• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.5
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• pp.414-418
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• 2004

A 'minimally complex problem set' for ab initio protein Structure prediction has been proposed. As well as consisting of non-redundant and crystallographically determined high-resolution protein structures, without disulphide bonds, modified residues, unusual connectivities and heteromolecules, it is more importantly a collection of protein structures. with a high probability of being the same in the crystal form as in solution. To our knowledge, this is the first attempt at this kind of dataset. Considering the lattice constraint in crystals, and the possible flexibility in solution of crystallographically determined protein structures, our dataset is thought to be the safest starting points for an ab initio protein structure prediction study.

• Biotechnology and Bioprocess Engineering:BBE
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• v.8 no.3
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• pp.167-172
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• 2003

Foam fractionation can be used to enrich a hydrophobic protein such as bromelain from an aerated dilute protein solution because the protein foams. On the other hand, a protein such as invertase, which is hydrophilic, is not likely to foam under similar aerated conditions. While a foam fractionation process may not be appropriate for recovering a hydrophilic protein alone, it is of interest to see how that non-foaming protein affects the foaming protein when the two are together in a mixture. The bromelain enrichment, activity and mass recovery were observed as a function of the solution pH in order to explore how invertase can affect the recovery of bromelain in a foam fractionation process.

• Journal of Microbiology and Biotechnology
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• v.18 no.5
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• pp.885-888
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• 2008

In this work, we demonstrate that glycolytic intermediates can serve as efficient energy sources to regenerate ATP during continuous-exchange cell-free (CECF) protein synthesis reactions. Through the use of an optimal energy source, approximately 10 mg/ml of protein was generated from a CECF protein synthesis reaction at greatly reduced reagent costs. Compared with the conventional reactions utilizing phosphoenol pyruvate as an energy source, the described method yields 10-fold higher productivity per unit reagent cost, making the techniques of CECF protein synthesis a more realistic alternative for rapid protein production.

• 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.

• 한국생물공학회:학술대회논문집
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• 2002.04a
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• pp.515-518
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• 2002

The method of foam fractionation can be applied to enrich proteins from a dilute protein solution if the proteins are hydrophobic and foam. If a protein, such as invertase, is hydrophilic, a dilute solution containing this protein may not foam. In that case, a batch foam fractionation process may not be appropriate for recovering a concentrated solution of that protein. In this paper, various concentrations of invertase were added to a dilute solution containing bromelain (a hydrophobic protein), in order to determine how the presence of a hydrophilic protein can affect the recovery of the desired hydrophobic protein. The effect of invertase on bromelain recovery was studied here at an initial bulk solution pH of 5 and an air superficial velocity of 4.6 cm/s.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.5
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• pp.455-461
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• 2006

In this study, we have described a method for the fabrication of a protein chip on silicon substrate using hydrophobic thin film and microfluidic channels, for the simultaneous detection of multiple targets in samples. The use of hydrophobic thin film provides for a physical, chemical, and biological barrier for protein patterning. The microfluidic channels create four protein patterned strips on the silicon surfaces with a high signal-to-noise ratio. The feasibility of the protein chips was determined in order to discriminate between each protein interaction in a mixture sample that included biotin, ovalbumin, hepatitis B antigen, and hepatitis C antigen. In the fabrication of the multiplexed assay system, the utilization of the hydrophobic thin film and the microfluidic networks constitutes a more convenient method for the development of biosensors or biochips. This technique may be applicable to the simultaneous evaluation of multiple protein-protein interactions.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.37 no.1
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• pp.18-23
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• 2004

Effect of initial protein concentration on the protein removal rate was assessed for seawater aquarium using a foam separator. Protein removal rate was increased and removal efficiency was decreased with the increase of initial protein concentration. Enrichment ratio was decreased and foam generation rate was increased with the increase of initial protein concentration. Total suspended solids (TSS) removal rate was increased with the increase of initial protein concentration, and TSS removal efficiency was decreased with the increase of initial protein concentration. Turbidity removal rate and removal efficiency were increased with the increase of initial protein concentration.

• BMB Reports
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• v.33 no.3
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• pp.195-201
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• 2000

A human gene has been reported that may encode the enzyme acetohydroxyacid synthase. Previously this enzyme was thought to be absent from animals although it is present in plants and many microorganisms. In plants, this enzyme is the target of a number of commercial herbicides and the use of these compounds may need to be reassessed if the human enzyme exists and proves to be susceptible to inhibition. Here we report the construction of several plasmid vectors containing the cDNA sequence for this protein, and their expression in Escherichia coli. High levels of expression were observed, but most of the protein proved to be insoluble. The small amounts of soluble protein contained little or no acetohydroxyacid synthase activity. Attempts to refold the insoluble protein were successful insofar as the protein became soluble. However, the refolded protein did not gain any acetohydroxyacid synthase activity. In vivo complementation tests of an E. coli mutant produced no evidence that the protein is active. Incorrect folding, or the lack of another subunit, may explain the data but we favor the interpretation that this gene does not encode an acetohydroxyacid synthase.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.7-16
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• 2003

In this paper, we propose a probabilistic framework to predict the interaction probability of proteins. The notion of domain combination and domain combination pair is newly introduced and the prediction model in the framework takes domain combination pair as a basic unit of protein interactions to overcome the limitations of the conventional domain pair based prediction systems. The framework largely consists of prediction preparation and service stages. In the prediction preparation stage, two appearance pro-bability matrices, which hold information on appearance frequencies of domain combination pairs in the interacting and non-interacting sets of protein pairs, are constructed. Based on the appearance probability matrix, a probability equation is devised. The equation maps a protein pair to a real number in the range of 0 to 1. Two distributions of interacting and non-interacting set of protein pairs are obtained using the equation. In the prediction service stage, the interaction probability of a protein pair is predicted using the distributions and the equation. The validity of the prediction model is evaluated fur the interacting set of protein pairs in Yeast organism and artificially generated non-interacting set of protein pairs. When 80% of the set of interacting protein pairs in DIP database are used as foaming set of interacting protein pairs, very high sensitivity(86%) and specificity(56%) are achieved within our framework.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.3
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• pp.184-190
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• 2004

The influences of impeller types on morphology and protein expression were investigated in a submerged culture of Aspergillus oryzae. The impeller types strongly affected mycelial morphology and protein production in batch and fed-batch fermentations. Cells that were cultured by propeller agitation grew in the form of a pellet, whereas cells that were cultured by turbine agitation grew in a freely dispersed-hyphal manner and in a clumped form. Pellet-grown cells showed high levels of protein production for both the intracellularly heterologous protein (${\beta}$-glucuronidase) and the extracellularly homologous protein (${\alpha}$-amylase). The feeding mode of the carbon source also influenced the morphological distribution and protein expression in fed-batch fermentation of A. oryzae. Pulsed-feeding mainly showed high protein expression and homogeneous distribution of pellet whereas continuous feeding resulted in less protein expression and heterogeneous distribution with pellet and dispersed-hyphae. The pellet growth with propeller agitation paralleling with the pulsed-feeding of carbon source showed a high level of protein production in the submerged fed-batch fermentation of recombinant A. oryzae.