• Archives of Pharmacal Research
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• v.25 no.6
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• pp.807-816
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• 2002

Dihydrofolate reductases (DHFR) of human, Candida albicans and E. coli were docked with their original ligands of X-ray crystal complex using QXP (Quick eXPlore), a docking program. Conditions to reproduce the crystal structures within the root mean square deviation (rmsd) of 2.00 $\AA$ were established. Applying these conditions, binding modes and species-specificities of a novel antibacterial compound, $N^4-(2-acetoxyethoxymethyl)-2-acetylpyridine$ thiosemicarbazone (MTSC), were studied. As the results, the docking program reproduced the crystal structures with average rmsd of six ligands as 0.91 $\AA$ ranging from 0.49 to 1.45 $\AA$. The interactions including the numbers of hydrogen bonds and hydrophobic interactions were the same as the crystal structures and superposition of the crystal and docked structures almost coincided with each other. For AATSC, the results demonstrated that it could bind to either the substrate or coenzyme sites of DHFR in all three species with different degrees of affinity. It confirms the experimentally determined kinetic behavior of uncompetitive inhibition against either the inhibitor or the coenzyme. The docked MTSC overlapped well with the original ligands and major interactions were consistent with the ones in the crystal complexes. The information generated from this work should be useful for future development of antibacterial and antifungal agents.

• Journal of the Korean Chemical Society
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• v.54 no.1
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• pp.71-76
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• 2010

The densities and viscosities of 2-bromopropane-methanol binary mixtures had been determined using an digital vibrating U-tube densimeter and Ubbelohde capillary viscometer respectively from (298.15 to 318.15) K. The dependence of densities and viscosities on temperature and concentration had been correlated. The excess molar volume and the excess viscosity of the binary system were calculated from the experimental density and viscosity data. The excess molar volumes were related to compositions by polynomial regression and regression parameters and total RMSD deviations were obtained; the excess viscosities was related to compositions by Redlich-Kister equation and regression coefficients and total RMSD deviation of the excess viscosity for 2-bromopropane and methanol binary system were obtained. The results showed that the model agreed very well with the experimental data.

• Proceedings of the Computational Structural Engineering Institute Conference
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• 2006.04a
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• pp.240-247
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• 2006

Piezoelectric sensor-based health monitoring technique using a two-step support vector machine (SYM) classifier is discussed for damage identification of a railroad track. An active sensing system composed of two PZT patches was investigated in conjunction with both impedance and guided wave propagation methods to detect two kinds of damage of the railroad track (one is a hole damage of 0.5cm in diameter at web section and the other is a transverse cut damage of 7.5cm in length and 0.5cm in depth at head section). Two damage-sensitive features were extracted one by one from each method; a) feature I: root mean square deviations (RMSD) of impedance signatures and b) feature II: wavelet coefficients for $A_0$ mode of guided waves. By defining damage indices from those damage-sensitive features, a two-dimensional damage feature (2-D DF) space was made. In order to minimize a false-positive indication of the current active sensing system, a two-step SYM classifier was applied to the 2-D DF space. As a result, optimal separable hyper-planes were successfully established by the two-step SYM classifier: Damage detection was accomplished by the first step-SYM, and damage classification was also carried out by the second step-SYM. Finally, the applicability of the proposed two-step SYM classifier has been verified by thirty test patterns.

• Proceedings of the Korean Society of Surveying, Geodesy, Photogrammetry, and Cartography Conference
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• 2010.04a
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• pp.253-255
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• 2010

Needs to study on distance measurement accuracy in aerial and satellite photogrammetry are rapidly increased. However, conventional studies show some confused definitions between measurement accuracy and measurement precision as well as standard deviation(STDEV) and root mean square error(RMSE or RMSD). So, Finite definitions of measurement accuracy and measurement precision as well as STDEV and RMSD are addressed in this paper. Experiment result show using correct definitions improve the distance measurement accuracy in aerial and satellite photogrammetry rapidly, but not the distance measurement accuracy in aerial and satellite photogrammetry.

• Atmosphere
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• v.28 no.2
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• pp.141-151
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• 2018

The KIAPS global model and data assimilation system were extended to assimilate brightness temperature from the Sondeur $Atmosph{\acute{e}}rique$ du Profil $d^{\prime}Humidit{\acute{e}}$ Intertropicale par $Radiom{\acute{e}}trie$ (SAPHIR) passive microwave water vapor sounder on board the Megha-Tropiques satellite. Quality control procedures were developed to assess the SAPHIR data quality for assimilating clear-sky observations over the ocean, and to characterize observation biases and errors. In the global cycle, additional assimilation of SAPHIR observation shows globally significant benefits for 1.5% reduction of the humidity root-mean-square difference (RMSD) against European Centre for Medium-Range Weather Forecasts (ECMWF) Integrated Forecast System (IFS) analysis. The positive forecast impacts for the humidity and temperature in the experiment assimilating SAPHIR were predominant at later lead times between 96- and 168-hour. Even though its spatial coverage is confined to lower latitudes of $30^{\circ}S-30^{\circ}N$ and the observable variable is humidity, the assimilation of SAPHIR has a positive impact on the other variables over the mid-latitude domain. Verification showed a 3% reduction of the humidity RMSD with assimilating SAPHIR, and moreover temperature, zonal wind and surface pressure RMSDs were reduced up to 3%, 5% and 7% near the tropical and mid-latitude regions, respectively.

• Journal of KIISE:Databases
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• v.34 no.5
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• pp.396-408
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• 2007

After the Human Genome Project finished the sequencing of a human DNA sequence, the concerns on protein functions are increasing. Since the structures of proteins are conserved in divergent evolution, their functions are determined by their structures rather than by their amino acid sequences. Therefore, if similarities between two protein structures are observed, we could expect them to have common biological functions. So far, a lot of researches on protein structure alignment have been performed. However, most of them use RMSD(Root Mean Square Deviation) as a similarity measure with which it is hard to judge the similarity level of two protein structures intuitively. In addition, they retrieve only one result having the highest alignment score with which it is hard to satisfy various users of different purpose. To overcome these limitations, we propose a novel protein structure alignment algorithm based on MRPD(Maximum of Residue Pair Distance) and SG (Similarity Graph). MRPD is more intuitive similarity measure by which fast tittering of unpromising pairs of protein pairs is possible, and SG is a compact representation method for multiple alignment results with which users can choose the most plausible one among various users' needs by providing multiple alignment results without compromising the time to align protein structures.

• Journal of the Korea institute for structural maintenance and inspection
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• v.14 no.6
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• pp.171-178
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• 2010

Pipeline structure is one of core underground infrastructure which transports primary sources. Since the almost pipeline structures are placed underground and connected each other complexly, it is difficult to monitor their structural health condition continuously. In order to overcome this limitation of recent monitoring technique, recently, a Ubiquitous Sensor Network (USN) system based on on-line and real-time monitoring system is being developed by the authors' research group. In this study, real-time pipeline health monitoring (PHM) methodology is presented based on electromechanical impedance methods using USN. Two types of damages including loosened bolts and notches are artificially inflicted on the pipeline structures, PZT and MFC sensors that have piezoelectric characteristics are employed to detect these damages. For objective evaluation of pipeline conditions, Damage metric such as Root Mean Square Deviation (RMSD) value was computed from the impedance signals to quantify the level of the damage. Optimal threshold levels for decision making are estimated by generalized extreme value(GEV) based statistical method. Throughout a series of experimental studies, it was reviewed the effectiveness and robustness of proposed PHM system.

• Proceedings of the Korean Society for Noise and Vibration Engineering Conference
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• 2006.11a
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• pp.603-606
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• 2006

We present a study on the development of a practical and quantitative technique for the assessment of the structural health condition with using piezoceramic(PZT) sensors. The electro-impedance-based technique with the PZT patches is very sensitive for evaluation of the incipient and small damage in a high frequency range, and however the commonly traditional modal analysis method is effective only for considerably larger damages in low frequency range. The paper presents the technique in detecting and characterizing real-time damage on the specimen that is an aluminum plate fastened with bolts and nuts by different torques and as well a plate with a crack. By using the special arrangement of the PZT sensors, the required longitudinal wave is generated through the specimen. A large number of experiments are conducted and the different conditions of the specimens, i.e. the location and extent of loosening bolts, and the plate with a crack are simulated. respectively. Since fixing and loosening the loosened bolt is controlled by a torque wrench, we can control exactly the experiment of the different torques. Compared with the simulated healthy condition, we can find whether or not there is a damage in the specimen with using an impedance analyzer with the PZT sensors. Several indices are discussed and used for assessing the different simulated damages. As for the location of bolt loosening, the RMSD is found to be the most appropriate index for numerical assessment and as well the RMSD shows strongly linear relationship for assessing the extent of the bolt loosening, and the frequency peak shift ${\Delta}F$ is used to assess the cracked plate. The possibility of repeatability of the pristine condition signatures is also presented and the appropriate frequency range and interval are uniquely selected through large numbers of experiments.

• Journal of Biosystems Engineering
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• v.43 no.2
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• pp.103-109
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• 2018

Purpose: This study has been conducted to develop a potato yield monitoring system, consisting of a segmentation algorithm to detect potatoes scattered on a soil surface and a counting system to count the number of potatoes and convert the data from two-dimensional images to masses. Methods: First, a segmentation algorithm was developed using top-hat filtering and processing a series of images, and its performance was evaluated in a stationary condition. Second, a counting system was developed to count the number of potatoes in a moving condition and calculate the mass of each using a mass estimation equation, where the volume of a potato was obtained from its two-dimensional image, and the potato density and a correction factor were obtained experimentally. Experiments were conducted to segment potatoes on a soil surface for different potato sizes. The counting system was tested 10 times for 20 randomly selected potatoes in a simulated field condition. Furthermore, the estimated total mass of the potatoes was compared with their actual mass. Results: For a $640{\times}480$ image size, it took 0.04 s for the segmentation algorithm to process one frame. The root mean squared deviation (RMSD) and average percentage error for the measured mass of potatoes using this counting system were 12.65 g and 7.13%, respectively, when the camera was stationary. The system performance while moving was the best in L1 (0.313 m/s), where the RMSD and percentage error were 6.92 g and 7.79%, respectively. For 20 newly prepared potatoes and 10 replication measurements, the counting system exhibited a percentage error in the mass estimation ranging from 10.17-13.24%. Conclusions: At a travel speed of 0.313 m/s, the average percentage error and standard deviation of the mass measurement using the counting system were 12.03% and 1.04%, respectively.

• The KIPS Transactions:PartD
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• v.12D no.2 s.98
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• pp.247-258
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• 2005

Protein structure is highly related to its function and comparing protein structure is very important to identify structural motif, family and their function. In this paper, we construct an integrated database system which has all the protein structure data and their literature. The structure queries from the web interface are compared with the target structures in database, and the results are shown to the user for future analysis. To constructs this system, we analyze the Flat-File of Protein Data Bank. Then we select the necessary structure data and store as a new formatted data. The literature data related to these structures are stored in a relational database to query the my kinds of data easily In our structure comparison system, the structure of matched pattern and RMSD valure are calculated, then they are showed to the user with their relational documentation data. This system provides the more quick comparison and nice analyzing environment.