• Bioinformatics and Biosystems
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• v.1 no.2
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• pp.103-108
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• 2006

Computational prediction of protein-ligand binding has been widely used as a tool to discover lead compounds fur new drugs. Prediction accuracy is determined in part by the scoring function used in docking calculations. Diverse scoring functions are available, and these can be classified into force-field based, empirical, and knowledge-based functions depending upon the basic assumptions made in development. Among these, force-field based functions consider physical interactions the most in detail. However, the force-field based functions have the drawback of not including the entropic effect while considering only the energy contribution such as dispersion or electrostatic forces. In this article, a method to take into account of the entropic effect using the colony energy is suggested when force-field based scoring functions is used by extracting conformational information obtained from the pre-existing docking program. An improved result for decoy discrimination is illustrated when the method is applied to the DOCK scoring function, and this implies that more accurate docking calculation is possible.

• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.124-131
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• 2015

단백질의 구조를 예측하기 위해서 구조가 알려져 있는 단백질 중 진화적으로 유사한 단백질의 구조 정보를 이용하는 Template Based Modeling (TBM) 방법이 현재까지 가장 효과적으로 많이 사용되고 있다. 단백질의 삼차 구조를 이루는 단위 중에서도 고리 부분은 효소 활성 부위 또는 리간드 결합 부위 등으로 작용하여 단백질의 생물학적 기능에 연관되어 있다. 하지만 진화적으로 가까운 단백질이어도 고리 부분은 서열이 잘 보존되지 않아 충분한 구조 정보를 주지 못하고 TBM 방법으로 고리 구조까지 정확히 예측을 할 수 없다. 따라서 TBM 방법으로 예측한 구조의 고리 부분을 주형 정보에 의존하지 않고 다시 예측하여 전체 구조를 정밀화하는 과정이 중요하다. 이번 연구에서는 이를 위해 자유 에너지를 고려한 고리 구조 예측 방법을 적용하여 그 효과를 검증해보았다.

• Journal of Naturopathy
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• v.8 no.2
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• pp.71-77
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• 2019

Purpose: The purpose of this study was to investigate the far-infrared emissivity of patented ocher quilt cotton fabrics and to investigate the microorganisms that survived the washing of cotton fabrics up to 20 times. Methods: A 16S rRNA assay was performed using a far-infrared radiometer and a single colony in which microorganisms grew in nutrient media. Results: The far-infrared emissivity of ocher quilt was 0.902 (90.2%) at 5~20 ㎛ at 40℃, and the radiation energy was 3.63 × 10² w/m². The number of viable cells was 2.0 × 10² cells/ml in ocher duvet cotton fabric, and no viable bacteria found in regular cotton fabric. The base sequence of 16S rRNA of B-2 strain isolated into single colonies was 1,419 bases, and the base sequence of strain A-4 was 1,284 bases. The base sequence of 16S rRNA of these two strains showed high homology with Bacillus spp. The B-2 bacteria showed high homology with 99.0% of the 16S rRNA sequence of B. aryabhattai EF114313 and 99.0% of the A-4 bacteria of B. bingmayongensis AKCS01000011. Consequently the colony strain B-2 finally identified as B. aryabhattai BJ-2 and A-4 as B. bingmayongensis BJ-4 strain. Concusions: Soil Bacillus strains survived in ocher quilt cotton fabric after 20 washing. The material can be useful because quilt cotton fabric emits a large amount of far-infrared and far-infrared radiation energy.

• Korean Journal of Microbiology
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• v.40 no.4
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• pp.320-327
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• 2004

Three hundreds thirty two bacterial colonies which were able to degrade crude oil were isolated from soil sam­ples that were contaminated with oil in Daejeon area. Among them, one bacterial strain was selected for this study based on its higher oil degrading ability, and this selected bacterial strain was identified as Acinetobactor sp. B2 through physiological-biochemical tests and analysis of its 16S rRNA sequence. Acinetobactor sp. B2 was able to utilize various carbohydrates but did not utilize trehalose and mannitol as a sole carbon source. Acinetobactor sp. B2 showed a weak resistance to antibiotics such as kanamycin, streptomycin, tetracycline and spectinomycin, but showed a high resistance up to mg/ml unit to heavy metals such as Ba, Li, Mn, AI, Cr and Pb. The optimal growth temperature of Acinetobactor sp. B2 was $30^{\circ}C.$ The lipase produced by Acinetobactor sp. B2 was purified by ammonium sulfate precipitation, DEAE-Toyopearl 650M ion exchange chromatography and Sephadex gel filtration chromatography. Its molecular mass was about 60 kDa and condition for the optimal activity was observed at $40^{\circ}C$ and pH 10, respectively. The activation energy of lipase for the hydrolysis of p­nitrophenyl palmitate was 2.7 kcal/mol in the temperature range of 4 to $37^{\circ}C,$ and the enzyme was unstable at the temperature higher than $60^{\circ}C.$ The Michaelis constant $(K_m)\;and\;V_{max}$ for p-nitrophenyl palmitate were 21.8 uM and $270.3\;{\mu}M\;min^{-1}mg^{-1},$ respectively. This enzyme was strongly inhibited by 10 mM $Cd^{2+},\;Co^{2+},\;Fe^{2+},\;Hg^{2+},$ EDTA and 2-Mercaptoethalol.

• Microbiology and Biotechnology Letters
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• v.38 no.2
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• pp.144-150
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• 2010

This study was aimed to screen bacteria of high alginate-degrading activity, to select the nitrogen source and concentration of NaCl and sodium alginate for the production of alginate-degrading enzyme, and to determine reaction conditions of enzyme. A novel alginate-degrading bacterium was isolated from abalone (Haliotis discus hannai) and named Methylobacterium sp. HJM27 by 16S rDNA sequence analysis. The optimum culture conditions for the production of alginate-degrading enzyme were 1.0% sodium alginate, 0.5% peptone, 0.3% yeast extract, 1.5% NaCl, $25^{\circ}C$ and 48 hours incubation time. The raw enzyme showed the highest activity at $25^{\circ}C$ and pH 9, and produced 1.217 g - reducing sugar per liter in 0.8% (w/v) sodium alginate for 30 minutes. Methylobacterium sp. HJM27 and its alginate-degrading enzyme would be useful for the production of bioenergy and biofunctional oligosaccharides from seaweed.