• Journal of Integrative Natural Science
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• v.3 no.1
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• pp.49-53
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• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Applied Chemistry for Engineering
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• v.5 no.2
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• pp.255-262
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• 1994

Arc melted Ti-5Bi alloy was oxidized by thermal oxidation method. In the present study free energy efficiency(${\eta}_e$) of titanium oxide electrode(TOE) was measured as a function of light intensity and light energy. Flat-band potential of TOE was measured as a function of the light intensity and the solution pH. The ${\eta}_e$ of TOE increased with the increase of light intensity and tight energy to maximum value of 3.2% and 13%, respectively, at $0.2W/cm^2$ and 4.0eV. The ${\eta}_e$ was strongly dependent on the magnitude of the bias voltage. Maximum value was found at 0.5V bias. Photocurrent of TOE was controlled by electron-hole pair generation in depletion layer. The flat-band potential of the illuminated TOE shifted to -0.065V/decade with increasing light intensity. With the decrease of pH of electrolyte, flat-band potential shifted to anodic direction. The experimental slope was in good agreement with the Nernstian value of 0.059V/pH decade.

• Bulletin of the Korean Chemical Society
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• v.21 no.4
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• pp.434-440
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• 2000

We present the results of computer simulation for the steady shear flows of rodlike molecules using nonequi-librium molecular dynamics simulation (NEMD) method. The model particle is a rigid rod composed of lin-early connected 6-sites and the Lennard-Jones 12-6 potential governs interactions between sites in different molecules. The system of rodlike molecules exhibits the change of orientational structure, that is, isotropic-nematic transition at high shear rates. We elucidate the nature of the ordered system developed from an isotro-pic phase by steady shear through an analysis of various quantities: orientational order parameters, orientational pair correlation functions, orientational distribution function, and snapshots of configurations. The effects of temperature and density on the shear rate dependence of orientational structure are described.

• Journal of Ginseng Research
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• v.44 no.2
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• pp.291-299
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• 2020

Background: Ginseng (G) and Ligustrum lucidum Ait (LLA) are core traditional Chinese medicines in treating myelosuppression formula. The present study was designed to profile effect of G and LLA herb pair (G-LLA) on myelosuppressed mice. Methods: The mice myelosuppression model was established by intraperitoneal (i.p.) injection of cyclophosphamide (Cy). Hematopoietic function of bone marrow was measured by hemopoietic progenitor cell culture and peripheral blood count, and serum hemopoietic factors were tested by enzyme-linked immunosorbent assay. Bone marrow cell cycle was performed by flow cytometry. HPLC was used to measure 20 potential chemical components related to myelosuppression, including ginsenoside Rg₁, Re, Rb₁, Rc, Rb₂, Rb₃, Rd, Rk₃, Rh₄, 20 (S)-Rg₃, 20 (R)-Rg₃, Rk₁, Rg₅, salidroside, and so on. Results: G, LLA, and G-LLA improved the amount of peripheral blood cells and bone marrow cells of myelosuppressed mice (P < 0.01). They significantly increased the colony quantity of colony-forming unit-granulocyte macrophage, burst-forming unit-erythroid, colony-forming unit-erythroid, and colony-forming unit-megakaryocyte and amount of G₂/M and S phase cells (P < 0.01). They also significantly decreased the amount of hematopoiesis-related cytokines (P < 0.01). The content of chemical components in G-LLA changed, and the change of rare saponin was the most obvious. Conclusion: These results show that G-LLA herb pair might produce synergistic or complementary compatibility effects on bone marrow suppression after chemotherapy. It suggests that the substance basis of G-LLA for treating bone marrow suppression may be effective chemical components.

• Smart Structures and Systems
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• v.15 no.4
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• pp.1121-1137
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• 2015

This study presents probabilistic-based damage identification technique for highlighting damage in metallic structures. This technique utilizes distributed piezoelectric transducers to generate and monitor the ultrasonic Lamb wave with narrowband frequency. Diagnostic signals were used to define the scatter signals of different paths. The energy of scatter signals till different times were calculated by taking root mean square of the scatter signals. For each pair of parallel paths an error function based on the energy of scatter signals is introduced. The resultant error function then is used to estimate the probability of the presence of damage in the monitoring area. The presented method with an autofocusing feature is applied to aluminum plates for method verification. The results identified using both simulation and experimental Lamb wave signals at different central frequencies agreed well with the actual situations, demonstrating the potential of the presented algorithm for identification of damage in metallic structures. An obvious merit of the presented technique is that in addition to damages located inside the region between transducers; those who are outside this region can also be monitored without any interpretation of signals. This novelty qualifies this method for online structural health monitoring.

• Journal of Microbiology and Biotechnology
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• v.18 no.10
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• pp.1634-1640
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• 2008

This study was focused on the screening of valuable genetic resources, such as promoters from metagenome, and describes a promoter trapping system with a bidirectional probe concept, which can select promoters or operons from various biological resources including metagenomic DNA. A pair of reporters, GFP and DsRed, facing the opposite direction without promoters, is an effective system that can function regardless of the direction of inserted promoters. The feasibility of this system was tested for the isolation of constitutively expressed promoters in E. coli from a soil metagenome, resulting in a potential pool of various promoters for practical application. The analyses of structural organization of the trapped genes demonstrated that constitutively expressible promoters in E. coli were broadly distributed within the metagenome, and suggested that some promoters were useful for the construction of expression vectors. Based on these observations, three constitutive promoters were employed in the expression vector system and their potentials for practical application were evaluated in terms of expression level, protein solubility, and effects on host growth.

• Journal of the Institute of Electronics Engineers of Korea TC
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• v.40 no.10
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• pp.150-158
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• 2003

In the beam pattern synthesis problem using line source, the relationship between source distribution function and beam pattern may be represented by Fourier transform pair. In this paper, a general method to synthesize the line source distribution for a desired lobe-like beam pattern is presented by developing the nonlinear inversion method based on an iterative sampling technique. This method can be applied to the synthesis of continuously distributed dielectric constants satisfying the desired inverse scattering coefficient patterns when illuminating by TE-polarized and TM-polarized plane waves to arbitrary dielectric material. Furthermore this method can also be applied to the synthesis of transmission line with arbitrary reflection coefficient patterns. Some bandstop spatial filter and dispersive transmission line filter are illustrated for generality.

• Bioinformatics and Biosystems
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• v.2 no.1
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• pp.17-23
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• 2007

Shot interfering RNA (siRNA) can be used to silence specific gene expression and have many potential therapeutic applications. However, how to design an effective siRNA is still not clear. Highly effective siRNA has sequence-specific properties which are low G/C content, low internal stability at the sense strand 3'-terminus, sense strand base bias(position 1 is G/C, position 19 is /AU). Recently, mRNA secondary structure playsan important role in RNAi. Target site of siRNA in high-ordered structure (i.e hairpin loop, multi loop) or base pair of many hydrogen bonds dramatically reduce function of siRNA mediated gene silencing. Possible off-target effects of siRNA is detecting from BLAST search.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.10
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• pp.4291-4295
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• 2015

Background: Chemokines and their receptors influence carcinogenesis and cysteine-cysteine chemokine receptor 5 (CCR5) directs spread of cancer to other tissues. A 32 base pair deletion in the coding region of CCR5 that might alter the expression or function of the protein has been implicated in a variety of immune-mediated diseases. The action of antiviral drugs being proposed as adjuvant therapy in cancer is dependent on CCR5 wild type status. In the present study, distribution of CCR5${\Delta}32$ polymorphism was assessed in North Indian esophageal cancer patients to explore the potential of using chemokine receptors antagonists as adjuvant therapy. Materials and Methods: DNA samples of 175 sporadic esophageal cancer patients (69 males and 106 females) and 175 unrelated healthy control individuals (69 males and 106 females) were screened for the CCR5${\Delta}32$ polymorphism by direct polymerase chain reaction (PCR). Results: The frequencies of wild type homozygous (CCR5/CCR5), heterozygous (CCR5/${\Delta}32$) and homozygous mutant (${\Delta}32/{\Delta}32$) genotypes were 96.0 vs 97.72%, 4.0 vs 1.71% and 0 vs 0.57% in patients and controls respectively. There was no difference in the genotype and allele frequencies of CCR5${\Delta}32$ polymorphism in esophageal cancer patients and control group. Conclusions: The CCR5${\Delta}32$ polymorphism is not associated with esophageal cancer in North Indians. As the majority of patients express the wild type allele, there is potential of using antiviral drug therapy as adjuvant therapy.

• BMB Reports
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• v.31 no.4
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• pp.370-376
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• 1998

Src-Homology 2 (SH2) domains have a capacity to bind phosphotyrosine-containing sequence context and play essential roles in various cellular signaling pathways. Due to the specific nature of the binding between SH2 domains and their counterpart proteins, inhibitors of SID domain binding have drawn extensive attention as a potential candidate for therapeutic agents. Here, we describe the binding assay system to screen for the ligands or blockers of the SH2 domains with an emphasis on the $p56^{lck}$ SH2 domain. In our assay system, SID domains expressed and purified as fusion proteins to Glutathione-S-transferase (GST) were covalently attached to 96-well microtitre plates through amide bond formation, which were subsequently allowed to bind the biotinylated phosphotyrosine (pY)containing synthetic pep tides. The binding of biotinylated pY peptides was detected by the horseradish peroxidase (HRP)-conjugated streptavidin. Using the various combinations of SH2 domain-pY peptides, we observed that: (1) The binding of pY-peptides to its counterpart SH2 domain is concentration-dependent and saturable; (2) The binding is highly specific for a particular combination of SH2 domain-pY peptide pair; and (3) The binding of Lck SH2-cognate pY-peptides is specifically competed by the nonbiotinylated peptides with expected relative affinity. These results indicate that the established assay system detects the SH2-pY peptide interaction with reproducible sensitivity and specificity and is suitable for screening the specific inhibitors of $p56^{lck}$ SH2 function.