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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
Fri Dec 09 2022
Journal Name
Molecules
Palm Raceme as a Promising Biomass Precursor for Activated Carbon to Promote Lipase Activity with the Aid of Eutectic Solvents
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This study concerns the role of activated carbon (AC) from palm raceme as a support material for the enhancement of lipase-catalyzed reactions in an aqueous solution, with deep eutectic solvent (DES) as a co-solvent. The effects of carbonization temperature, impregnation ratio, and carbonization time on lipase activity were studied. The activities of Amano lipase from Burkholderia cepacia (AML) and lipase from the porcine pancreas (PPL) were used to investigate the optimum conditions for AC preparation. The results showed that AC has more interaction with PPL and effectively provides greater enzymatic activity compared with AML. The optimum treatment conditions of AC samples that yield the highest enzymatic activity were 0.5 (NaOH (

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Publication Date
Tue Dec 01 2009
Journal Name
Iraqi Journal Of Physics
Spectrophotometrically Analysis of PMMA as a low – Doses Dosimeter
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Polymethylmethacrylate film (PMMA) of thickness 75 μm was evaluated Spectrophotometrically for using it as a low-doses gamma radiation dosimeter. The doses were examined in the range 0.1 mrad-10 krad. Within an absorption band of 200-400 nm, the irradiated films showed an increase in the absorption intensity with increasing the absorbed doses. Calibration curves for the changes in the absorption differences were obtained at 218, 301, and 343 nm. At 218 nm the response for the absorbed doses is a linear in the range 10 mrad- 10 krad. Hence it is recommended to be adopted as an environmental low doses dosimeter

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Publication Date
Tue Jun 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
Bayes Estimator as a Function of Some Classical Estimator
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Maximum likelihood estimation method, uniformly minimum variance unbiased estimation method and minimum mean square error estimation, as classical estimation procedures, are frequently used for parameter estimation in statistics, which assuming the parameter is constant , while Bayes method assuming the parameter is random variable and hence the Bayes estimator is an estimator which minimize the Bayes risk for each value the random observable and for square error lose function the Bayes estimator is the posterior mean. It is well known that the Bayesian estimation is hardly used as a parameter estimation technique due to some difficulties to finding a prior distribution.

The interest of this paper is that

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Publication Date
Fri Aug 09 2024
Journal Name
Theory And Practice In Language Studies
Fallacy as a Strategy of Argumentation in Political Debates
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This study aims to study argumentation in political debates by figuring out the logical fallacies employed in the debates of Clinton and Trump, the presidential nominees of the 2016 elections, and Biden and Trump, the leading contenders in the 2020 United States presidential election. The study attempts to answer the questions: (1) What relevance fallacies are adopted in the debate between Trump and Clinton? (2) What rhetorical devices are used to influence the audience and gain voters besides fallacies in the debates selected? The study analyses two texts from two arguments using Damer's (2009) taxonomy of relevance fallacy and rhetorical devices based on Perrine’s (1969) model of communication and interpersonal rhetoric to answe

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Publication Date
Fri Jan 01 2021
Journal Name
Water Pollution And Management Practices
Existence of Antibiotics in Wastewater as a Pollution Indicator
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Publication Date
Sun Mar 01 2015
Journal Name
Baghdad Science Journal
Terrestrial Invertebrates as a Bioindicators of Heavy Metals Pollution
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Bioaccumulation of heavy metals in the terrestrial invertebrates in Al-Jadriyia district Baghdad- Iraq were investigated. Forth terrestrial invertebrates snails, slug, isopods, and diplopods , were selected for this study. The results showed that all invertebrate groups have the ability in accumulate considerable amounts of heavy metals. Higher levels of zinc and copper were observed in the isopods specimens, it's about ( 60.50±0.58 ) and ( 96.00±0.58 ) ppm respectively , while higher levels of lead were observed in the diplopods specimens ,it's about ( 23.00±1.15 ) ppm ,but the higher levels of both iron and cadmium were observed in snail specimens , it's about ( 590.00±1.15 ) and ( 9.50±1.15 ) ppm respectively .but the

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Publication Date
Sun May 22 2022
Journal Name
International Journal Of Early Childhood Special Education
The impact of using learning acceleration model on the achievement of mathematics for third intermediate grade students
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The current study aims at identifying the impact of using learning acceleration model on the achievement of mathematics for third intermediategrade students. Forachieving this, the researchers chose the School (Al-Kholood Secondary School for Girls) affiliated to the General Directorate of Babylon Education / Hashemite Education Department for the academic year (2021/2021), The sample reached to (70) female students from the third intermediate grade, with (35) female students for each of the two research groups. The two researchers prepared an achievement test consisting of (25) objective items of multiple choice type, The psychometric properties of the test were confirmed, and after the completion of the experiment, the achievement test wa

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Publication Date
Sun Aug 01 2021
Journal Name
Journal Of Engineering
Practical comparation of the accuracy and speed of YOLO, SSD and Faster RCNN for drone detection
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Convolutional Neural Networks (CNN) have high performance in the fields of object recognition and classification. The strength of CNNs comes from the fact that they are able to extract information from raw-pixel content and learn features automatically. Feature extraction and classification algorithms can be either hand-crafted or Deep Learning (DL) based. DL detection approaches can be either two stages (region proposal approaches) detector or a single stage (non-region proposal approach) detector. Region proposal-based techniques include R-CNN, Fast RCNN, and Faster RCNN. Non-region proposal-based techniques include Single Shot Detector (SSD) and You Only Look Once (YOLO). We are going to compare the speed and accuracy of Faster RCNN,

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Engineering
Speed Controller of Three Phase Induction Motor Using Sliding Mode Controller
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In this paper, an adaptive integral Sliding Mode Control (SMC) is employed to control the speed of Three-Phase Induction Motor. The strategy used is the field oriented control as ac drive system. The SMC is used to estimate the frequency that required to generates three phase voltage of Space Vector Pulse Width Modulation (SVPWM) invertor . When the SMC is used with current controller, the quadratic component of stator current is estimated by the controller. Instead of using current controller, this paper proposed estimating the frequency of stator voltage since that the slip speed is function of the quadratic current . The simulation results of using the SMC showed that a good dynamic response can be obtained under load

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Publication Date
Sat Dec 18 2021
Journal Name
Egyptian Journal Of Chemistry
Coumarin based-histone deactylace HADC inhibitors
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Coumarins have been recognized as anticancer competitors. HDACis are one of the interesting issues in the field of antitumor research. In order to achieve an increased anticancer efficacy, a series of hybrid compounds bearing coumarin scaffolds have been designed and synthesized as novel HDACis, In this review we present a series of novel HDAC inhibitors comprising coumarin as a core e of cap group of HDAC inhibitors that have been designed, synthesized and assessed for their enzyme inhibitory activity as well as antiproliferative activity. Most of them exhibited potent HDAC inhibitory activity and significant cytotoxicity

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