• Journal of the Korea Convergence Society
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• v.10 no.3
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• pp.23-30
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• 2019

The purpose of this study is to find out the structure of the substance that affects antidiabetic using the candidate drug information for diabetes treatment. A quantitative structure activity relationship model based on machine learning method was constructed and major molecular descriptors were determined for each experimental data variables from coefficient values using a partial least squares algorithm. The results of the analysis of the molecular access system fingerprint data reflecting the candidate drug structure information were higher than those of the in vitro data analysis in terms of goodness-of-fit, and the major molecular expression factors affecting the antidiabetic effect were also variously derived. If the proposed method is applied to the new drug development environment, it is possible to reduce the cost for conducting candidate screening experiment and to shorten the search time for new drug development.

• KIPS Transactions on Software and Data Engineering
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• v.11 no.1
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• pp.11-18
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• 2022

De novo drug design is the process of developing new drugs that can interact with biological targets such as protein receptors. Traditional process of de novo drug design consists of drug candidate discovery and drug development, but it requires a long time of more than 10 years to develop a new drug. Deep learning-based methods are being studied to shorten this period and efficiently find chemical compounds for new drug candidates. Many existing deep learning-based drug design models utilize recurrent neural networks to generate a chemical entity represented by SMILES strings, but due to the disadvantages of the recurrent networks, such as slow training speed and poor understanding of complex molecular formula rules, there is room for improvement. To overcome these shortcomings, we propose a deep learning model for SMILES string generation using variational autoencoders with self-attention mechanism. Our proposed model decreased the training time by 1/26 compared to the latest drug design model, as well as generated valid SMILES more effectively.

• Proceedings of the Korea Information Processing Society Conference
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• 2017.04a
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• pp.810-811
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• 2017

신약 개발은 고부가가치를 창출하는 차세대 전략 산업으로 주목받고 있지만, 동물 실험과 임상 시험에 막대한 비용이 필요한 고위험-초고소득(high risk-super high return) 산업이다. 따라서 신약 후보군의 선정이 매우 중요하며 약물 유사도를 랭킹함수를 사용하는 top-k 질의 처리를 통해 후보군을 효과적으로 선정할 수 있다. 본 논문에서는 ChEMBL 데이터베이스[4]에 존재하는 화합물들 중 사용자가 원하는 특성을 갖는 k개의 화합물들을 후보군으로 추천해주는 검색 엔진을 개발하였다.

• The Journal of the Korea institute of electronic communication sciences
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• v.13 no.3
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• pp.579-586
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• 2018

With the beginning of the new era of bigdata, information extraction or prediction are an important research area. Here, we present the acquisition of semi-automatically curated large-scale biological database and the prediction of enzyme reaction annotation for analyzing the pharmacological activities of drugs. Because the xenobiotic metabolism of pharmaceutical drugs by cellular enzymes is an important aspect of pharmacology and medicine. In this study, we apply and analyze similarity models to predict bimolecular reactions between human enzymes and their corresponding substrates. Thirteen models select to reflect the characteristics of each cluster in the similarity model. These models compare based on sensitivity and AUC. Among the evaluation models, the Simpson coefficient model showed the best performance in predicting the reactivity between the enzymes. The whole similarity model implement as a web service. The proposed model can respond dynamically to the addition of reaction information, which will contribute to the shortening of new drug development time and cost reduction.

• Journal of Life Science
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• v.33 no.6
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• pp.490-497
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• 2023

Pregnant women may need to take medications to treat preexisting diseases or diseases that develop during pregnancy. However, some drugs may be fetotoxic and lead to, for example, teratogenicity and growth retardation. Predicting the fetotoxicity of drugs is thus important for the health of the mother and fetus. The fetotoxicity of many drugs has not been established because various challenges hinder the ability of researchers to determine their fetotoxicity. The need exists for in silico-based fetotoxicity assessment models, as they can modernize the testing paradigm, improve predictability, and reduce the use of animals and the costs of fetotoxicity testing. In this study, we collected data on the fetotoxicity of drugs and constructed fetotoxicity prediction models based on various machine learning algorithms. We optimized the models for more precise predictions by tuning the hyperparameters. We then performed quantitative performance evaluations. The results indicated that the constructed machine learning-based models had high performance (AUROC >0.85, AUPR >0.9) in fetotoxicity prediction. We also analyzed the feature importance of our model's predictions, which could be leveraged to identify the specific features of drugs that are strongly associated with fetotoxicity. The proposed model can be used to prescreen drugs and drug candidates at a lower cost and in less time. It provides a predictive score for fetotoxicity risk, which may be beneficial in the design of studies on fetotoxicity in human pregnancy.

• Journal of the Korean Data and Information Science Society
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• v.23 no.6
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• pp.1085-1091
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• 2012

Phase I clinical trials are designed to identify an appropriate dose; the maximum tolerated dose, which assures safety of a new drug by evaluating the toxicity at each dose-level. The adjusted maximum tolerated dose estimation is presented by stopping rule in phase I clinical trial on this research. The suggested maximum tolerated dose estimation is compared to the standard method3 and NM method using a Monte Carlo simulation study.

• Journal of the Korea Society of Computer and Information
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• v.25 no.6
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• pp.109-117
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• 2020

An edutainment system aims to help learners to recognize problems effectively, grasp and classify important information needed to solve the problems and convey the contents of what they have learned. Edutainment contents can be usefully applied to education and training in the both scientific and industrial areas. Our present work proposes an edutainment system that can be applied to a drug discovery process including virtual screening by using intuitive multi-modal interfaces. In this system, a stereoscopic monitor is used to make three-dimensional (3D) macro-molecular images, with supporting multi-modal interfaces to manipulate 3D models of molecular structures effectively. In this paper, our system can easily solve a docking simulation function, which is one of important virtual drug screening methods, by applying gaming factors. The level-up concept is implemented to realize a bio-game approach, in which the gaming factor depends on number of objects and users. The quality of the proposed system is evaluated with performance comparison in terms of a finishing time of a drug docking process to screen new inhibitors against target proteins of human immunodeficiency virus (HIV) in an e-drug discovery process.

• The Korean Journal of Pesticide Science
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• v.5 no.3
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• pp.1-11
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• 2001

New technologies will have a large impact on the discovery of new herbicide site of action. Genomics, combinatorial chemistry, and bioinformatics help take advantage of serendipity through tile sequencing of huge numbers of genes or the synthesis of large numbers of chemical compounds. There are approximately $10^{30}\;to\;10^{50}$ possible molecules in molecular space of which only a fraction have been synthesized. Combining this potential with having access to 50,000 plant genes in the future elevates tile probability of discovering flew herbicidal site of actions. If 0.1, 1.0 or 10% of total genes in a typical plant are valid for herbicide target, a plant with 50,000 genes would provide about 50, 500, and 5,000 targets, respectively. However, only 11 herbicide targets have been identified and commercialized. The successful design of novel herbicides depends on careful consideration of a number of factors including target enzyme selections and validations, inhibitor designs, and the metabolic fates. Biochemical information can be used to identify enzymes which produce lethal phenotypes. The identification of a lethal target site is an important step to this approach. An examination of the characteristics of known targets provides of crucial insight as to the definition of a lethal target. Recently, antisense RNA suppression of an enzyme translation has been used to determine the genes required for toxicity and offers a strategy for identifying lethal target sites. After the identification of a lethal target, detailed knowledge such as the enzyme kinetics and the protein structure may be used to design potent inhibitors. Various types of inhibitors may be designed for a given enzyme. Strategies for the selection of new enzyme targets giving the desired physiological response upon partial inhibition include identification of chemical leads, lethal mutants and the use of antisense technology. Enzyme inhibitors having agrochemical utility can be categorized into six major groups: ground-state analogues, group specific reagents, affinity labels, suicide substrates, reaction intermediate analogues, and extraneous site inhibitors. In this review, examples of each category, and their advantages and disadvantages, will be discussed. The target identification and construction of a potent inhibitor, in itself, may not lead to develop an effective herbicide. The desired in vivo activity, uptake and translocation, and metabolism of the inhibitor should be studied in detail to assess the full potential of the target. Strategies for delivery of the compound to the target enzyme and avoidance of premature detoxification may include a proherbicidal approach, especially when inhibitors are highly charged or when selective detoxification or activation can be exploited. Utilization of differences in detoxification or activation between weeds and crops may lead to enhance selectivity. Without a full appreciation of each of these facets of herbicide design, the chances for success with the target or enzyme-driven approach are reduced.