• Journal of the Korea Society of Computer and Information
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• v.27 no.8
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• pp.49-59
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• 2022

In this paper, we designed a new enzyme function prediction model PSCREM based on a study that compared and evaluated CNN and LSTM/GRU models, which are the most widely used deep learning models in the field of predicting functions and structures using protein sequences in 2020, under the same conditions. Sequence evolution information was used to preserve detailed patterns which would miss in CNN convolution, and the relationship information between amino acids with functional significance was extracted through overlapping RNNs. It was referenced to feature map production. The RNN family of algorithms used in small CNN-RNN models are LSTM algorithms and GRU algorithms, which are usually stacked two to three times over 100 units, but in this paper, small RNNs consisting of 10 and 20 units are overlapped. The model used the PSSM profile, which is transformed from protein sequence data. The experiment proved 86.4% the performance for the problem of predicting the main classes of enzyme number, and it was confirmed that the performance was 84.4% accurate up to the sub-sub classes of enzyme number. Thus, PSCREM better identifies unique patterns related to protein function through overlapped RNN, and Overlapped RNN is proposed as a novel methodology for protein function and structure prediction extraction.

• Proceedings of the Korea Information Processing Society Conference
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• 2003.11a
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• pp.389-392
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• 2003

인터넷상의 생물학 자원들을 이용하는 에이전트 시스템들에는 몇 가지 특징들이 있는데, 그중 하나가 바로 사용자 에이전트와 공개 데이터베이스들을 대신하는 에이전트들간의 자원 이용과정에서 발생하는 정보를 효율적으로 중계하고 조정하는 역할을 하는 기능이 존재해야 한다는 것이다. 공개 데이터베이스 자원들을 이용하는 경우 서로 다른 데이터 양식과 용어 체계, 제공하는 정보의 양과 정보를 제공하는데 걸리는 시간 등의 차이점이 존재하며, 또한 하나의 UI 에이전트로부터 복수 개의 질의를 수행하는 경우나 복수 개의 UI 에이전트들로부터 복수 개의 질의가 이루어지는 경우, 다양한 형태와 제공 정보로 인해 발생하는 자원들의 특성이 존재하게 된다. 이를 해결하기 위해서는 자원들의 다양성에 대한 고려, 메시지 트랜잭션의 관리와 더불어 다양한 플랫폼들에서 운용이 가능한 메시지 형식을 띠고 있어야 한다. 본 논문에서는 현재 개발중인 단백질 구조예측 연구를 지원하는 APSS 시스템 내에서의 사용자 에이전트와 여러 분석 및 자원 에이전트들 간의 효율적인 메시지 중재 및 조정기능을 갖는 CODY 에이전트를 설계하였고 이에 관하여 기술하고자 한다.

• Journal of Life Science
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• v.12 no.1
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• pp.113-119
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• 2002

The cloning and expression of Phosphotyrosine Protein Phosphatase into E. coli provides important tools of understanding of its functions and signal transduction mechanisms. The abundant soluble protein of the Phosphotyrosine Protein Phosphatase A (PtpA) and the active site mutant PtpA(C9S) were produced using the expression vector pET26 in E. coli and pIJ6021 with the thiostrepton in S. lividans. The enzyme activity of both proteins extracted by Ni-NTA column had same results from the expression vector pET26 and pIJ6021. The enzyme activity of phosphatase was found in the protein of PtpA, but not in that of C9S. The western blot detected by penta His-tag antibody resulted in the inducer, thiostrepton was not a good trigger to induce a large amount of PtpA protein. The overexpression of both proteins had no significantly different effect on the A factor cascade related to the secondary metabolite and mycelium formation between PtpA and C9S. However, overproduction of PtpA protein using pIJ6021 in S. lividans brought about a dramatic decrease in the amount of phosphotyrosine proteins (p200, p90, and p65), but no significantly phenotypic variation in S. lividans. This indicates that PtpA has an important proteome role in signal transduction mechanism of producing massive amount of phosphotyrosine protein in Streptomyces sp.

• Korean Journal of Microbiology
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• v.36 no.3
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• pp.181-186
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• 2000

The cellulosome of Clo.~tr~rlil~m tl\ulcornererfnocellum consistmg of 26 dfferent polypeptides contains calcium. The polypeptides dissociated when calcium was removed. Most of dockerill region in the catalytic polypeptides cleavcd during dmociation. The dissociated polypeptides were well separated by MonoQ column chromatography into CipA containing fraction, a fraction still complexed wit11 91 kDa (CelK-a). 60 IiDa and 57 kDa polypeptides, and fractious contailling mainly single polypeptide of 46 kDa (CelA-a) or 71 1d)a polypeptide (CelS-trj Most or the fractions hydrolyzed c~ystalliue cellulose The purified 71 kDa polypeptide was strictly dependent on calcium for crystalline cellulose hydvolyzing activities a1 $60^{\circ}C$~$70^{\circ}C$ but 46 kDa polypeptide was not. 46 M)a polypeptide digested cellodextri~~ as cellobiose or cellotriose unit, and glucose was produced together with cellobiose and cellotriose froln cellotetraosc. It seems that cellulosome produces final product, cellobiose, through coordinated ~qulation of activities of vannus subunits.

• The KIPS Transactions:PartD
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• v.10D no.4
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• pp.679-688
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• 2003

Motif databases are used in the function and structure prediction of proteins which appear on new and rapid release of raw data from genome sequencing projects. Recently, the frequency of use about these databases increases continuously. However, existing motif databases were developed and extended independently and were integrated mainly by using a web-based cross-reference, thus these databases have a heterogeneous search result problem, a complex query process problem and a duplicate database entry handling problem. Therefore, in this paper, we suppose physical motif resource integration and describe the integrated search method about a family-based protein prediction for solving above these problems. Finally, we estimate our implementation of the motif integration database and prediction system for predicting protein motifs.

• Korean Journal of Food Science and Technology
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• v.15 no.3
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• pp.252-261
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• 1983

Isopropyl alcohol extracted filefish protein concentrate (FPC) and NaOH hydrolyzed filefish protein isolate (FPI) were used for the investigation on the effect of processing conditions on the molecular distribution and functional properties. The molecular distribution of FPC on polyacrylamide gel showed a resemblance to that of fish muscle, but that of alkaline hydrolyzed FPI showed the severe degradation of protein. The content of several amino acids in FPI were lower than those of FPC. The pepsin digestibility of the FPC dried at high temperature was relatively high. FPC didn't exhibit a significant difference in nitrogen solubility at the pH range of 3.0-9.0, while FPI showed a wide difference with the pH change. FPI was more suspensible and rehydrated in water than FPC. Although the aeration capacity of FPI was very low, foam viscosity was higher than that of FPC. In contrast with aeration capacity, FPI presented higher emulsion capacity and lower emulsion viscosity than FPC. The size of fat globule in the emulsion of FPC was larger than that of FPI. In general, most functional properties decreased with the increment in drying temperature, except water holding capacity.

• The Journal of the Korea Contents Association
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• v.19 no.11
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• pp.632-643
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• 2019

In recent years, large scale damages from arbovirus infections by mosquitoes have been reported worldwide due to factors such as change in global climate, increased overseas travel, and increased logistics movement between countries. Among them, Zika virus and dengue virus belonging to genus Flavivirus are representative. In this study, we performed in-depth analyses of the envelope (E) protein that perform essential functions for host infection of Zika virus and dengue virus based on bioinformatics databases. The domain analysis of E protein was performed to determine the type, location, and function, and homology analysis for each domain. From these results, EDIII showing low homology was identified. The homology and immunogenicity of each peptide constituting EDIII were analyzed and three-dimensional structures were modeled. Furthermore, we discussed their biological meaning and how they could be used.

• Korean Journal of Food Science and Technology
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• v.20 no.5
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• pp.625-630
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• 1988

Phosphorylation of soy protein by sodium trimetaphosphate and acetylation of soy protein by acetic anhydride were performed. Then, the functional properties of modified soy proteins were compared with that of unmodified soy protein. Isolated soy protein prepared from defatted soybean flake had protein content of 92.7% as moisture-free basis. The phosphorylated soy protein showed higher solubility, foaming properties, and water holding capacity than unmodified soy protein. Acetylation of soy protein increased emulsification activity and foaming properties greatly, whereas decreased the solubility at pH 8.0. Isoelectric pHs of phosphorylated and acetylated soy protein were shifted to acidic regions(pH 3.0 and pH 4.0) from pH 5.0, which was the isoelectric pH of unmodified soy protein. Soy protein seems to be aggregated during phosphorylation and acetylation procedure, judging form Sepharose CL-4B gel filtration profiles. The modified soy proteins showed increased mobilities to anode direction in disc-gel electrophoresis.

• Korean Journal of Microbiology
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• v.32 no.1
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• pp.12-19
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• 1994

KEM1 is known to control the spindle pole body or microtubule function, probably in response to the cellular nutritional conditions in Saccharomyces cerevisiae. Transposon insertions were performed in the cloned KEM1 gene using mini-Tn10-LUK element carrying E. coli ${\beta}$-galactosidase structural gene. A collection of ranfom Tn10-LUK insertions defined an approximately 3.5 kb region required for the KEM1 function. From this collection functional KEM1::lacZ protein fusions were identified. Indirect immunofluorescence using anti-${\beta}$-galacatosidase antibodies localized the KEM1::lacZ fusion protein to the periphery of the nucleus.

• Journal of KIISE:Software and Applications
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• v.37 no.1
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• pp.74-79
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• 2010

The amino acid composition of a protein provides basic information for solving many problems in bioinformatics. We propose a new method that uses biologically relevant similarity between amino acids to determine the amino acid composition, where the BOLOSUM matrix is exploited to define a similarity measure between amino acids. Futhermore, to extract more information from a protein sequence than conventional methods for determining amino acid composition, we exploit the concepts of spectral analysis of signals such as radar and speech signals-the concepts of time-dependent analysis, time resolution, and frequency resolution. The proposed method was applied to predict subcellular localization of proteins, and showed significantly improved performance over previous methods for amino acid composition estimation.