• Proceedings of the Korean Society for Bioinformatics Conference
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• 2004.11a
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• pp.250-261
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• 2004

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is introduced. This method utilizes secondary structure prediction information and fragment assembly. The secondary structure prediction of proteins is performed with the PREDICT method which uses PSI-BLAST to generate profiles and a distance measure in the pattern space. In order to predict the tertiary structure of a protein sequence, we assemble fragments in the fragment library constructed as a byproduct of PREDICT. The tertiary structure is obtained by minimizing the potential energy using the conformational space annealing method which enables one to sample diverse low lying minima of the energy function. We apply PROFESY for prediction of some proteins with known structures, which shows good performances. We also participated in CASP5 and applied PROFESY to new fold targets for blind predictions. The results were quite promising, despite the fact that PROFESY was in its early stage of development. In particular, the PROFESY result is the best for the hardest target T0161.

• BMB Reports
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• v.42 no.4
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• pp.189-193
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• 2009

During development lymphoid tissue inducer (LTi) cells are the first hematopoietic cells to enter the secondary lymphoid anlagen and induce lymphoid tissue neogenesis. LTi cells induce lymphoid tissue neogensis by expressing a wide range of proteins that are associated with lymphoid organogenesis. Among these proteins, membrane-bound lymphotoxin (LT) $\alpha1\beta2$ has been identified as a critical component to this process. LT$\alpha1\beta2$ interacts with the LT$\beta$-receptor on stromal cells and this interaction induces up-regulation of adhesion molecules and production of chemokines that are necessary for the attraction, retention and organization of other cell types. Constitutive expression of LT$\alpha1\beta2$ in adult LTi cells can result in the formation of a lymphoid-like structure called tertiary lymphoid tissue. In this review, we summarize the function of fetal and adult LTi cells and their involvement in secondary and tertiary lymphoid tissue development in murine models.

• Journal of KIISE:Computing Practices and Letters
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• v.6 no.1
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• pp.21-35
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• 2000

MIDAS-II is the storage system for BADA DBMS developed at ETRI. This paper describes the extension of MIDAS-II for incorporating the tertiary storage device such as an optical disk jukebox or a tape library, enabling MIDAS-II to function as a storage system of the data server that stores a massive amount of multimedia data. The MIDAS-II disk volume structure is extended to efficiently function as a volume for the tertiary storage device with multiple platters, which canstore huge amount of data of the order of tera bytes. The storage structure of the LOB is changed to efficiently manage the LOB data in the tertiary storage device. The data structures of the shared memory, the process structure, and the utilities in MIDAS-II are also extended to efficiently incorporating the tertiary storage device. The functionalities of each MIDAS-II API function are expanded to handle the tertiary storage device, while the prototypes of those functions are intact in order not to affect the existing application programs. The performance evaluation shows that the extended MIDAS-II works effectively with the tertiary storage device. All these extensions and the performance evaluation are conducted in the SunOS 5.4 environment.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.1
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• pp.41-49
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• 1998

A linear undecapeptide, Substance P (SP) is involved in a wide variety of physiological processes such as pain, inflammation, salivation, and hypertension. Tertiary structure of SP in dodecylphosphocholine (DPC) micelles has been investigated by CD, NMR spectroscopy, and DGII calculation. CD spectrum of SP in the presence of 7.5 mM DPC micelles does not show any favorable secondary structure. The tertiary structure determined by NMR spectroscopy and DGII calculation shows that the Phe7-Phr8-Gly9-Leu10 region adopts a turn structure, while the N-terminal region is quite flexible. Both prolines in SP exist preferentially as the trans isoforms and the aromatic ring of Phe7 protrudes outward. Conformation of SP may be restrained by the contact of the Phe7 aromatic ring with the hydrophobic side chains of the DPC micelles and this interaction induces a turn structure. Structure of SP in aqueous solution in the presence of DPC micelles can represent a good model to study the conformation recognized by the receptor near neutral membrane.

• Proceedings of the Korean Geotechical Society Conference
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• 2002.11b
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• pp.3-17
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• 2002

Tertiary Pohang basin distributed in south weatern part of the korean peninsula, is composed of Chunbuk formation as the basal conglomerate, Hakjon formation, Duho formation and intrusive basalt which is 15 Ma by absolute age data. The basement of the basin is represented by Cretaceous sedimentary rocks, Hakjon welded tuff and Chilpo welded tuff and rhyolite. The fault systems at the basement of the Pohang basin are consist of NNE direction fault, WNW to EW trend fault. NNE fault is not only strike-slip fault but also normal fault. n fault has sinistral strike-slip sene and the EW fault is strike-slip and normal fault. In the Tertiary basin, the fault system is represented by nm strike-slip fault, EW normal fault and NNE thrust fault. By these fault relationships and geometries, it is interpreted that NNE sinistral strike-slip fault and nomal fault have acted at Creceous times. At Tertiary tines, NNE dextralstrike-slip fault and EW normal fault has created. Progressively Tertiary Pohang basin was influenced by the trenspression to make thrust fault and fold, namely as inversion tectonics.

• Journal of KIISE:Computing Practices and Letters
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• v.5 no.6
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• pp.674-685
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• 1999

MIDAS-II는 한국전자통신연구원에서 개발한 바다 DBMS의 저장 시스템이다. MIDAS-II 볼륨은 데이터의 논리적 저장 단위인 파일을 저장하는 영역을 가리킨다. 본 논문에서는, MIDAS-II가 대용량 멀티미디어 데이터 서버의 저장 시스템으로 기능하도록 광 디스크 쥬크박스 또는 테이프 라이브러리와 같이 복수 개의 저장 매체 (platter , 예를 들어 디스크 또는 카트리지 테이프)로 구성된 Tera 바이트 급의 3창 저장 장치를 장착할 경우 이를 위한 볼륨 구조의 설계 및 구현에 대해 기술한다. 본 논문에서 제안하는 볼륨 구조는 3차 저장 장치 접근 시 성능 제고를 위하여 디스크 캐쉬 영역을 두고 있으며, 3차 저장 장치의 저장 매체별 관리 기능을 제공한다. Abstract MIDAS-II is the storage systemfor BADA DBMS developed at ETRI. A volume of MIDAS-II is the area where the files, the logical unit for storing data, are stored. This paaper describes the design and implementation of a new MIDAS-II volume structure for the tertiary storage device such as an optical disk juke box or a tape library equipped with multiple platters(disks or cartridge tapes, for example ). Incorporating thetertirary storage device of the order of tera bytes into MIDAS-II enables it to function as a storage system for a massive amount fo multimedia eata server. The volume structure for the tertiary storage device proposed in this paper features disk caching for performing improvement and direct control of theindividual platter.

• Bulletin of the Korean Chemical Society
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• v.19 no.5
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• pp.569-575
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• 1998

Investigation of the structure of the gangliosides has proven to be very important in the understanding of their biological roles. We have determined the tertiary structure of asialoganglioside GM1 $(GA_1)$ using NMR spectroscopy and distance geometry calculations. All of the structures are very similar except the glycosidic torsion angles in the ring IV and ring III linkages. There are two low-energy structures for GA1, G1 and G2. G1 differs from G2 only in the IV-III glycosidic linkages and the orientation of acetamido group in ring III. There is a stable intramolecular hydrogen bond between the third hydroxyl group in ring I and the ring oxygen atom in ring II. Also, there may be a weak hydrogen bond between the second hydroxyl group in ring IV and the acetamido group in ring III. Small coupling constants of $^3J_{IH3,IOH3}\; and\; ^3J_{IVH2,IVOH2}$ support this result. Overall structural features of $(GA_1)$ are very similar to those of $(GM_1)$. It implicates that specificities of the sugar moieties in GM1 are caused not by their tertiary foldings, but mainly by the electrostatic interactions between the polar sialic acid and its receptors. Since it is evident that $(GA_1)$ is more hydrophobic than $(GA_1)$, a receptor with a hydrophobic binding site can recognize the $(GA_1)$ better than $(GA_1)$. Studies on the conformational properties of $(GA_1)$ may lead to a better understanding of the molecular basis of its functions.

• Bulletin of the Korean Chemical Society
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• v.10 no.1
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• pp.12-15
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• 1989

Various tertiary amides have been subjected to the reduction by borane-THF in the presence of trimethyl borate at $0^{\circ}C$ and the product ratio of alcohol and amine have been analyzed in order to find out the possible way to obtain one product exclusively on the basis of the structure of amides. In the case of N,N-dimethyl derivatives of both linear aliphatic and aromatic amides the corresponding alcohols were produced predominantly. However, the bulkier tertiary amides such as N,N-diethyl and hindered acid derivatives afforded amines rather than alcohols. The mechanism of borane reduction of tertiary amides is also discussed.

• Journal of the Korean Magnetic Resonance Society
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• v.4 no.1
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• pp.41-49
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• 2000

To design more efficient peptide antagonist against the HBV, preSl(21-47) which carries the HBV receptor binding site for hepatocytes was synthesized and the solution structure of preSl(21-47) was investigated using CD spectroscopy and NMR spectroscopy in membrane-mimicking environments. According to CD spectra, preSl(21-47) has a random structure in aqueous solution, while conformational change was induced by addition of TFE and SDS micelle. Tertiary structures as determined by NMR spectroscopy shows that preSl(21-47) has a very flexible structure even in SDS micelle.

• Proceedings of the Zoological Society Korea Conference
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• 1998.10b
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• pp.271.2-271
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• 1998

No Abstract, See Full Text