• Proceedings of the Korea Information Processing Society Conference
• /
• 2002.11c
• /
• pp.2403-2406
• /
• 2002

현재의 단백질 구조비교 시스템들 사이의 호환성이나 상호작용성의 문제를 해결하고 단백질 구조를 비교하는 시스템을 신속히 개발하기 위해서 단백질 3차구조를 표현하기 위한 데이터를 추출하여 XML과 같은 표준 형식으로 기술된 데이터를 제공하는 것이 바람직하다. 이에 따라 단백질의 2차구조 구성요소와 그들 사이의 관계를 이용하여 단백질 구조를 기술하는 PSA가 제안되었으며, PSA를 기반으로 하여 단백질 데이터의 XML 표현기법인 PSAML이 제안되었다. 본 논문에서는 PSAML 데이터의 생성을 위하여 PDB에서 제공되는 데이터를 PSAML 형식으로 변환시키는 도구를 설계하고 구현하였다. 변환도구는 XML DOM과 Java를 이용하여 구현되었으며, 생성된 데이터는 단백질 구조 및 유사성을 비교하기 위한 단백질 구조비교 시스템에서 사용될 수 있다.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
• /
• 2005.04a
• /
• pp.211-214
• /
• 2005

Bench-scale experiments conducted to evaluation of the biostimulation and bioaugmentation techniques in treatment of petroleum contaminated soil. The soil bioreactors were operated for a 52 day-period. PDB population in the stimulated treatments increased from $7{\times}10^4MPN/g$ soil in zero day to $7{\times}10^7MPN/g$ soil after 23 days. However, despite the initially higher PDB population in the augmented treatments, it was decreased PDB population with respect to time. The average biodegradation rate in the augmented treatments were greater than of the stimulated treatment in the early stage, but the average biodegradation rate in the latter stage were calculated $3{\sim}5mg/kg-day$ in the augmented treatments and 10.38mg/kg-day in the stimulated treatments. The TPH removal rate was calculated $20{\sim}30%$ in the augmented treatments and 53% in the stimulated treatments.

• Journal of KIISE:Information Networking
• /
• v.29 no.6
• /
• pp.706-711
• /
• 2002

In this paper, we implement a diffserv-capable router on the linux system and evaluate its performance. The router supports the packet marking for the input finks that is different from the previous implementation. The edge diffserv-capable router can guarantee the performance of each class, even in a congested condition. We compare the performance of the diffserv-capable router with that of the normal router in terms of PDBs (per domain behaviors), which are defined with traffic conditioning rules and PHBs (per hop behaviors).

• 한국해양학회지
• /
• v.29 no.2
• /
• pp.164-170
• /
• 1994

The well preserved ostracodes of the Chunbuk Formation in Pohang Basin were analyzed isotopically to understand paleoceanographic conditions of the southeastern park of Korean peninsula which Songhacdong, and Mulcheonri areas range from - 2.2 to - 0.7% (PDB), - 0.7 to 0.0% , and -20.0 to - 0.8%, and their corresponding paleotemperatures range from ca 20 to 27$^{\circ}C$ (average = 24$^{\circ}C$), 17 to 20$^{\circ}C$ (average = 18$^{\circ}C$), and 20 to 26$^{\circ}C$ (average=23$^{\circ}C$),respectively. Assuming the $\delta$/SUP 18/O composition of the Middle Miocene seawater was about - 0.34% (SMOW), the paleotemperatures of the Middle Miocene shallow seawater in the Pohang Basin was almost equal to or slightly higher than the present summer temperature (ca 16 to 20$^{\circ}C$) near Pohang area. Carbon isotopic value of Cyhere omotenipponica is - 0.8% (PDB), reflecting marine carbonate carbon composition. Carbon isotopic compositions of other ostracodes such as Aurial okumurai, Trachyleberis niitsmai, Urocythereis sp., Urocythereis cf. gorokuensis, and Acanthocythereis mutsuensis range from - 5.2 to - 3.4% (PDB), which might have secreted their shells out of equilibrium with ambient seawater. This disequilibrium was most likely to have resulted from metabolic (=vital) effect, rather than temperature of productivity.

• Proceedings of the Korean Geotechical Society Conference
• /
• 2003.03a
• /
• pp.761-766
• /
• 2003

In environmental and economical views Plastic Board Drain(PBD) has many problems which is generally used in improving soft grounds. In order to improve these, Rags drain and Sponge drain are developed in this study, and the application to drains is presented though comparing with PDB and Sand drain In consolidation effects. Test results show that the consolidation effects, including consolidation rate and stregth, increase in order of Sand and Rags, PDB and Sponge drain.

• Journal of the Korean Geosynthetics Society
• /
• v.7 no.4
• /
• pp.37-45
• /
• 2008

A pilot test using environmentally friendly drains, was carried out to evaluate their applicability potential in the field. The pilot test site was divided into 5 different areas, with several combinations of vertical and horizontal drains installed for evaluation. Conventional natural fiber drains (FDB), new developed straw drain board (SDB) and plastic drain board (PDB) were used as vertical drains, while sand and fiber mats were used as horizontal drains. Surface settlement rates and excess pore pressure generation/dissipation tendency of PDB and FDB are almost identical except those of SDB. Cone tip resistance obtained from cone penetration test measured at the end of 1st consolidation stage for upper soft layer definitely increased irrespective of types of vertical drains. The monitoring and site investigation test data obtained at the pilot test site prove the vertical natural fiber drains can be used as substitutes of conventional plastic and sand material.

• Proceedings of the Korean Information Science Society Conference
• /
• 2003.10b
• /
• pp.826-828
• /
• 2003

이제까지 Protein이나 RNA와 같은 분자의 구조는, 대부분 X-ray crystallography나 Nuclear Magnetic Resonance (NMR) 방법을 통해 분석이 이루어 졌다. 이 방법들은 실제 분자를 직접 원자레벨에서 분석하는 방법으로, 분자를 구성하는 모든 원자의 3차원 좌표 정보를 얻어 낼 수 있다. 원자의 3차원 좌표 정보는 분자의 전체적인 모양과 구조를 이해하는데 유용한 정보이다. 하지만, 분자의 구조를 좀 더 완벽히 이해하기 위해서는 원자 레벨의 좌표 정보 보다는 좀 더 높은 차원에서의 구조 정보가 필요하다. 특히 분자의 구조를 예측하거나, 분자들 사이에 결합 관계를 예측하기 위해서는, 원자 레벨의 정보만으로는 필요한 모든 정보를 얻을 수 없다. 이러한 경우, 분자의 2차원 또는 3차원 구조 요소 (structural elements)가 더욱 좋은 정보를 제공해 줄 수 있다. Protein 분자의 경우. 이미 3차원 좌표 정보를 이용해서, 2차원 구조 요소를 알아내는 자동화된 방법이 알려져 있다. 그러나 RNA의 경우 protein에 비해 알려진 결정 구조가 적기 때문에. 아직까지 2차원 구조 요소나 3차원 구조 요소를 알아내는 자동화된 방법이 알려져 있지 않다. 따라서, 이제까지는 RNA의 구조 요소를 알아내기 위해, 사람이 직접 RNA분자의 3차원 좌표 정보를 분석함으로써 많은 시간과 노력이 필요했다. 이 때문에, 우리는 RNA의 원자들의 3차원 좌표 정보를 이용해서, 2차원 구조요소와 3차원 구조 요소 정보를 자동화된 방법으로 밝혀내는 알고리즘을 개발하였다. 우리는 분자를 구성하고 있는 원자들의 3차원 좌표 정보를 Protein data bank (PDB)에서 가져왔다. 우리의 알고리즘은 PDB file형태의 데이터라면 protein-RNA 복합체나 RNA 분자 모두에서 RNA의 2차원 구조 요소나 3차원 구조 요소를 얻어낼 수 있다. 우리의 연구는 RNA의 원자레벨의 3차원 좌표 정보를 이용해서 RNA의 구조 요소를 뽑아내는 첫 번째 시도로, 우리의 알고리즘을 통해 얻어진 구조 정보는 RNA의 구조 예측 연구나. protein-RNA complex의 결합 예측 연구에 많은 도움을 줄 수 있으리라 기대된다.

• Applied Biological Chemistry
• /
• v.50 no.1
• /
• pp.77-81
• /
• 2007

In order to minimize the mycelial pellet size of a high phosphate-solubilizing fungus, Aspergillus sp. PS-104 in liquid media, one of the critical obstacles during the submerged culture of filamentous fungi, an investigation was focused on the culture conditions (media and inoculum size) and additives (different soils, surfactants and polyethylene glycol 200). When the fungus was cultured in PDB, SDB and YPD media. their pellet sizes decreased in the order of SDB=YPD>PDB. At the higher concentrations of initial inoculum ranging from $1{\times}10^3$ to $1{\times}10^7$ conidia/ml, the smaller size of pellet was formed in the PDB medium. In addition, the pellet size was effectively reduced by 1/6${\sim}$1/4 by the addition of 0.1% soil containing zeolite, diatomite, loess, kaoline and talc, excluding bentonite. The addition of 0.1% Tween 80, Triton X-100 and PEG 200 also decreased the pellet size, but SDS completely inhibited the fungal growth.

• Korean Journal of Microbiology
• /
• v.30 no.3
• /
• pp.187-192
• /
• 1992

The spatial and temporal distribution of petroleum-degrading bacteria(PDB) was studied at six sampling sites in Kyeonggi Bay of the Yellow Sea fiom March 1990 to October 1991. In addition, petroleum-degrading potcntial of natural ~iiai-ineb acterial population was studied at different culturc contlitions. During the period o f stutly. thc heterotrophic bacterial number and PDB number were n1e;rsured in the range of 7 000-108.400 CFU/nil. 0-2.800 MPN1100 mi. respectively. The spatial tlistribution of PDB wa\ highly affected by presence of petroleum hydrocarbon. In laboratory cxperirncnt. petrolcu~n biodegradation wac enhanced hy addition of yeast cxtracl. cell free cxtr:~ct. anti rnixctl culture of PI)B.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2005.09a
• /
• pp.325-330
• /
• 2005

We are generally interested in the analysis, detection and prediction of structural motifs in proteins, in order to infer compatibility of amino acid sequence to structure in proteins of known three-dimensional structure available in the Protein Data Bank. In this context, we are analyzing some of the well-characterized structural motifs in proteins. We have analyzed simple structural motifs, such as, ${\beta}$-turns and ${\gamma}$-turns by evaluating the statistically significant type-dependent amino acid positional preferences in enlarged representative protein datasets and revised the amino acid preferences. In doing so, we identified a number of ‘unexpected’ isolated ${\beta}$-turns with a proline amino acid residue at the (i+2) position. We extended our study to the identification of multiple turns, continuous turns and to peptides that correspond to the combinations of individual ${\beta}$ and ${\gamma}$-turns in proteins and examined the hydrogen-bond interactions likely to stabilize these peptides. This led us to develop a database of structural motifs in proteins (DSMP) that would primarily allow us to make queries based on the various fields in the database for some well-characterized structural motifs, such as, helices, ${\beta}$-strands, turns, ${\beta}$-hairpins, ${\beta}$-${\alpha}$-${\beta}$, ${\psi}$-loops, ${\beta}$-sheets, disulphide bridges. We have recently implemented this information for all entries in the current PDB in a relational database called ODSMP using Oracle9i that is easy to update and maintain and added few additional structural motifs. We have also developed another relational database corresponding to amino acid sequences and their associated secondary structure for representative proteins in the PDB called PSSARD. This database allows flexible queries to be made on the compatibility of amino acid sequences in the PDB to ‘user-defined’ super-secondary structure conformation and vice-versa. Currently, we have extended this database to include nearly 23,000 protein crystal structures available in the PDB. Further, we have analyzed the ‘structural plasticity’ associated with the ${\beta}$-propeller structural motif We have developed a method to automatically detect ${\beta}$-propellers from the PDB codes. We evaluated the accuracy and consistency of predicting ${\beta}$ and ${\gamma}$-turns in proteins using the residue-coupled model. I will discuss results of our work and describe databases and software applications that have been developed.