• The KIPS Transactions:PartA
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• v.16A no.3
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• pp.153-158
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• 2009

Analysis of 3-dimensional (3D) protein structure plays an important role of structural bioinformatics. The protein structure visualization is the one of the structural bioinformatics and the most fundamental problem. As the number of known protein structure increases rapidly and the study of protein-protein interaction is prevalent, the fast visualization of large scale protein structure becomes essential. The fast protein structure visualization system we proposed is sophisticated and well designed visualization system using geometry instancing technique. Because this system is optimized for recent 3D graphics hardware using geometry instancing technique, its rendering speed is faster than other visualization tools.

• Journal of Internet Computing and Services
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• v.16 no.2
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• pp.117-125
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• 2015

The information about protein structure gives the clues for the function of protein. It is needed for the improvement for the efficacy and fast development of protein drugs. So, the studies visualizing the structure of protein effectively increase. Most studies of visualization focus on the structural prediction for protein or the improvement on the rendering speed. However, studies of information delivery depending on the form of protein visualization are very limited. The major objective of this study is to analyze the information representation goodness-of-fit for the patterns of the hybrid visualization with primary and secondary structures of protein. Those hybrid visualizations included the patterns which updated current representative visualization services, Chimera, PDB and Cn3D. Information factor to analyze information representation goodness-of-fit is assorted by protein primary structure, secondary protein structure, the location of amino acid and ratio information about protein secondary structure, based on the result of subject-analysis. Subject is the group of experts who are involved in protein drug development over 5 years. The result of this study shows the meaningful difference in the information representation goodness-of-fit by the patterns of hybrid visualization and proves the difference in the information by the pattern of visualization.

• The KIPS Transactions:PartD
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• v.11D no.7 s.96
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• pp.1517-1526
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• 2004

Entering the post genome era with an increasing amount of protein data available in public databases, the study of tertiary structure of pro-teins has been artively in progress. To analyze the structure of a protein effectively, it is necessary to visualize the tertiary structure of a protein. Rececntly, many visualization tools based on Java technology have been developed to visualize a protein whose structure has been known. In this paper, we describe a new protein visualization system, named JProtein. It is designed to be an easy-to-use, platform neutral melocular visualization tool. The JProtein system is developed using Java3D technology. Java3D is an API providing a programming interface for 3D representations. The system informs us the angle and the distance of the interacting atoms in amino acids which are visualized, providing several 3D representation models of a protein molecule. In particular, the JProtein system presents synchronous stereo view as well as asynchronous one.

• Genomics & Informatics
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• v.6 no.1
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• pp.50-53
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• 2008

We have released five Java Application Programming Interface (API) packages for viewing three-dimensional structures of proteins from the Protein Data Bank. To this end, the user interface of an earlier version has been refactored in an object-oriented fashion, in which refactoring is the process of changing a software system to improve its internal structure, without altering the external behavior. Various GUI design and features have been provided conveniently thanks to the Model-View-Control (MVC) model, which is an architectural pattern used in software engineering. Availability: The source code and API specification can be downloaded from https://sourceforge.net/projects/j3dpsv/.

• Proceedings of the Materials Research Society of Korea Conference
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• 2011.05a
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• pp.10.2-10.2
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• 2011

The design and synthesis of protein-like polymers is a fundamental challenge in materials science. A biomimetic approach is to explore the impact of monomer sequence on non-natural polymer structure and function. We present the aqueous self-assembly of two peptoid polymers into extremely thin two-dimensional (2D) crystalline sheets directed by periodic amphiphilicity, electrostatic recognition and aromatic interactions. Peptoids are sequence-specific, oligo-N-substituted glycine polymers designed to mimic the structure and functionality of proteins. Mixing a 1:1 ratio of two oppositely charged peptoid 36 mers of a specific sequence in aqueous solution results in the formation of giant, free-floating sheets with only 2.7 nm thickness. Direct visualization of aligned individual peptoid chains in the sheet structure was achieved using aberration-corrected transmission electron microscopy. Specific binding of a protein to ligand-functionalized sheets was also demonstrated. The synthetic flexibility and biocompatibility of peptoids provide a flexible and robust platform for integrating functionality into defined 2D nanostructures. In the later part of my talk, we describe the use of metal ions to construct two-dimensional hybrid films that have the ability to self-heal. Incubation of biomimetic peptoid polymers with specific divalent metal ions results in the spontaneous formation of uniform multilayers at the air-water interface. We anticipate that ease of synthesis and transfer of these two-dimensional materials may have many potential applications in catalysis, gas storage and sensing, optics, nanomaterial synthesis, and environmentally responsive scaffolds.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.215-220
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• 2005

Generally, enzymes in the starch biosynthesis pathway exist in many isoforms, contributing to the difficulties in the dissection of their specific roles in controlling starch properties. In this study, we present an algorithm as an alternative method to classify isoforms of starch biosynthesis enzymes based on their conserved secondary structures. Analysis of the predicted secondary structure of plant soluble starch synthase I (SSI) and soluble starch synthase II (SSII) demonstrates that these two classes of isoform can be reclassified into three subsets, SS-A, SS-B and SS-C, according to the differences in the secondary structure of the protein at C-terminus. SS-A reveals unique structural features that are conserved only in cereal plants, while those of SS-B are found in all plants and SS-C is restricted to barley. These findings enable us to increase the accuracy in the estimation of evolutionary distance between isoforms of starch synthases. Moreover, it facilitates the elucidation of correlations between the functions of each enzyme isoforms and the properties of starches. Our secondary structure analysis tool can be applicable to study the functions of other plant enzyme isoforms of economical importance.

• Journal of Life Science
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• v.21 no.5
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• pp.631-646
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• 2011

Mesenchymal stem cells (MSC) are multipotent and can be isolated from diverse human tissues including bone marrow, fat, placenta, dental pulp, synovium, tonsil, and the thymus. They function as regulators of tissue homeostasis. Because of their various advantages such as plasticity, easy isolation and manipulation, chemotaxis to cancer, and immune regulatory function, MSCs have been considered to be a potent cell source for regenerative medicine, cancer treatment and other cell based therapy such as GVHD. However, relating to its supportive feature for surrounding cell and tissue, it has been frequently reported that MSCs accelerate tumor growth by modulating cancer microenvironment through promoting angiogenesis, secreting growth factors, and suppressing anti-tumorigenic immune reaction. Thus, clinical application of MSCs has been limited. To understand the underlying mechanism which modulates MSCs to function as tumor supportive cells, we co-cultured human adipose tissue derived mesenchymal stem cells (ASC) with cancer cell lines H460 and U87MG. Then, expression data of ASCs co-cultured with cancer cells and cultured alone were obtained via microarray. Comparative expression analysis was carried out using DAVID (Database for Annotation, Visualization and Integrated Discovery) and PANTHER (Protein ANalysis THrough Evolutionary Relationships) in divers aspects including biological process, molecular function, cellular component, protein class, disease, tissue expression, and signal pathway. We found that cancer cells alter the expression profile of MSCs to cancer associated fibroblast like cells by modulating its energy metabolism, stemness, cell structure components, and paracrine effect in a variety of levels. These findings will improve the clinical efficacy and safety of MSCs based cell therapy.

• Journal of Veterinary Science
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• v.24 no.4
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• pp.51.1-51.17
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• 2023

Background: To date, various genotypes of infectious bronchitis virus (IBV) have co-circulated and in Korea, GI-15 and GI-19 lineages were prevailing. The spike protein, particularly S1 subunit, is responsible for receptor binding, contains hypervariable regions and is also responsible for the emerging of novel variants. Objective: This study aims to investigate the putative major amino acid substitutions for the variants in GI-19. Methods: The S1 sequence data of IBV isolated from 1986 to 2021 in Korea (n = 188) were analyzed. Sequence alignments were carried out using Multiple alignment using Fast Fourier Transform of Geneious prime. The phylogenetic tree was generated using MEGA-11 (ver. 11.0.10) and Bayesian analysis was performed by BEAST v1.10.4. Selective pressure was analyzed via online server Datamonkey. Highlights and visualization of putative critical amino acid were conducted by using PyMol software (version 2.3). Results: Most (93.5%) belonged to the GI-19 lineage in Korea, and the GI-19 lineage was further divided into seven subgroups: KM91-like (Clade A and B), K40/09-like, QX-like (I-IV). Positive selection was identified at nine and six residues in S1 for KM91-like and QX-like IBVs, respectively. In addition, several positive selection sites of S1-NTD were indicated to have mutations at common locations even when new clades were generated. They were all located on the lateral surface of the quaternary structure of the S1 subunits in close proximity to the receptor-binding motif (RBM), putative RBM motif and neutralizing antigenic sites in S1. Conclusions: Our results suggest RBM surrounding sites in the S1 subunit of IBV are highly susceptible to mutation by selective pressure during evolution.