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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
Mon Jul 10 2023
Journal Name
Journal Of Engineering
Bearing Capacity of a Strip Model Footing on Loose Sand Reinforced With Pomegranate Sticks Mat
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A series of laboratory model tests has been carried out to investigate the using of pomegranate sticks mat as reinforcement to increase the bearing capacity of footing on loose sand. The influence of depth and length of pomegranate sticks layer was examined. In the present research single layer of pomegranate sticks reinforcement was used to strengthen the loose sand stratum beneath the strip footing. The dimensions of the used foundation were 4*20 cm. The reinforcement layer has been embedded at depth 2, 4 and 8 cm under surcharge stresses . Reinforcing layer with length of 8 and 16 cm were used. The final model test results indicated that the inclusion of pomegranate sticks reinforcement is very effective in improvement the loading cap

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Publication Date
Wed Nov 03 2021
Journal Name
Al-ghary Journal Of Economic And Administrative Sciences
The Role of Marketing Vigilance in Analyzing the Strategic Position of Tourism Organization: A Survey Study of the Opinions of a Sample of Travel and Tourism Companies
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The study aims at studying and analyzing the subject of marketing vigilance as it is one of the modern approaches in the marketing field that can be used to face changes in the competitive and strategic environment and that represents quick reactions on the part of the institution to ensure its survival and distinctiveness other aims are: Consolidating the strength of the marketing organization and its success continuously, represented by changes in the market share, awareness of the institution's position in the market and its relations with competing tourism companies, diversification of tourism services, as well as an analysis of the competitive strategic position of tourism institutions for the purpose of conducting a r

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Publication Date
Sun Dec 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The impact of wages and benefits systems on the performance of employees A field study in the General Company for Food Industries in the city of Baghdad
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The research aims to find out the impact of wages and benefits systems on the performance of employees, which included the research community on a sample of employees in the company, and the sample consisted of (50) employees and an employee, A questionnaire composed as prepared (23) paragraph, use the promised statistically methods in data collected by the questionnaire analysis. The research reached a number of results, the most prominent of which were: There is a correlation between wage systems, benefits and performance of employees, and the presence of the impact of the systems of wages and benefits to the performance of employees. The research was presented a set of recommendations including: increasing the effectiveness of

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Publication Date
Mon Jan 01 2018
Journal Name
Portugaliae Electrochimica Acta
A Kinetic Study of Oxalic Acid Electrochemical Oxidation on a Manganese Dioxide Rotating Cylinder Anode
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Publication Date
Sun Mar 26 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation and Characterization of Montelukast Sodium ( SMLT ) as a Dual Sustained Release Buccal Strips
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An oral bi layer  sustained release (SR) strips of Sodium  Montelukast SMLT , which is selective  leukotriene  antagonist  , used  for  patients  suffered from mid-night asthma , were prepared successfully ,using different polymers, like guar  gum , carrageenan , and xanthan gum , by solvent casting method .

The results obtained by this study revealed  ,that best  fast  dissolving  film of  SMLT was  loaded  in carrageenan   polymer 57%  w\w (30mg.) ,  with  acceptable  physical properties, like film thickness , elastic endurance and  surface pH  .

Besides  to that , the  disintegration  t

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Publication Date
Sat Jan 01 2011
Journal Name
Iraqi Journal Of Physics
Characteristics of Zinc Oxide Film Prepared by Chemical Spray Deposition as a Gas Sensor
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Zinc oxide thin films were deposited by chemical spray pyrolysis onto glass substrates which are held at a temperature of 673 K. Some structural, electrical, optical and gas sensing properties of films were studied. The resistance of ZnO thin film exhibits a change of magnitude as the ambient gas is cycled from air to oxygen and nitrogen dioxide

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Publication Date
Sat Dec 01 2012
Journal Name
Journal Of Engineering
Effect Of Technology Based Learning As A Supplement To Traditional Technology On Student's Achievement
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This paper describes a practical study on the impact of learning's partners, Bluetooth Broadcasting system, interactive board, Real – time response system, notepad, free internet access, computer based examination, and interaction classroom, etc, had on undergraduate student performance, achievement and involving with lectures. The goal of this study is to test the hypothesis that the use of such learning techniques, tools, and strategies to improve student learning especially among the poorest performing students. Also, it gives some kind of practical comparison between the traditional way and interactive way of learning in terms of lectures time, number of tests, types of tests, student's scores, and student's involving with lectures

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Publication Date
Fri Sep 24 2021
Journal Name
Indonesian Journal Of Chemistry
Molecular Imprinted of Nylon 6 for Selective Separation of Procaine by Solid-Phase Extraction
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The study is based on the selective binding ability of the drug compound procaine (PRO) on a surface imprinted with nylon 6 (N6) polymer. Physical characterization of the polymer template was performed by X-ray diffraction and DSC thermal analysis. The imprinted polymer showed a high adsorption capacity to trap procaine (237 µg/g) and excellent recognition ability with an imprinted factor equal to 3.2. The method was applied to an extraction column simulating a solid-phase extraction to separate the drug compound in the presence of tinoxicam and nucleosimide separately and in a mixture of them with a recovery rate more than the presence of tinoxicam and nucleosimide separately and in a mixture of them with a recovery rate of more t

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Publication Date
Sat Jun 30 2018
Journal Name
Iraqi Journal Of Medical Sciences
CLINICAL UTILITY OF URINARY ANTIGEN TEST AND MOLECULAR METHOD FOR DETECTION OF LEGIONELLA PNEUMOPHILA
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Background: Legionella pneumophila (L. pneumophila) is gram-negative bacterium, which causes Legionnaires’ disease as well as Pontiac fever. Objective: To determine the frequency of Legionella pneumophila in pneumonic patients, to determine the clinical utility of diagnosing Legionella pneumonia by urinary antigen testing (LPUAT) in terms of sensitivity and specificity, to compares the results obtained from patients by urinary antigen test with q Real Time PCR (RT PCR) using serum samples and to determine the frequency of serogroup 1 and other serogroups of L. pneumophila. Methods: A total of 100 pneumonic patients (community acquired pneumonia) were enrolled in this study during a period between October 2016 to April 2017; 92 sam

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of the competitiveness for commercial banks in Iraq for a period of 2004 – 2012
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This study was conducted on a sample of commercial banks in Iraq, chosen according number of considerations for twenty banks, contained two public banks and eighteen private banks.                                                                                             &

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