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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Wed Jan 01 2014
Journal Name
Scienceasia
A combined compact genetic algorithm and local search method for optimizing the ARMA(1,1) model of a likelihood estimator
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In this paper, a compact genetic algorithm (CGA) is enhanced by integrating its selection strategy with a steepest descent algorithm (SDA) as a local search method to give I-CGA-SDA. This system is an attempt to avoid the large CPU time and computational complexity of the standard genetic algorithm. Here, CGA dramatically reduces the number of bits required to store the population and has a faster convergence. Consequently, this integrated system is used to optimize the maximum likelihood function lnL(φ1, θ1) of the mixed model. Simulation results based on MSE were compared with those obtained from the SDA and showed that the hybrid genetic algorithm (HGA) and I-CGA-SDA can give a good estimator of (φ1, θ1) for the ARMA(1,1) model. Anot

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Publication Date
Tue Jun 01 2021
Journal Name
Al-khwarizmi Engineering Journal
Effect of Environmental Factors on the Accuracy of a Quality Inspection System Based on Transfer Learning
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In this research, a study is introduced on the effect of several environmental factors on the performance of an already constructed quality inspection system, which was designed using a transfer learning approach based on convolutional neural networks. The system comprised two sets of layers, transferred layers set from an already trained model (DenseNet121) and a custom classification layers set. It was designed to discriminate between damaged and undamaged helical gears according to the configuration of the gear regardless to its dimensions, and the model showed good performance discriminating between the two products at ideal conditions of high-resolution images. So, this study aimed at testing the system performance at poo

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Publication Date
Tue Jun 01 2021
Journal Name
Al-khwarizmi Engineering Journal
Effect of Environmental Factors on the Accuracy of a Quality Inspection System Based on Transfer Learning
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In this research, a study is introduced on the effect of several environmental factors on the performance of an already constructed quality inspection system, which was designed using a transfer learning approach based on convolutional neural networks. The system comprised two sets of layers, transferred layers set from an already trained model (DenseNet121) and a custom classification layers set. It was designed to discriminate between damaged and undamaged helical gears according to the configuration of the gear regardless to its dimensions, and the model showed good performance discriminating between the two products at ideal conditions of high-resolution images.

So, this study aimed at testing the system performance at poor s

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Publication Date
Tue Sep 01 2020
Journal Name
Baghdad Science Journal
A Comparative Study on the Active Constituents, Antioxidant Capacity and Anti-Cancer Activity of Cruciferous Vegetable Residues
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This study is pointed out to estimate the effectiveness of two solvents in the extraction and evaluating the active ingredients and their antioxidant activity as well as anti-cancer efficiency. Therefore, residues from four different Brassica vegetables viz. broccoli, Brussels sprout, cauliflower, and red cherry radish were extracted using two procedures methods: methanolic and water crude extracts. Methanol extracts showed the highest content of total phenolic (TP), total flavonoids (TF), and total tannins (TT) for broccoli and Brussels sprouts residues. Methanolic extract of broccoli and Brussels sprouts residues showed the highest DPPH· scavenging activity (IC50 = 15.39 and 18.64 µg/ml). The methanol and water ex

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Publication Date
Tue Dec 22 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Accounting Disclosure for non-current intangible assets according to international accounting standard (IAS16, 36): A Comparative Study of the State Company for Travelers and delegates Transportations
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The Accounting Disclosure for non-current intangible assets is necessary to rely on accounting information by decision makers in the economic unity, two international accounting standards issued (IAS16,36), which aims to provide the foundations of the recognition, measurement and disclosure of appropriate assets Non-current tangible. (IAS16) allowed to use re-evaluation approach to measure assets entrance due to the inadequacy of the accounting information resulting from the application of the historical cost of the entrance under increasing technical developments and continuing that leave clear their effects on non-current intangible assets, As well as the requirements of what came (IAS36) the importance of accounting for the impairment

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Publication Date
Sat Jun 06 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
A comparative study of the mechanical and electrical activities of the heart according to the energy systems of advanced players
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The study aims to identify the mechanical and electrical activities of the heart according to the energy systems of advanced players and to detect the differences between the energy systems in terms of the mechanical and electrical activities of the heart for advanced players. It was clear from the results of the significance of the differences between the three groups according to the energy systems of the advanced players in all research variables that (the non-oxygenic system "Lactic"), which represents the advanced players in the arches (800 m, 1500 m) was the first in most tests of mechanical and electrical activities of the heart, which is (Margaria-Kalamen, Wingate, systolic muscle strength of the heart FC, Stroke Volume SV

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Publication Date
Sat Dec 01 2018
Journal Name
Al-khwarizmi Engineering Journal
Production of Protease Enzyme from Wheat Straw
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      Protease enzyme production was studied and optimized as  a first step to collect information about solid state fermenter) to produce protease enzyme. A local isolated Aspergillus niger was used for this study with constant spores feeding in every experiment at (105/g). Experiments carried out in conical flasks with (250 ml) containing (10 g) of wheat straw as a substrate with different conditions included temperature, pH, hydration ratio, and fermentation time, the results comprised by measuring protease activity (u). The results showed that the best activity can be obtained at (T = 32°C, t= 100 hrs, pH= 2.5 and hydration ratio is 1:3). On the other hand the results is courage to p

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Publication Date
Wed Sep 15 2021
Journal Name
Al-academy
representations of body language in the contemporary Iraqi theatrical show "Imagine That as a model": عمار عبد سلمان محمد
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There is no doubt that each of the arts has a material from which the aesthetic achievement is built, so the researcher found that the art of theater, especially the show, whose artistic achievement is based on the body of the actor who emits the formal language (body language), is the focus of interest and active presence, because the body possesses its spiritual qualities that made him and the ability to The formation of things by (his body language), so the researcher studied this theatrical phenomenon and divided it into four chapters. In the first chapter, the research problem included the following question: (Is there a phenomenon of body language in the contemporary theatrical show "Imagine that" as a model) so It is of cognitive

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Publication Date
Thu Aug 17 2023
Journal Name
Migration Letters
Employing the Teleological-Causal Presumption between Al-Khwarizmi and Ibn Yaish’s Explanations of Al-Mufasal (even) as a Model
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It is a moral presumption that includes the object for its sake, and it is called the object for it or the object for its sake, which is the present tense after (lam, ki, fa, willn, and then), and it is not an excuse for the occurrence of the matter (1), and it requires a connection between the two sides of (a cause with a cause) united by a reason for a specific purpose (2). The object has a reason or an excuse, because it is an explanation of what came before it, of the cause. The reason for the occurrence of the action, being the motive for causing the action and the bearer of it (3), indicates that the infinitive is restricted to a special reason. So if I said: (I came to you with the hope of honoring you), then I attributed the coming

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Restructuring of the public industrial sector companies Wayshift to private shareholding companies and mixed (Iraqi experience as a model)
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That the main feature of  the economics many countries in general is a tendency towards defining the role of the public sector in economic activity and the tendency towards encourage the private sector to investment in public projects especially in countries those tendency towards market economy actually.

That increased economic development proven failure in achieving more economic growth both individually in many countries especially developing countries socialist, by researchers this led one way or another to direction of corrective reforms in their economic was one of them in Transformation of public companies into Shareholding companies contributes to the public sector in resources and expertise

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