• Genomics & Informatics
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• v.13 no.1
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• pp.15-24
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• 2015

Fatty acid synthase (FASN, EC 2.3.1.85), is a multi-enzyme dimer complex that plays a critical role in lipogenesis. This lipogenic enzyme has gained importance beyond its physiological role due to its implications in several clinical conditions-cancers, obesity, and diabetes. This has made FASN an attractive pharmacological target. Here, we have attempted to predict the theoretical models for the human enoyl reductase (ER) and ${\beta}$-ketoacyl reductase (KR) domains based on the porcine FASN crystal structure, which was the structurally closest template available at the time of this study. Comparative modeling methods were used for studying the structure-function relationships. Different validation studies revealed the predicted structures to be highly plausible. The respective substrates of ER and KR domains-namely, trans-butenoyl and ${\beta}$-ketobutyryl-were computationally docked into active sites using Glide in order to understand the probable binding mode. The molecular dynamics simulations of the apo and holo states of ER and KR showed stable backbone root mean square deviation trajectories with minimal deviation. Ramachandran plot analysis showed 96.0% of residues in the most favorable region for ER and 90.3% for the KR domain, respectively. Thus, the predicted models yielded significant insights into the substrate binding modes of the ER and KR catalytic domains and will aid in identifying novel chemical inhibitors of human FASN that target these domains.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.38 no.10
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• pp.1139-1145
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• 2014

Creation of a human skeleton model and characterization of the variation in the bone shape are fundamentally important in many applications of biomechanics. In this paper, we present a parametric shape modeling method for femurs that is based on extracting the main parameter of variations of the femur shape from a 3D model database by using statistical shape analysis. For this shape analysis, principal component analysis (PCA) is used. Application of the PCA to 3D data requires bringing all the models in correspondence to each other. For this reason, anatomical landmarks are used for guiding the deformation of the template model to fit the 3D model data. After subsequent application of PCA to a set of femur models, we calculate the correlation between the dominant components of shape variability for a target population and the anatomical parameters of the femur shape. Finally, we provide tools for visualizing and creating the femur shape using the main parameter of femur shape variation.

• KIPS Transactions on Software and Data Engineering
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• v.5 no.2
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• pp.69-78
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• 2016

Ischemic stroke is a disease that the brain tissues cannot function by reducing blood flow due to thrombosis or embolisms. Due to the nature of the disease, it is most important to identify the status of cerebral vessel and the medical images are necessarily used for its diagnosis. Among many indicators, brain MRI is most widely utilized because experts can effectively obtain the semantic information such as cerebral anatomy aiding the diagnosis with it. However, in case of emergency diseases like ischemic stroke, even though a intelligent system is required for supporting the prompt diagnosis and treatment, the current systems have some difficulties to provide the information of medical images intuitively. In other words, as the current systems have managed the medical images based on the basic meta-data such as image name, ID and so on, they cannot consider semantic information inherent in medical images. Therefore, in this paper, to provide core information like cerebral anatomy contained in brain MRI, we suggest a template-driven medical images mapping method. The key idea of the method is defining the mapping characteristics between anatomic feature and representative images by using template images that can be representative of the whole brain MRI image set and revealing the semantic relations that only medical experts can check between images. With our method, it will be possible to manage the medical images based on semantic.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.3
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• pp.147-154
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• 2018

This paper focuses on the development of a support system that can rapidly generate the design data of a hot-form die with cooling channels, commonly known as hot stamping technology. We propose a new process for designing hot-form dies based on our (automated) system, whose main features are derived from the analysis of the design requirements and design process in the current industry. Our design support system consists of two modules, which allow for the generation of a 3D geometry model and its 2D drawings. The module for 3D modeling automation is implemented as a type of CATIA template model based on CATIA V5 Knowledgeware. This module automatically creates a 3D model of a hot-form die, including the cooling channels, that depends on the shape of the forming surface and the number of STEELs (subsets of die product) and cooling channels. It also allows for both the editing of the positions and orientations of the cooling channels and testing for the purpose of satisfying the constraints on the distance between the forming surface and cooling channels. Another module for the auto-generation of the 2D drawings is being developed as a plug-in using CAA (CATIA SDK) and Visual C++. Our system was evaluated using the S/W test based on a user defined scenario. As a result, it was shown that it can generate a 3D model of a hot form die and its 2D drawings with hole tables about 29 times faster than the conventional manual method without any design errors.

• Journal of KIISE:Computing Practices and Letters
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• v.12 no.2
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• pp.129-140
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• 2006

The existing CBD development methods deal with the analysis phase in a superficial manner. Applying such a superficial analysis to business applications with a number of subsystems makes analysis models be inconsistent with levels and styles, only depending on experiences of the analysts. This inconsistent analysis might cause more serious problems during the subsequent development phases, resulting in the failure of the projects. In this paper, we propose a rule-based analysis pattern that provides an analysis template for business applications. This pattern analyzes the concepts of business applications by using external events and internal rules that process the events. Employing this pattern, a huge business application can be developed by a couple of co-analysts who work together in a consistent and systematic manner. This paper also describes an efficient way to develop business components with the suggested analysis pattern using banking deposit case study through UML Components development process.

• Bulletin of the Korean Chemical Society
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• v.33 no.8
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• pp.2508-2512
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• 2012

Cold shock proteins (CSPs) are a family of proteins induced at low temperatures. CSPs bind to single-stranded nucleic acids through the ribonucleoprotein 1 and 2 (RNP 1 and 2) binding motifs. CSPs play an essential role in cold adaptation by regulating transcription and translation via molecular chaperones. The solution nuclear magnetic resonance (NMR) or X-ray crystal structures of several CSPs from various microorganisms have been determined, but structural characteristics of psychrophilic CSPs have not been studied. Therefore, we optimized the purification process to obtain highly pure Lm-Csp and determined the three-dimensional structure model of Lm-Csp by comparative homology modeling using MODELLER on the basis of the solution NMR structure of Bs-CspB. Lm-Csp consists of a ${\beta}$-barrel structure, which includes antiparallel ${\beta}$ strands (G4-N10, F15-I18, V26-H29, A46-D50, and P58-Q64). The template protein, Bs-CspB, shares a similar ${\beta}$ sheet structure and an identical chain fold to Lm-Csp. However, the sheets in Lm-Csp were much shorter than those of Bs-CspB. The Lm-Csp side chains, E2 and R20 form a salt bridge, thus, stabilizing the Lm-Csp structure. To evaluate the contribution of this ionic interaction as well as that of the hydrophobic patch on protein stability, we investigated the secondary structures of wild type and mutant protein (W8, F15, and R20) of Lm-Csp using circular dichroism (CD) spectroscopy. The results showed that solvent-exposed aromatic side chains as well as residues participating in ionic interactions are very important for structural stability. Further studies on the three-dimensional structure and dynamics of Lm-Csp using NMR spectroscopy are required.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.277-287
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• 2003

Acetolactate synthase (ALS, EC 4.1.3.18; also referred to as acetohydroxy acid synthase) catalyzes the first common step in the biosynthesis of valine, leucine, and isoleucine in microorganisms and plants. Recently X-ray structure of yeast ALS was available. Pair-wise alignment of yeast and tobacco ALS sequences revealed 63% sequence similarity. Using Deep View and automatic modeling on Swiss model server, we have generated reliable models of tobacco ALS based on yeast ALS template with a calculated pair-wise RMSD of 0.86 Angstrom. Functional roles of four residues located on the subunit interface (H142, El43, M350, and R376) were examined by site-directed mutagenesis. Seven mutants were generated and purified, of which three mutants (H142T, M350V, and R376F) were found to be inactivated under various assay conditions. The H142k mutant showed moderately altered kinetic properties. The E143A mutant increased 10-fold in K$_m$ value while other parameters remained unchanged. The M350C mutant was strongly resistant to three tested herbicides, while the R376k mutant can bind with herbicide carder at similar affinity to that of wild type enzyme, as determined by tryptophan quenching study. Except M350V mutant, all other mutants were ate to bind with cofactor FAD. Taken together, it is likely that residues H142 and E143 are located at the active site, while residues M350 and R376 are possibly located at the overlapping region of active site and herbicide binding site of the enzyme. Our data also allows us to hypothesize that the interaction between side chains of residues M350 and R376 are probably essential for the correct conformation of the active site. It remains to be elucidated that, whether the herbicide, upon binding with enzyme, inactivates the enzyme by causing change in the active site allosterically, which is unfavorable for catalytic activity.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.14 no.10
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• pp.5169-5175
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• 2013

We present a framework for 3D hand gesture design and modeling. We adapted two different pattern matching techniques, Dynamic Time Warping (DTW) and Hidden Markov Models (HMMs), to support the registration and evaluation of 3D hand gestures as well as their recognition. One key ingredient of our framework is a concept for the convenient gesture design and registration using HMMs. DTW is used to recognize hand gestures with a limited training data, and evaluate how the performed gesture is similar to its template gesture. We facilitate the use of visual sensors and body sensors for capturing both locative and inertial gesture information. In our experimental evaluation, we designed 18 example hand gestures and analyzed the performance of recognition methods and gesture features under various conditions. We discuss the variability between users in gesture performance.

• Korean Journal of Computational Design and Engineering
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• v.19 no.2
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• pp.138-147
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• 2014

In manufacturing companies, different types of production have been developed based on diverse production strategies and differentiated technologies. The production systems have become smart, factories are filled with unmanned manufacturing lines, and sustainable manufacturing technologies are under development. Nowadays, the digital manufacturing technology is being adopted and used in manufacturing industries. When this technology is applied, a lot of efforts, time and cost are required and training professionals in-house is limited. In this paper, we introduce e-FEED system (electronic based Front End Engineering and Design) that is the integrated design and analysis system for optimized manufacturing line development on virtual environment. This system provides the functions that can be designed easily using library and template based on standardized modules and analyzed automatically the logistic and capacity simulation by one-click and verified the result using visual reports. Also, we can review the factory layout using automatically created 3D virtual factory and increase the knowledge reuse by e-FEED system.

• BMB Reports
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• v.45 no.5
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• pp.275-280
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• 2012

Nicotinic acetylcholine receptors (nAChRs) are a diverse family of homo- or heteropentameric ligand-gated ion channels. Understanding the physiological role of each nAChR subtype and the key residues responsible for normal and pathological states is important. ${\alpha}$-Conotoxin neuropeptides are highly selective probes capable of discriminating different subtypes of nAChRs. In this study, we performed homology modeling to generate the neuronal ${\alpha}3$, ${\beta}2$ and ${\beta}4$ subunits using the x-ray structure of the ${\alpha}1$ subunit as a template. The structures of the extracellular domains containing ligand binding sites in the ${\alpha}3{\beta}2$ and ${\alpha}3{\beta}4$ nAChR subtypes were constructed using MD simulations and ligand docking processes in their free and ligand-bound states using ${\alpha}$-conotoxin GIC, which exhibited the highest ${\alpha}3{\beta}2$ vs. ${\alpha}3{\beta}4$ discrimination ratio. The results provide a reasonable structural basis for such a discriminatory ability, supporting the idea that the present strategy can be used for future investigations on nAChR-ligand complexes.