• Proceedings of the Korean Biophysical Society Conference
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• 1996.07a
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• pp.10-10
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• 1996

High-resolution solution conformation of a novel conotoxin, [Pro 7,13] $\alpha$A-conotoxin $P_{IVA}$, GCCGSYPNAACHPCSCKDROSYCGQ-N $H_2$, has been determined by two-dimensional $^1$H nmr methods in combination with distance geometry calculation to rmsd values of 0.90 $\AA$ and 1.16 $\AA$ for the backbone and heavy atoms, respectively. Total of 324 NOE-derived interproton distance restraints including 33 long-range NOE restraints a well as 11 $\Phi$ and 7 $\chi$$^1$ torsion angle restraints were used for computation of structures. (omitted)d)

• Bulletin of the Korean Chemical Society
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• v.28 no.2
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• pp.211-219
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• 2007

The subtle but significant differences and thereby the lack of consensus in active site structures among the crystal structures of cyclin-dependent kinase 2 (CDK2) has hampered structure-based drug design. In this study, we devised a simple but effective ‘mutation, pharmacophore-guided docking, followed by mutation' strategy to generate an “average” CDK2 structure, which was used for ligand docking study to successfully reproduce 30 out of 32 X-ray ligand positions within 2.0 A of heavy atom RMSD. This novel docking method was applied for structure-based 3D QSAR with CoMSIA study of a series of structurally related ligands, which showed a good discrimination between CDK2 binders and nonbinders.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.126-130
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• 2016

Epidermal growth factor receptor(EGFR)는 HER family에 속하는 tyrosine kinase receptor로서 다양한 하류경로로 신호를 전달하여 세포 증식, 혈관 형성, 세포 사멸을 억제하는 역할을 한다. EGFR이 폐암의 형성에 중요한 역할을 하고 많은 상피세포 종양에서 비정상적으로 활성화됨에 따라 암 치료에 중요한 역할을 하고 있어 EGFR tyrosine kinase inhibitor(TKI)에 관한 많은 연구가 이루어졌다. 위와 같은 약 개발에 있어서 현재 가상 시뮬레이션을 통한 약 후보물질 개발이 진행되고 있다. 특히, Molecular docking 시뮬레이션은 기존의 실험적인 기술(X-ray crystallography, NMR)로는 연구하기가 어려웠던 protein과 ligand간의 상호작용을 예측하여 이에 대한 정보를 제공할 수 있다. 하지만, 우선적으로 Molecular docking 시뮬레이션은 정확한 validation을 기반으로 진행되어야 신뢰할 수 있는 정보를 얻을 수 있다. 따라서 이번 연구에서는 EDISON에서 제공하는 Dock 프로그램과 일반적으로 잘 알려진 Glide, Autodock 프로그램으로 protein data bank(PDB)에서 제공하는 EGFR wild type cocrystal을 redocking하는 방식을 통하여 최상위 rank pose의 RMSD 값을 통한 validation 성능을 비교함으로써 어떤 프로그램이 EGFR과 ligand 간의 결합예측을 하는데 있어서 보다 더 정확한 결과를 낼 수 있는지 알아보고자 하였고 시뮬레이션 결과 Autodock에서 가장 우수한 결과 값을 보여주었다.

• Bulletin of the Korean Chemical Society
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• v.16 no.7
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• pp.649-653
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• 1995

Solution-state structure of native F430 was determined by using NMR methods and NMR-based distance geometry (DG) computations. Structures were generated with loose NOE-derived interproton distance restraints (2.0-2.5 Å, 2.0-3.5 Å and 2.0-4.5 Å for strong, medium, and weak NOE cross-peak intensities, respectively). 2D NOESY back-calculations of structures were subsequently carried out for establishing the consistence between experimental data and DG-model structures. The back-calculated 2D NOESY spectra of resulting DG structures were well consistent with experimental 2D NOESY spectra. Superposition of 20 independent structures with macrocyclic ring atoms and all atoms of F430 afforded pairwise root mean square deviations (RMSD) of 0.025-0.125 Å and 0.64-1.3 Å, respectively. The macrocyclic rings of structures are well converged to a unique conformation with saddle-shaped deformation whereas most of side chains are not converged. The average dihedral angle (N1-N2-N3-N4, 27.78±1.50°) of 20 DG-structures exhibits that the macrocyclic ring conformation is puckered as much as 12,13-diepimeric F430 (28.75±4.07°).

• Journal of Industrial and Engineering Chemistry
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• v.67
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• pp.293-300
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• 2018

Lipocalins are diverse group of small extracellular proteins found in various organisms. In this study, members of 10 non-homologous lipocalin-ligand crystal complex structures were remodeled using rigid and flexible ligand modes to validate the prediction efficiency of molecular docking simulation. The modeled ligand conformations indicated a high prediction accuracy in rigid ligand mode using cluster based analysis for most cases whereas the flexible ligand mode required further considerations such as ligand binding energy and RMSD for some cases. This in silico study is expected to serve as a platform in the screening of novel ligands against lipocalin family of proteins.

• Structural Monitoring and Maintenance
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• v.9 no.3
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• pp.221-235
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• 2022

Among nondestructive damage detection methods, impedance-based methods have been recognized as an effective technique for damage identification in many kinds of structures. This paper proposes a method to detect cracks in metal structures by combining electro-mechanical impedance (EMI) responses and artificial neural networks (ANN). Firstly, the theories of EMI responses and impedance-based damage detection methods are described. Secondly, the reliability of numerical simulations for impedance responses is demonstrated by comparing to pre-published results for an aluminum beam. Thirdly, the proposed method is used to detect cracks in the beam. The RMSD (root mean square deviation) index is used to alarm the occurrence of the cracks, and the multi-layer perceptron (MLP) ANN is employed to identify the location and size of the cracks. The selection of the effective frequency range is also investigated. The analysis results reveal that the proposed method accurately detects the cracks' occurrence, location, and size in metal structures.

• Journal of Integrative Natural Science
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• v.16 no.1
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• pp.33-38
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• 2023

The follicle stimulating hormone receptor (FSHR) is a glycoprotein hormone, that belongs to the GPCR superfamily. FSHR plays a major role in reproduction. The aberrant activation of FHS receptor leads to infertility and several reproductive disorders. The recently recognized roles of the FSHR in diverse extragonadal tissues is also closely related to Alzheimer's disease and cancers. Analysing the structural characteristics of the receptor is important in understanding the pathophysiology of diseases associated with the receptor. In this present study, homology modelling of FSHR-TM domain was developed using four different templates. Totally 20 models were developed using single template-based approach and selected three based on the validation of RC plot, RMSD, ProSA, QMEAN and ERRAT values. The developed models would be useful for further research on the structural characteristics and binding characteristics of the FSHR-TM domain.

• Korean Journal of Remote Sensing
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• v.31 no.6
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• pp.549-560
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• 2015

With the global scale impact of atmospheric $CO_2$ in global warming and climate system, it is necessary to monitor the $CO_2$ concentration continuously on a global scale, where satellite remote sensing has played a significant role recently. In this study, global monthly $CO_2$ concentrations obtained by satellite remote sensing were compared with ground-based measurements at Anmyeon-do and Gosan Korean Global Atmosphere Watch Center. Atmospheric $CO_2$ concentration has increased from 371.87 ppm in January 1999 to 405.50 ppm in December 2013 at Anmyeon-do station (KMA, 2013). Comparison of the continuous measurements by flask air sampling at Anmyeon-do shows the same trend and seasonal variations with those of global monthly mean dataset. Nevertheless, the trends of $CO_2$ over Northeast Asia showed the higher than those of global and the trends also changes with different slope. $CO_2$ products derived from Greenhouse Gases Observing Satellite (GOSAT) and Atmospheric Infrared Sounder (AIRS) were compared with ground-based measurement at Anmyeon-do. The monthly mean values of GOSAT and AIRS data are systemically lower than those obtained at Anmyeon-do, however, the seasonal cycle of satellite products present the similar trend with values of global and Anmyeon-do. The accuracy of $CO_2$ products from GOSAT and AIRS were evaluated statistically for two years from January 2011 to December 2012. GOSAT showed good correlation with the correlation coefficient, RMSD and bias of 0.947, 5.610 and -5.280 to ground-based measurements respectively, while AIRS showed reasonable comparison with 0.737, 8.574 and -7.316 at Anmyeon-do station, respectively.

• Korean Journal of Remote Sensing
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• v.32 no.2
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• pp.73-86
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• 2016

In this study, an algorithm to estimate Aerosol Optical Thickness (AOT) over small cities during nighttime has been developed by using the radiance from artificial light sources in small cities measured from Visible Infrared Imaging Radiometer Suite (VIIRS) sensor's Day/Night Band (DNB) aboard the Suomi-National Polar Partnership (Suomi-NPP) satellite. The algorithm is based on Beer's extinction law with the light sources from the artificial lights over small cities. AOT is retrieved for cloud-free pixels over individual cities, and cloud-screening was conducted by using the measurements from M-bands of VIIRS at infrared wavelengths. The retrieved nighttime AOT is compared with the aerosol products from MODerate resolution Imaging Spectroradiometer (MODIS) aboard Terra and Aqua satellites. As a result, the correlation coefficients over individual cities range from around 0.6 and 0.7 between the retrieved nighttime AOT and MODIS AOT with Root-Mean-Squared Difference (RMSD) ranged from 0.14 to 0.18. In addition, sensitivity tests were conducted for the factors affecting the nighttime AOT to estimate the range of uncertainty in the nighttime AOT retrievals. The results of this study indicate that it is promising to infer AOT using the DNB measaurements over small cities in Korea at night. After further development and refinement in the future, the developed retrieval algorithm is expected to produce nighttime aerosol information which is not operationally available over Korea.

• Journal of Life Science
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• v.25 no.11
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• pp.1304-1310
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• 2015

The period circadian clock gene 3 (PER3) plays a role in the mammalian circadian clocksystem. A regular exercise regime may affect the PER3 transcription in skeletal muscle. Although the effects of day length on circadian and circannual processes are well established in humans and mice, the influence of exercise on these processes in the horse has not been investigated. The present study investigated the expression of the PER3 gene following exercise in a thoroughbred breed of Korean horse. In addition, a comprehensive in silico nonsynonymous single nucleotide polymorphism (nsSNP) analysis of the horse PER3 gene and predicted effects of nsSNPs on proteins were examined. The expression of PER3 in skeletal muscle was significantly upregulated after exercise. Four nsSNPs were functionally annotated and analyzed by computational prediction. The total free energy and RMSD values of PER3 gene showed causative mutations. The results showed that nsSNP s395916798 (G72R) was associated with residues that have stabilizing effects on structure and function of PER3 gene. This study documented role of PER3 gene in phenotypic adaptation related to exercise in skeletal muscle. Further, the SNPs in PER3 could serve as useful biomarkers of early recovery after exercise in racehorses.