• Bulletin of the Korean Chemical Society
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• 제34권4호
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• pp.1043-1046
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• 2013

Prediction of physicochemical properties of organic molecules is an important process in chemistry and chemical engineering. The MSEP approach developed in our lab calculates the molecular surface electrostatic potential (ESP) on van der Waals (vdW) surfaces of molecules. This approach includes geometry optimization and frequency calculation using hybrid density functional theory, B3LYP, at the 6-31G(d) basis set to find minima on the potential energy surface, and is known to give satisfactory QSPR results for various properties of organic molecules. However, this MSEP method is not applicable to screen large database because geometry optimization and frequency calculation require considerable computing time. To develop a fast but yet reliable approach, we have re-examined our previous work on organic molecules using two semi-empirical methods, AM1 and PM3. This new approach can be an efficient protocol in designing new molecules with improved properties.

• 한국식품저장유통학회지
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• 제5권1호
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• pp.1-6
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• 1998

Physicochemical properties of early cultivar of Satsuma mandarin(Citrus unshiu Marc. var. miyagawa) according to harvesting year during 1990 to 1995 were investigated. Climatic conditions of every year affected the quality of citrus fruits. Compared to other harvesting years, flesh ratio and soluble solids were higher, but acid content was lower on citrus fruits produced in 1994, as for good climatic conditions during growth of fruits. Especially, acid content of fruits produced in 1993 was higher, compared to those of years, as for low mean temperature and high rainfalls. Fruit weight, peel thickness and soluble solids had a good linear correlation to fruits size, but acid content and flesh ratio had not correlation derived from difference of individual fruits. From the climatic data, the prediction of fruit quality would be possible in some degree before harvest. It seemed recommend to ably the flexibe method by harvesting year for the quality stanardization of citrus fruit.

• Computers and Concrete
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• 제17권4호
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• pp.523-539
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• 2016

Alkali-activated binder (AAB) is increasingly being considered as an eco-friendly and sustainable alternative to portland cement (PC). The present study evaluates 30 different AAB mixtures containing fly ash and/or slag activated by sodium hydroxide and sodium silicate by correlating their properties from micro to specimen level using regression. A model is developed to predict compressive strength of AAB as a function of volume fractions of microstructural phases (physicochemical properties) and ultrasonic pulse velocity (elastic properties and density). The predicted models are ranked and then compared with the experimental data. The correlations were found to be quite reasonable (R2 = 0.89) for all the mixtures tested and can be used to estimate the compressive strengths for similar AAB mixtures.

• Genomics & Informatics
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• 제21권2호
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• pp.25.1-25.12
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• 2023

Adaptation of infections and hosts has resulted in several metabolic mechanisms adopted by intracellular pathogens to combat the defense responses and the lack of fuel during infection. Human tuberculosis caused by Mycobacterium tuberculosis (MTB) is the world's first cause of mortality tied to a single disease. This study aims to characterize and anticipate potential antigen characteristics for promising vaccine candidates for the hypothetical protein of MTB through computational strategies. The protein is associated with the catalyzation of dithiol oxidation and/or disulfide reduction because of the protein's anticipated disulfide oxidoreductase properties. This investigation analyzed the protein's physicochemical characteristics, protein-protein interactions, subcellular locations, anticipated active sites, secondary and tertiary structures, allergenicity, antigenicity, and toxicity properties. The protein has significant active amino acid residues with no allergenicity, elevated antigenicity, and no toxicity.

• International Journal of Computer Science & Network Security
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• 제21권3호
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• pp.41-47
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• 2021

Detection of protein-protein interactions (PPIs) remains essential for the development of therapies against diseases. Experimental studies to detect PPI are longer and more expensive. Today, with the availability of PPI data, several computer models for predicting PPIs have been proposed. One of the big challenges in this task is feature extraction. The relevance of the information extracted by some extraction techniques remains limited. In this work, we first propose an extraction method based on correlation relationships between the physicochemical properties of amino acids. The proposed method uses a correlation matrix obtained from the hydrophobicity and hydrophilicity properties that it then integrates in the calculation of the bigram. Then, we use the SVM algorithm to detect the presence of an interaction between 2 given proteins. Experimental results show that the proposed method obtains better performances compared to the approaches in the literature. It obtains performances of 94.75% in accuracy, 95.12% in precision and 96% in sensitivity on human HPRD protein data.

• 통합자연과학논문집
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• 제5권1호
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• pp.1-5
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• 2012

Quantitative structure-activity relationship (QSAR) methodologies have been applied for many years, to correlate the relationship between physicochemical properties of chemical substances and their biological activities to generate a statistical model for prediction of the activities of new chemical entities. The basic principle behind the QSAR models is that, how structural variation is responsible for the difference in biological activities of the compounds. 3D-QSAR has emerged as a natural extension to the classical Hansch and Free-Wilson approaches, which develops the 3D properties of the ligands to predict their biological activities using various chemometric techniques (PLS, G/PLS, ANN etc). It has served as a valuable predictive tool in the design of pharmaceuticals and agrochemicals. This review seeks to provide different 3D-QSAR approaches involved in drug designing process to develop structure-activity relationships and also discussed the fundamental limitations, as well as those that might be overcome with the improved methodologies.

• Advances in concrete construction
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• 제1권3호
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• pp.201-213
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• 2013

While recognizing the problem of reinforcement corrosion and premature structural deterioration of reinforced concrete (RC) structures as a combined effect of mechanical and environmental actions (carbonation, ingress of chlorides), emphasis is given on the effect of the latter, as most severe and unpredictable action. In this study, a simulation tool, based on proven predictive models utilizing principles of chemical and material engineering, for the estimation of concrete service life is applied on an existing reinforced concrete bridge (${\O}$resund Link) located in a chloride environment. After a brief introduction to the structure of the models used, emphasis is given on the physicochemical processes in concrete leading to chloride induced corrosion of the embedded reinforcement. By taking under consideration the concrete, structural and environmental properties of the bridge investigated, an accurate prediction of its service life is taking place. It was observed that the proposed, and already used, relationship of service lifetime- cover is almost identical with a mean line between the lines derived from the minimum and maximum critical values considered for corrosion initiation. Thus, an excellent agreement with the project specifications is observed despite the different ways used to approach the problem. Furthermore, different scenarios of concrete cover failure, in the case when a coating is utilized, and extreme deicing salts attack are also investigated.

• Molecules and Cells
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• 제27권5호
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• pp.547-556
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• 2009

Parathyroid hormone is the most important endocrine regulator of calcium concentration. Its N-terminal fragment (1-34) has sufficient activity for biological function. Recently, site-directed mutagenesis studies demonstrated that substitutions at several positions within shorter analogues (1-14) can enhance the bioactivity to greater than that of PTH (1-34). However, designing the optimal sequence combination is not simple due to complex combinatorial problems. In this study, support vector machines were introduced to predict the biological activity of modified PTH (1-14) analogues using mono-substituted experimental data and to analyze the key physicochemical properties at each position that correlated with bioactivity. This systematic approach can reduce the time and effort needed to obtain desirable molecules by bench experiments and provide useful information in the design of simpler activating molecules.

• Advances in environmental research
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• 제1권4호
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• pp.257-276
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• 2012

QSAR models for chlorinated alkenes were developed between $E_{HOMO}$ and their chlorine and carbon content. The aim is to provide valid QSAR model which is statistically validated for $E_{LUMO}$ prediction. Different molecular descriptors, $N_{Cl}$, $N_C$ and $E_{HOMO}$ have been used to take into account relevant information provided by molecular features and physicochemical properties. The best model were selected using Partial Least Square (PLS) and Multiple Linear Regression (MLR) led to models with satisfactory predictive ability for a data set of 15 chlorinated alkene compounds.

• Computers and Concrete
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• 제10권5호
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• pp.523-539
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• 2012

Silica fume has long been used as a mineral admixture to improve the durability and produce high strength and high performance concrete. And in marine and coastal environments, penetration of chloride ions is one of the main mechanisms causing concrete reinforcement corrosion. In this paper, we proposed a numerical procedure to predict the chloride diffusion in a hydrating silica fume blended concrete. This numerical procedure includes two parts: a hydration model and a chloride diffusion model. The hydration model starts with mix proportions of silica fume blended concrete and considers Portland cement hydration and silica fume reaction respectively. By using the hydration model, the evolution of properties of silica fume blended concrete is predicted as a function of curing age and these properties are adopted as input parameters for the chloride penetration model. Furthermore, based on the modeling of physicochemical processes of diffusion of chloride ion into concrete, the chloride distribution in silica fume blended concrete is evaluated. The prediction results agree well with experiment results of chloride ion concentrations in the hydrating concrete incorporating silica fume.