• Bulletin of the Korean Chemical Society
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• v.29 no.9
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• pp.1755-1760
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• 2008

Energy minimization and conformational studies of molecular ions generated by ESI (electrospray ionization) tandem mass spectrometry (MS/MS) can be used for the discrimination of stereoisomeric permethylated and sodium cationized trisaccharides. Sets of fucose-containing trisaccharides having different internal and terminal linkages have been synthesized to analyze the reducing terminal linkage positions using BT and IT fusion approaches. A detailed investigation has been undertaken on the conformational behaviors of four trisaccharide fragments from human milk and blood group determinants of Type 1 and Type 2, namely Fuc($\alpha$1- 3)Gal($\beta$1-3)GalNAc and Fuc($\alpha$1-3)Gal($\beta$1-X)GlcNAc where X = 3, 4 and 6 using molecular modeling methods. Three dimensional rigid and adiabatic phi-psi-energy maps (Surfer program) describing the energy as a function of rotation around corresponding glycosidic linkages were calculated by SYBYL molecular modeling and MM4 force field programs conjunction with cleavage energies of ESI MS/MS for the side group orientations. This approach predicted conformational behaviors exhibited by isomer saccharides for future applications on biologically active glycoconjugates and to exploit a faster method of synthesizing a series of structural isomeric oligosaccharides.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.869-880
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• 2012

Identification of the selective chemical features for Aurora-B inhibitors gained much attraction in drug discovery for the treatment of cancer. Hence to identify the Aurora-B critical features various techniques were utilized such as pharmacophore generation, virtual screening, homology modeling, molecular dynamics, and docking. Top ten hypotheses were generated for Aurora-B and Aurora-A. Among ten hypotheses, HypoB1 and HypoA1 were selected as a best hypothesis for Aurora-B and Aurora-A based on cluster analysis and ranking score, respectively. Test set result revealed that ring aromatic (RA) group in HypoB1 plays an essential role in differentiates Aurora-B from Aurora-A inhibitors. Hence, HypoB1 used as 3D query in virtual screening of databases and the hits were sorted out by applying drug-like properties and molecular docking. The molecular docking result revealed that 15 hits have shown strong hydrogen bond interactions with Ala157, Glu155, and Lys106. Hence, we proposed that HypoB1 might be a reasonable hypothesis to retrieve the structurally diverse and selective leads from various databases to inhibit Aurora-B.

• Proceedings of the PSK Conference
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• 2000.10a
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• pp.59-60
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• 2000

• Applied Biological Chemistry
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• v.41 no.8
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• pp.563-567
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• 1998

Computer aided molecular modeling can help to predict the three dimensional structure of the polypeptide without the sample. The study on soybean Bowman-Birk protease inhibitor (SBI) is valuable, because it has been recently known that SBI possesses anticarcinogenic activities and immune-stimulating properties. SBI has several isoinhibitors, whose isolation and characterization were reported in 1990. Among these, DII inhibits trypsin only. The different inhibitory specificities cannot be explained only by their different primary sequences, but is possible with further assistance by the study on their different three dimensional structures. The study on the three dimensional structure of DII using homology method is reported in this paper.

• Macromolecular Research
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• v.9 no.3
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• pp.129-142
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• 2001

To efficiently demonstrate the molecular motion, physical properties, and mechanical properties of polycarbonates, we studied the differences between bisphenol-A polycarbonate(BPA-PC) and tetramethyl bisphenol-A-polycarbonate(TMBPA-PC) using molecular modeling techniques. To investigate the conformations of BPA-PC and TMBPA-PC and the effect of the conformation on mechanical properties, we performed conformational energy calculation, molecular dynamics calculation, and stress-strain curves based on molecular mechanics method. From the result obtained from conformational energy calculations of each segment, the molecular motions of the carbonate and the phenylene group in BPA-PC were seen to be more vigorous and have lower restriction to mobility than those in TMBPA-PC, respectively. In addition, from the results of radial distribution function, velocity autocorrelation function, and power spectrum, BPA-PC appeared to have higher diffusion constant than TMBPA-PC and is easier to have various conformations because of the less severe restrictions in molecular motion. The result of stress-strain calculation for TMBPA-PC seemed to be in accordance with the experimental value of strain-to-failure ∼4%. From these results of conformational energy calculations of segments, molecular dynamics, and mechanical properties, it can be concluded that TMBPA-PC has higher modulus and brittleness than BPA-PC because the former has no efficient relaxation mode against the external deformations.

• KIISE Transactions on Computing Practices
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• v.20 no.10
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• pp.534-542
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• 2014

Multiscale modeling is a new simulation approach which can manage different spatial and temporal scales of system. In this study, as part of multiscale modeling research, we propose the way of combining two different simulation methods, molecular dynamics(MD) and stochastic rotation dynamics(SRD). Our conceptual implementations are based on LAMMPS, one of the well-known molecular dynamics programs. Our prototype of multiscale modeling follows the form of the third party implementation of LAMMPS. It added MD to SRD in order to simulate the boundary area of the simulation box. Because it is important to guarantee the seamless simulation, we also designed the overlap zones and communication zones. The preliminary experimental results showed that our proposed scheme is properly worked out and the execution time is also reduced.

• BMB Reports
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• v.49 no.6
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• pp.349-354
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• 2016

The archaeon Sulfolobus solfataricus P1 carboxylesterase is a thermostable enzyme with a molecular mass of 33.5 kDa belonging to the mammalian hormone-sensitive lipase (HSL) family. In our previous study, we purified the enzyme and suggested the expected amino acids related to its catalysis by chemical modification and a sequence homology search. For further validating these amino acids in this study, we modified them using site-directed mutagenesis and examined the activity of the mutant enzymes using spectrophotometric analysis and then estimated by homology modeling and fluorescence analysis. As a result, it was identified that Ser151, Asp244, and His274 consist of a catalytic triad, and Gly80, Gly81, and Ala152 compose an oxyanion hole of the enzyme. In addition, it was also determined that the cysteine residues are located near the active site or at the positions inducing any conformational changes of the enzyme by their replacement with serine residues.

• Smart Structures and Systems
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• v.13 no.4
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• pp.685-709
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• 2014

Carbon nanotubes are due to their outstanding mechanical properties destined for a wide range of possible applications. Since the knowledge of the material behavior is vital regarding the possible applications, experimental and theoretical studies have been conducted to investigate the properties of this promising material. The aim of the present research is the calculation of mechanical properties and of the mechanical behavior of single wall carbon nanotubes (SWCNTs). The numerical simulation was performed on basis of a molecular mechanics approach. Within this approach two different issues were taken into account: (i) the nanotube geometry and (ii) the modeling of the covalent bond. The nanotube geometry is captured by two different approaches, the roll-up and the exact polyhedral model. The covalent bond is modeled by a structural molecular mechanics approach according to Li and Chou. After a short introduction in the applied modeling techniques, the results for the Young's modulus for several SWCNTs are presented and are discussed extensively. The obtained numerical results are compared to results available in literature and show an excellent agreement. Furthermore, deviations in the geometry stemming from the different models are given and the resulting differences in the numerical findings are shown. Within the investigation of the deformation mechanisms occurring in SWCNTs, the basic contributions of each individual covalent bond are considered. The presented results of this decomposition provide a deeper understanding of the governing deformation mechanisms in SWCNTs.

• Bulletin of the Korean Chemical Society
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• v.35 no.1
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• pp.62-68
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• 2014

Coptis chinensis 3'-hydroxy-N-methylcoclaurine 4'-O-methyltransferase (HOMT), an essential enzyme in the berberine biosynthetic pathway, catalyzes the methylation of 3'-hydroxy-N-methylcoclaurine (HMC) producing reticuline. A 3D model of HOMT was constructed by homology modeling and further subjected to docking with its ligands and molecular dynamics simulations. The 3D structure of HOMT revealed unique structural features which permitted the methylation of HMC. The methylation of HMC was proposed to proceed by deprotonation of the 4'-hydroxyl group via His257 and Asp258 of HOMT, followed by a nucleophilic attack on the SAM-methyl group resulting in reticuline. HOMT showed high substrate specificity for methylation of HMC. The study evidenced that Gly117, Thr312 and Asp258 in HOMT might be the key residues for orienting substrate for specific catalysis.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.18 no.5
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• pp.414-422
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• 2005

This paper shows the results of atomistic modeling for the Interaction between spherical nano abrasive and substrate In chemical mechanical polishing processes. Atomistic modeling was achieved from 2-dimensional molecular dynamics simulations using the Lennard-jones 12-6 potentials. We proposed and investigated three mechanical models: (1) Constant Force Model; (2) Constant Depth Model, (3) Variable Force Model, and three chemical models, such as (1) Chemically Reactive Surface Model, (2) Chemically Passivating Surface Model, and (3) Chemically Passivating-reactive Surface Model. From the results obtained from classical molecular dynamics simulations for these models, we concluded that atomistic chemical mechanical polishing model based on both Variable Force Model and Chemically Passivating-reactive Surface Model were the most suitable for realistic simulation of chemical mechanical polishing in the atomic scale. The proposed model can be extended to investigate the 3-dimensional chemical mechanical polishing processes in the atomic scale.