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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 13 2021
Journal Name
Palarch's Journal Of Archaeology Of Egypt / Egyptology
A WEIGHTED MEASUREMENT TO DIAGNOSED REASONS OF THE LOW SUCCESS RATIOS IN MATHEMATIC SUBJECT FOR THE THIRD INTERMEDIATE SCHOOLS AMONG A SAMPLE IN IRAQ
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Objective: To suggest a weighted measure to diagnose the reasons for the low student success ratios in mathematics concerning the third grade of intermediate schools in light of components educational system represented by: [Students, Teachers, Curriculum, and Environmental reasons (others reasons)] assuming differentiated and interrelated components, Also the effectiveness forming of these components according to the gender variable. Methods: Data collection tools were prepared by constructing two questionnaires for each of (Students and Teachers), which included a number of items that involved some domains for studied components of educational system, which demonstrated a high level of validity and reliability in the pilot study, in addi

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Publication Date
Sun Dec 31 2023
Journal Name
Nativa,
Benthic invertebrate at three sites on the Tigris River, Iraq
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The study was conducted from November 2021 to May 2022 at the three study sites within the Baghdad governorate. The study aims to identify the impact of human activities on the Tigris River, so an area free of human activities was chosen and represented the first site. A total of 48 types were diagnosed, 6204 ind/m3 spread over three sites. The following environmental indicators were evaluated: Constancy Index (S), Relative abundance index (Ra), Richness Index (between 17.995 and 23.251), Shannon Weiner Index (0.48-1.25 bit/ind.), Uniformity Index (0.124 -0.323). The study showed that the highest percentage recorded was for the phylum Annileda 34%; and the stability index shows that taxes (Stylaria sp., Aoelosoma sp., Branchinra sowerby, Ch

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Publication Date
Thu Dec 01 2016
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
THE OCCURRENCE OF THREE MONOGENEAN PARASITE SPECIES FOR THE FIRST TIME IN IRAQ ON GILLS OF THE COMMON CARP CYPRINUS CARPIO LINNAEUS, 1758 (CYPRINIFORMES, CYPRINIDAE)
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    The monogeneans Gyrodactylus dzhalilovi Ergens & Ashurova, 1984, G. magnus Konovalov, 1967 and G. matovi Ergens & Kakachava-Avramova, 1966 were recorded in this study for the first time in Iraq from gills of the common carp Cyprinus carpio Linnaeus, 1758 collected from Tigris River in Baghdad city. The description, measurements and illustrations of these parasites were given.

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Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The Role of Moral Intelligence of Internal Auditors in Support of the Performance of Internal Audit Process - Study for Opinions of a Sample of Internal Auditors in Iraq
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Abstract

      The  aim of  the research to define the concept of moral intelligence and its dimensions and its relationship to some personal characteristics with the internal auditors and identify the importance of the employment of moral intelligence dimensions of (empathy, conscience, self- control, respect, kindness, tolerance, fairness) in the internal audit and the extent of support for the performance of the internal audit process in light of these dimensions. And that by answering the following question : Is there a role for moral intelligence  of  internal auditors in support the performance of internal audit process ? How are employ these dimensions i

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Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Ijarah and lease ending with ownership and its implications for the bank's profits: A case study in the Emirates Islamic Bank and Emirates NBD
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The formula of Ijarah and Ijarah ending with ownership is one of the investment formulas in Islamic banks, so this research has shed light on it in order to benefit from the experiences of the research sample banks, This research aims to find a reliable way for Iraqi Islamic banks, namely (leasing and leasing ending with ownership) in order to invest their money without usurious interests, The problem of the research emerges through the lack of awareness of the Iraqi Islamic banks to work with different Islamic financing formulas and their inability to invest their money through the adoption of their administrations for different formulas, including the leasing, and this is reflected in the decrease and fluctuation of its profits, Theref

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Publication Date
Mon Aug 01 2011
Journal Name
Journal Of Engineering
DESIGN OF A CONTINUOUS SLIDING MODE CONTROLLER FOR THE ELECTRONIC THROTTLE VALVE SYSTEM
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Lowering the emission, fuel economy and torque management are the essential
requirements in the recent development in the automobile industry. The main engine control
input that satisfies the above requirements is the throttling angle which adjusts the air mass
flow rate to the engine port. Due to the uncertainty and the presence of the nonlinear
components in its dynamical model, the sliding mode control theory is utilized in this work
for the throttle valve angle control system to design a robust controller for this system in the
presence of a nonlinear spring and Coulomb friction. A continuous sliding mode control law
which consists of a saturation function, instead of a signum function, and the integral of
ano

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Publication Date
Wed Mar 25 2015
Journal Name
Comptes Rendus Chimie
A novel method for the synthesis of biodiesel from soybean oil and urea
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The increasing demand for energy has encouraged the development of renewable resources and environmentally benign fuel such as biodiesel. In this study, ethyl fatty esters (EFEs), a major component of biodiesel fuel, were synthesized from soybean oil using sodium ethoxide as a catalyst. By-products were glycerol and difatty acyl urea (DFAU), which has biological characteristics, as antibiotics and antifungal medications. Both EFEs and DFAU have been characterized using Fourier transform infrared (FTIR) spectroscopy, and 1H nuclear magnetic resonance (NMR) technique. The optimum conditions were studied as a function of reaction time, reactant molar ratios, catalyst percentage and the effect of organic solvents. The conversion ratio of soybea

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Publication Date
Sun Aug 13 2023
Journal Name
Arpn Journal Of Engineering And Applied Sciences
A NEW APPROACH FOR MODELLING THE VIBRATION OF BEAMS UNDER MOVING LOAD EFFECT
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In this paper, a new equivalent lumped parameter model is proposed for describing the vibration of beams under the moving load effect. Also, an analytical formula for calculating such vibration for low-speed loads is presented. Furthermore, a MATLAB/Simulink model is introduced to give a simple and accurate solution that can be used to design beams subjected to any moving loads, i.e., loads of any magnitude and speed. In general, the proposed Simulink model can be used much easier than the alternative FEM software, which is usually used in designing such beams. The obtained results from the analytical formula and the proposed Simulink model were compared with those obtained from Ansys R19.0, and very good agreement has been shown. I

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Publication Date
Tue Oct 13 2015
Journal Name
Plos Medicine
P2RX7 Purinoceptor: A Therapeutic Target for Ameliorating the Symptoms of Duchenne Muscular Dystrophy
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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Synthesis, Characterization and study biologicalactivity of several 1-cyclopentene-1,2-dicarboxylimidyl Containing oxadiazole and Benzothiazole
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In this work involved prepared of several new 1-cyclopentene-1,2-dicarboxylimide linked to oxadiazole and benzothiazole moiety were synthesized by two steps: The first step 2-amino-substituted-1,3,4-oxadiazoles and substituted-2-aminobenzothiazole were reaction with 1-cyclopentene-1,2-dicarboxyl anhydride producing N-( 5- substituted-1,3,4-oxadiazole-2-yl)-1-cyclopentene-1,2-dicarboxyl amic acids and N-(Substitutedbenzothiazole-2-yl)-1-cyclopentene-1,2-dicarboxyl amic acids which in turn were dehydrated in the second step via fusion method to afford he desirable N-(5-substituted-1,3,4-oxadiazole-2-yl)-1-cyclopentene-1,2-dicarboxylimides and N-(Substituted benzothiazole-2-yl)1-cyclopentene-1,2-dicarboxylimides respectively. Struct

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