• Proceeding of EDISON Challenge
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• 2015.03a
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• pp.212-216
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• 2015

Oseltamivir, also known as Tamifu, is an inhibitor of neuraminidase protein which plays an essential role in proliferation and replication of influenza virus. Binding to the active site of neuraminidase, the oseltamivir prevents the protein from enzyme reaction. Conformational change of the protein(neuraminidase) should be accompanied by the enzyme reaction, but the drug inhibits the protein to deform. In this study, we examine the influence of oseltamivir on protein's conformational change in the structural and mechanical point of view. Finite element analysis of the protein can be an useful approach to investigate the influence of oseltamivir on the deformation of a protein. We suggest the finite element based protein model, and then perform the linear static analysis with the displacement loading condition based on the first two largest motion which can be obtained from the normal mode analysis. The results show that it takes more energy to change shape of the protein with an oseltamivir attached than the protein without an oseltamivir.

• Korean Journal of Community Nutrition
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• v.25 no.3
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• pp.226-235
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• 2020

Objectives: Decreasing muscle strength in old age has become a significant health problem because it increases the risk of falls or fractures and transfers to other diseases. The precise role of dietary protein intake in preventing or reducing muscle weakness is unclear. This study examined the relationship between handgrip strength and protein intake in Korean female elderly. Methods: This was a cross-sectional study that used data from the Seventh Korean National Health and Nutrition Examination Surveys (KNHANES) on female subjects aged 65 years and older. Low handgrip strength (LHGS) was defined as a handgrip strength below than 18 kg. Dietary intake data were obtained using the 1-day 24-hour recall method. Multiple regression was performed to test whether there is an independent relationship between the grip strength and protein intake, and the association between protein intake and LHGS was confirmed through multiple logistic regression. Results: The mean age of the 2,083 elderly females was 73.3 ± 0.1 years, and the prevalence of LHGS was 35% (n=734). Elderly women with an LHGS consumed less energy, total protein, and animal-based protein than those in the normal group. A multiple regression analysis after adjusting for covariate revealed a significant positive association between the handgrip strength and energy, protein, and animal-based protein intake. Multiple logistic regression analysis showed that the odds ratio (OR) of LHGS in female elderly with the highest quartiles of consumption of energy [OR, 0.65; 95% confidence interval (CI), 0.43-0.82; P for trend=0.004], and animal-based protein [OR, 0.59; CI, 0.40-0.87; P for trend=0.037] were significantly lower than those in the lowest quartiles. Conclusions: The energy intake and animal-based protein intake were negatively associated with the LHGS. These results suggest that adequate energy intake and protein intake, particularly those from animal-based sources, for elderly women in Korea are beneficial in lowering the risk of LHGS.

• BMB Reports
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• v.37 no.1
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• pp.28-34
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• 2004

The discovery of biochemical and cellular functions of unannotated gene products begins with a database search of proteins with structure/sequence homologues based on known genes. Very recently, a number of frontier groups in structural biology proposed a new paradigm to predict biological functions of an unknown protein on the basis of its three-dimensional structure on a genomic scale. Structural proteomics (genomics), a research area for structure-based functional discovery, aims to complete the protein-folding universe of all gene products in a cell. It would lead us to a complete understanding of a living organism from protein structure. Two major complementary experimental techniques, X-ray crystallography and NMR spectroscopy, combined with recently developed high throughput methods have played a central role in structural proteomics research; however, an integration of these methodologies together with comparative modeling and electron microscopy would speed up the goal for completing a full dictionary of protein folding space in the near future.

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.15 no.2
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• pp.111-120
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• 2015

Protein named entity identification is one of the most essential and fundamental predecessor for extracting information about protein-protein interactions from biomedical literature. In this paper, we explore the use of abstracts of biomedical literature in MEDLINE for protein name identification and present the results of the conducted experiments. We present a robust and effective approach to classify biomedical named entities into protein and non-protein classes, based on a rich set of features: orthographic, keyword, morphological and newly introduced Protein-Score features. Our procedure shows significant performance in the experiments on GENIA corpus using Random Forest, achieving the highest values of precision 92.7%, recall 91.7%, and F-measure 92.2% for protein identification, while reducing the training and testing time significantly.

• The Journal of Natural Sciences
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• v.9 no.1
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• pp.25-29
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• 1997

To study the mechanism of lipocortin-1, the 37 kDa protein, one of the annxin superfamily thought to be a second messenger during the Glucocorticoid dependent anti-inflammatory action, the gene for lipocortin-1 binding protein was isolated using the yeast two hybrid assay, the yeast based genetic assay recognizing the protein-protein interaction. The results showed that this gene has a weak homology to the for the human serine proteinase.

• Journal of Microbiology and Biotechnology
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• v.15 no.5
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• pp.1022-1027
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• 2005

Based on plasmid display technology by the complexes of fusion protein and the encoding plasmid DNA, an in vitro selection method for high affinity DNA-binding protein was developed and experimentally demonstrated. The GAL4 DNA-binding domain (GAL4 DBD) was selected as a model DNA-binding protein, and enhanced green fluorescent protein (EGFP) was used as an expression reporter for the selection of target proteins. Error prone PCR was conducted to construct a mutant library of the model. Based on the affinity decrease with increased salt concentration, mutants of GAL4 DBD having high affinity were selected from the mutant protein library of protein-encoding plasmid complex by this method. Two mutants of (Lys33Glu, Arg123Lys, Ile127Lys) and (Ser47Pro, Ser85Pro) having high affinity were obtained from the first generation mutants. This method can be used for rapid in vitro selection of high affinity DNA-binding proteins, and has high potential for the screening of high affinity DNA-binding proteins in a sequence-specific manner.

• Genomics & Informatics
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• v.11 no.3
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• pp.155-160
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• 2013

Structural information has been a major concern for biological and pharmaceutical studies for its intimate relationship to the function of a protein. Three-dimensional representation of the positions of protein atoms is utilized among many structural information repositories that have been published. The reliability of the torsional system, which represents the native processes of structural change in the structural analysis, was partially proven with previous structural alignment studies. Here, a web server providing structural information and analysis based on the backbone torsional representation of a protein structure is newly introduced. The web server offers functions of secondary structure database search, secondary structure calculation, and pair-wise protein structure comparison, based on a backbone torsion angle representation system. Application of the implementation in pair-wise structural alignment showed highly accurate results. The information derived from this web server might be further utilized in the field of ab initio protein structure modeling or protein homology-related analyses.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.12
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• pp.1674-1680
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• 2004

The objective of this study was to compare the Dutch DVE/OEB system and the NRC-2001 model in the prediction of supply of protein to dairy cows from processed field tick beans. Comparisons were made in terms of 1) ruminally synthesized microbial CP, 2) truly absorbed protein in the small intestine, and 3) degraded protein balance. The results showed that the predicted values from the DVE/OEB system and the NRC-2001 model had significant correlations with high R (>0.90) values. However, using the DVE/OEB system, the overall average microbial protein supply based on available energy was 16% higher and the truly absorbed protein in the small intestine was 9% higher than that predicted by the NRC-2001 model. The difference was also found in the prediction of the degraded protein balances (DPB), which was 5% lower than that predicted based on data from the NRC-2001 model. These differences are due to considerably different factors used in calculations in the two models, although both are based on similar principles. It need to mention that this comparison was based on the limited data, the full comparison involving various types of concentrate feeds will be investigated in the future.

• Journal of Life Science
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• v.14 no.6 s.67
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• pp.997-1002
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• 2004

This paper deals with the WASPIFA (Web-based Assistant System for Protein-protein Interaction and Function Analysis) system that can provide the comprehensive information on Protein-protein interaction and function concerned with function analysis. Different from existing systems for protein function and protein-protein interaction analysis, which provide fragmentary information restricted to specific field, our system furnishes end-user with comprehensive and synthetic information on the input sequence to be analyzed, including function and annotation information, domain information, and interaction relationship information. The synthetic information that our system contains as local databases has been extracted from many resources related to function, annotation, motif and domain by various pre-processing. Employing our system, end-users can evaluate and judge the synthetic results to do protein interaction and function analysis effectively. In addition, the WASPIFA system is equipped with automatic system management and data update function that facilitates system manager to maintain and manage it efficiently.

• The KIPS Transactions:PartD
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• v.12D no.1 s.97
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• pp.51-62
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• 2005

After figuring out the function of an amino acid sequence, we can infer the function of the other amino acids that have similar sequence composition. Besides, it is possible that we alter protein whose function we know, into useful protein using genetic engineering method. In this process. an original protein amino sequence produces various protein sequences that have different sequence composition. Here, a systematic technique is needed to manage protein version sequences and reference data of those sequences. Thus, in this paper we proposed a technique of managing protein version sequences based on local sequence alignment and a technique of managing protein historical reference data using Trigger This method automatically determines the similarity between an original sequence and each version sequence while the protein version sequences are stored into database. When this technique is employed, the storage space that stores protein sequences is also reduced. After storing the historical information of protein and analyzing the change of protein sequence, we expect that a new useful protein and drug are able to be discovered based on analysis of version sequence.