• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.35-38
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• 2000

An early step toward evaluating a predicted RNA secondary structure is to visualize the predicted structure in graphical form. This talk will present an algorithm for efficiently drawing RNA secondary structures. The algorithm represents the direction and space for a structural element using vector and vector space, and generates nearly overlap-free polygonal displays. The algorithm and a graphical user interface have been implemented in a working program called VizQFolder on IBM PC compatibles.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.133-138
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• 2003

The prediction of protein secondary structure has been an important bioinformatics tool that is an essential component of the template-based protein tertiary structure prediction process. It has been known that the predicted secondary structure information improves both the fold recognition performance and the alignment accuracy. In this paper, we describe several novel ideas that may improve the prediction accuracy. The main idea is motivated by an observation that the protein's structural information, especially when it is combined with the evolutionary information, significantly improves the accuracy of the predicted tertiary structure. From the non-redundant set of protein structures, we derive the 'potential' parameters for the protein secondary structure prediction that contains the structural information of proteins, by following the procedure similar to the way to derive the directional information table of GOR method. Those potential parameters are combined with the frequency matrices obtained by running PSI-BLAST to construct the feature vectors that are used to train the support vector machines (SVM) to build the secondary structure classifiers. Moreover, the problem of huge model file size, which is one of the known shortcomings of SVM, is partially overcome by reducing the size of training data by filtering out the redundancy not only at the protein level but also at the feature vector level. A preliminary result measured by the average three-state prediction accuracy is encouraging.

• 대한화학회지
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• 제42권2호
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• pp.161-171
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• 1998

알켄-오존 반응에서 생성된 중간 생성물로써 primary ozonide (POZ),secondary ozonide (SOZ)그리고 carbonyl oxide의 분자구조, vibrational frequencies그리고 infrared(IR)스펙트럼의 세기 등에 대한 이론적 연구를 high level ab initio 양자역학적 방법(CISD,CCSD)을 사용하여 수행하였다. 일반적으로, polarization function은 결합각과 결합길이를 감소시키는 경향을 보였고 반면, electron correlation effect는 결합길이와 결합각을 약간 증가시키는 경향을 보이고 있다. Carbonyl oxide의 분자구조는 zwitterionic form이 diradical form보다 더 안정한 것으로 예측되었으며, 두 형태의 에너지는 차이는 TZ2P CISD level에서 약 22.4 kcal/mol인 것으로 계산되었다. 또한, POZ과 SOZ의 분자구조 및 harmonic vibrational frequencies들을 실험결과와 비교 분석하였으며 IR세기에 근거하여 각 vibrational mode를 assign 하였다.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.65-65
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• 2003

After many genome projects, algorithms and software to process explosively growing biological information have been developed. To process huge amount of biological information, high performance computing equipments are essential. If we use the remote resources such as computing power, storages etc., through a Grid to share the resources in the Internet environment, we will be able to obtain great efficiency to process data at a low cost. Here we present the performance improvement of the protein secondary structure prediction (PSIPred) by using the Grid platform, distributing protein sequence data on the Grid where each computer node analyzes its own part of protein sequence data to speed up the structure prediction. On the Grid, genome scale secondary structure prediction for Mycoplasma genitalium, Escherichia coli, Helicobacter pylori, Saccharomyces cerevisiae and Caenorhabditis slogans were performed and analyzed by a statistical way to show the protein structural deviation and comparison between the genomes. Experimental results show that the Grid is a viable platform to speed up the protein structure prediction and from the predicted structures.

• 한국자기공명학회논문지
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• 제16권2호
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• pp.162-171
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• 2012

SAV2228 has an OB (Oligomer-Binding)-motif which is frequently used for nucleic acid recognition. To characterize the activity of translation initiation factor-1 (IF-1) from Staphylococcus aureus, SAV2228 was expressed and purified in Escherichia coli. We acquired 3D NMR spectra showing well dispersed and homogeneous signals which allow us to assign 94.4% of all $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$ and $^{13}CO$ resonances. We could predict a secondary structure of SAV2228 using TALOS and CSI from NMR data. SAV2228 was consisted of one ${\alpha}$-helix and five ${\beta}$-sheets. The predicted secondary structure, ${\beta}-{\beta}-{\beta}-{\alpha}-{\beta}-{\beta}$, was similar to other bacterial IF-1, but it was not completely same to the eukaryotic one. Assigned NMR peaks and secondary structre prediction can be used for the study on interaction with nucleic acid in the future.

• 한국전산유체공학회지
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• 제10권1호
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• pp.63-66
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• 2005

A computational fluid dynamics(CFD) analysis has been made for fully developed turbulent flow in a triangular bare rod bundle with a pitch to diameter ratio (P/D) of 1.123. The nonlinear turbulence models predicted the turbulence-driven secondary flow in the triangular subchannel. The nonlinear quadratic κ-ε models by Speziale[1] and Myong-Kasagi[2] predicted turbulence structure in the rod bundle fairly well. The nonlinear quadratic and cubic k-ε models by Shih et al.[3] and Craft et al.[4] showed somewhat weaker anisotropic turbulence. The differential Reynolds stress model by Launder et al.[5} appeared to over predict the turbulence anisotropy in the rod bundle.

• 한국전산유체공학회:학술대회논문집
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• 한국전산유체공학회 2003년도 The Fifth Asian Computational Fluid Dynamics Conference
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• pp.71-73
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• 2003

A CFD analysis has been made for fully developed turbulent flows in a triangular bare rod bundle with pitch to diameter ratio (P/D) of 1.123. The nonlinear turbulence models predicted the turbulence­driven secondary flow in the triangular subchannel. The nonlinear quadratic $\kappa-\omega$ models by Speziale and Myong-Kasagi predicted turbulence structure in the rod bundle fairly well. The nonlinear quadratic and cubic $\kappa-\omega$ models by Shih et al. and Craft et al. showed somewhat weaker anisotropic turbulence. The differential Reynolds stress model appeared to overpredict the turbulence anisotropy in the rod bundle.

• 대한기계학회:학술대회논문집
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• 대한기계학회 2003년도 추계학술대회
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• pp.598-603
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• 2003

A CFD analysis has been performed to investigate turbulent heat transfer in a triangular rod bundle with a pitch-to-diameter ratio(P/D) of 1.06. Anisotropic turbulence models predicted the turbulence-driven secondary flow in the triangular subchannel and the distributions of time mean velocity and temperature showing significantly improved agreement with the measurements over the linear standard ${\kappa}-{\varepsilon}$. The anisotropic turbulence models predicted turbulence structure in large flow region fairly well but could not predict the very high turbulent intensity of azimuthal velocity observed in narrow flow region(gap).

• Nuclear Engineering and Technology
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• 제36권2호
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• pp.153-164
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• 2004

A computational fluid dynamics (CFD) analysis has been performed to investigate the turbulent flow and heat transfer in a triangular rod bundle with pitch-to-diameter ratios (P/D) of 1.06 and 1.12. Anisotropic turbulence models predicted the turbulence-driven secondary flow in a triangular subchannel and the distributions of the time mean velocity and temperature, showing a significantly improved agreement with the measurements from the linear standard $k-{\epsilon}$ model. The anisotropic turbulence models predicted the turbulence structure for a rod bundle with a large P/D fairly well, but could not predict the very high turbulent intensity of the azimuthal velocity observed in the narrow flow region (gap) for a rod bundle with a small P/D.

• 한국동물학회:학술대회논문집
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• 한국동물학회 1998년도 공동 춘계학술대회
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• pp.37.1-37
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• 1998

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