• Genomics & Informatics
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• 제15권2호
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• pp.69-80
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• 2017

In this study, cytolethal distending toxin (CDT) producer isolates genome were compared with genome of pathogenic and commensal Escherichia coli strains. Conserved genomic signatures among different types of CDT producer E. coli strains were assessed. It was shown that they could be used as biomarkers for research purposes and clinical diagnosis by polymerase chain reaction, or in vaccine development. cdt genes and several other genetic biomarkers were identified as signature sequences in CDT producer strains. The identified signatures include several individual phage proteins (holins, nucleases, and terminases, and transferases) and multiple members of different protein families (the lambda family, phage-integrase family, phage-tail tape protein family, putative membrane proteins, regulatory proteins, restriction-modification system proteins, tail fiber-assembly proteins, base plate-assembly proteins, and other prophage tail-related proteins). In this study, a sporadic phylogenic pattern was demonstrated in the CDT-producing strains. In conclusion, conserved signature proteins in a wide range of pathogenic bacterial strains can potentially be used in modern vaccine-design strategies.

• 농약과학회지
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• 제7권2호
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• pp.117-122
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• 2003

신농약 살균제를 개발할 목적으로 선도화합물 2-페닐이미노티아졸린 유도체 1의 분자수정을 통하여 새로운 화합물 히드록시에틸 2-이미노티아졸런 유도체 3을 모델링하고 합성하였다. 2-이미노티아졸린 유도체 3의 히드록시에틸기의 산소 원자는 인접기 참여를 통하여 2-이미노티아졸린 골격의 2 위치의 이미노탄소에 접근이 가능하며 따라서 그들의 생물활성에 영향을 줄 것으로 예상되었다. 감마-클로로아세토아세트아닐리드 유도체 5와 히드록시에틸티오우레아 6을 반응시켜 29종의 히드록시에틸 2-이미노티아졸린 유도체 3을 높은 수율로 합성하였다.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.70-70
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• 2003

Active sites and substrate bindings of 1-aminoxyclopropane-1-carboxylate oxidase (MD-ACO1) catalyzing the oxidative conversion of ACC to ethylene have been determined based on site-directed mutagenesis and comparative modeling methods. Molecular modeling based on the crystal structure of Isopenicillin N synthase (IPNS) provided MD-ACO1 structure. MD-ACO1 protein folds into a compact jelly roll shape, consisting of 9 ${\alpha}$-helices, 10 ${\beta}$-strands and several long loops. The MD-ACO1/ACC/Fe(II)/Ascorbate complex conformation was determined from automated docking program, AUTODOCK. The MD-ACO1/Fell complex model was consistent with well known binding motif information (HIS177-ASP179-HIS234). The cosubstrate, ascorbate is placed between iron binding pocket and Arg244 of MD-ACO1 enzyme, supporting the critical role of Arg244 for generating reaction product. These findings are strongly supported by previous biochemical data as well as site-directed mutagenesis data. The structure of enzyme/substrate suggests the structural mechanism for the biochemical role as well as substrate specificity of MD-ACO1 enzyme.

• 한국전기전자재료학회:학술대회논문집
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• 한국전기전자재료학회 2005년도 하계학술대회 논문집 Vol.6
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• pp.240-241
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• 2005

In this paper, Latin Hypercube Sampling based the neural network model for the electrical characteristics of $HfO_2$ thin films grown by metal organic molecular beam epitaxy was investigated. The accumulation capacitance and the hysteresis index are extracted to be the main responses to examine the characteristics of $HfO_2$ thin films. X-ray diffraction was used to analyze the characteristic variation for the different process conditions. The initial weights and biases are selected by Latin Hypercube Sampling method. This modeling methodology can allow us to optimize the process recipes and improve the manufacturability.

• 통합자연과학논문집
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• 제5권1호
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• pp.32-37
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• 2012

Chemokine receptor antagonists have potential applications in field of drug discovery. Although the chemokine receptors are G-protein-coupled receptors, their cognate ligands are small proteins (8 to 12 kDa), and so inhibiting the ligand/receptor interaction has been challenging. The application of structure-based in-silico methods to drug discovery is still considered a major challenge, especially when the x-ray structure of the target protein is unknown. Such is the case with human CCR2 and CCR5, the most important members of the chemokine receptor family and also a potential drug target. Herein, we review the success stories of combined receptor modeling/mutagenesis approach to probe the allosteric nature of chemokine receptor binding by small molecule antagonists for CCR2 and CCR5 using Rhodopsin as template. We also urged the importance of recently available ${\beta}2$-andrenergic receptor as an alternate template to guide mutagenesis. The results demonstrate the usefulness and robustness of in-silico 3D models. These models could also be useful for the design of novel and potent CCR2 and CCR5 antagonists using structure based drug design.

• 정보과학회 컴퓨팅의 실제 논문지
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• 제20권12호
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• pp.700-705
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• 2014

애너그램은 주어진 문자들을 재배열하여 숨겨진 단어를 찾아내는 철자바꾸기 놀이로, 문제를 빨리 풀어내는 사람들은 제약 만족 네트워크의 병렬적 탐색에 의해 문제를 해결한다. 본 연구에서는 이러한 인지적 현상을 모델링한 분자 애너그램 풀이 알고리즘을 제시하였다. 문자를 DNA 서열로 인코딩하고, 문자 DNA 가닥을 연결하여 바이그램과 단어 서열을 만들었다. DNA 혼성화, 연결, 젤 전기영동, 추출 연산을 수행해 문자와 바이그램 집합으로부터 답을 찾는 데 필요한 바이그램을 추출한 후, 추출한 바이그램과 단어 집합으로부터 다시 네 가지 DNA 연산을 반복하여 답을 찾는다. 분자 실험 결과 분자 컴퓨터는 정답인 단어와 오답인 단어를 구분해낼 수 있었다. 이를 통해 인간의 병렬적 사고과정을 분자 컴퓨터로 모델링할 수 있는 가능성을 보였다.

• Bulletin of the Korean Chemical Society
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• 제29권7호
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• pp.1311-1314
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• 2008

Bacillus halodurans O-methyltransferase (BhOMT) is an S-adenosylmethionine dependent methyltransferase. In our previous study, three dimensional structure of the BhOMT has been determined by comparative homology modeling and automated docking study showed that two hydroxyl groups at 3'- and 4'-position in Bring and structural rigidity of C-ring resulting from the double bond characters between C2 and C3 of flavonoid, were key factors for interaction with BhOMT. In the present study, BhOMT was cloned and expressed. Binding assay was performed on purified BhOMT using fluorescence experiments and binding affinity of luteolin, quercetin, fisetin, and myricetin were measured in the range of $10^7$. Fluorescence quenching experiments indicated that divalent cation plays a critical role on the metal-mediated electrostatic interactions between flavonoid and substrate binding site of BhOMT. Fluorescence study confirmed successfully the data obtained from the docking study and these results imply that hydroxyl group at 7-position of luteolin, quercetin, fisetin, and myricetin forms a stable hydrogen bonding with K211 and carboxyl oxygen of C-ring forms a stable hydrogen bonding with R170. Hydroxyl group at 3'-and 4'-position in the B-ring also has strong $Ca^{2+}$ mediated electrostatic interactions with BhOMT.

• 한국고분자학회:학술대회논문집
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• 한국고분자학회 2006년도 IUPAC International Symposium on Advanced Polymers for Emerging Technologies
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• pp.108-108
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• 2006

The role of conformational entropy of polymer chains in polymer crystallization is investigated by molecular modeling and theory. The entropy of folded loops dominates at experimentally relevant temperatures to dictate short equilibrium lamellar thicknesses, which are much smaller than the extended chain thickness. Also the entropic barriers control the kinetics of polymer crystallization. These results based on chain entropy are different from the classical views of how polymer chains crystallize.

• Communications for Statistical Applications and Methods
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• 제10권1호
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• pp.203-210
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• 2003

In a standard Metropolis-type Monte Carlo simulation, the proposal distribution cannot be easily adapted to "local dynamics" of the target distribution. To overcome some of these difficulties, Duane et al. (1987) introduced the method of hybrid Monte Carlo(HMC) which combines the basic idea of molecular dynamics and the Metropolis acceptance-rejection rule to produce Monte Carlo samples from a given target distribution. In this paper, using the HMC within Gibbs sampler, an asymptotical estimate of the smoothing mean and a general solution to state space modeling in Bayesian framework is obtaineds obtained.

• Applied Biological Chemistry
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• 제40권6호
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• pp.597-599
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• 1997