic.     

The role of strap muscles in phonation—In vivo caninelaryngeal model

In spite of the presumed importance of the strap muscles on laryngealvalving and speech production, there is little research concerning the physiological role and the functional differences among the strap muscles. Generally, the strap muscles have been shown to cause a decrease in the fundamental frequency (F₀) of phonation during contraction. In this study, an in vivo canine laryngeal model was used to show the effects of strap muscles on the laryngeal function by measuring the F₀, subglottic pressure, vocal intensity, vocal fold length, cricothyroid distance, and vertical laryngeal movement. Results demonstrated that the contraction of sternohyoid and sternothyroid muscles corresponded to a rise in subglottic pressure, shortened cricothyroid distance, lengthened vocal fold, and raised F₀ and vocal intensity. The thyrohyoid muscle corresponded to lowered subglottic pressure, widened cricothyroid distance, shortened vocal fold, and lowered F₀ and vocal intensity. We postulate that the mechanism of altering F₀ and other variables after stimulation of the strap muscles is due to the effects of laryngotracheal pulling, upward or downward, and laryngotracheal forward bending, by the external forces during strap muscle contraction.     

A single current density component imaging by MRCDI without subject rotations

Magnetic resonance current density imaging (MRCDI) is a useful method for measuring electrical current density distribution inside a subject. Due to the requirement of subject rotations in MRCDI, MRCDI has not been widely applied to in vivo studies. In this paper, we propose a new current density image (CDI) reconstruction method by which a single component of the current density can be imaged by MRCDI without subject rotations. After measuring one of the two magnetic field components, produced by the current density component passing through the measurement plane, we have reconstructed the current density component images in the spatial frequency domain. Even though the proposed method has a limitation that the area of magnetic field measurement should be much larger than that of the current density, the proposed method is expected to expedite MRCDI applications to in vivo studies.