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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
Sun Jan 01 2017
Journal Name
Dissertation/thesis
A Model To Evaluate the Online Training for Global Virtual Teams in Global Software Projects
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Publication Date
Mon Jan 19 2026
Journal Name
Iraqi Journal Of Science
Magnetohydrodynyamic Flow for a Viscoclastic Fluid with the Generalized Oldroyd-B Model with Fractional Derivative
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This paper deals with the Magnetohydrodynyamic (Mill)) flow for a viscoclastic fluid of the generalized Oldroyd-B model. The fractional calculus approach is used to establish the constitutive relationship of the non-Newtonian fluid model. Exact analytic solutions for the velocity and shear stress fields in terms of the Fox H-function are obtained by using discrete Laplace transform. The effect of different parameter that controlled the motion and shear stress equations are studied through plotting using the MATHEMATICA-8 software.

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Publication Date
Sun Sep 04 2016
Journal Name
Baghdad Science Journal
Degradation of Brilliant Green by Using a bentonite Clay- Based Fe Nano Composite Film as a Heterogeneous Photo- Fenton Catalyst.
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This paper aims to study the chemical degradation of Brilliant Green in water via photo-Fenton (H2O2/Fe2+/UV) and Fenton (H2O2/Fe2+) reaction. Fe- B nano particles are applied as incrustation in the inner wall surface of reactor. The data form X- Ray diffraction (XRD) analysis that Fe- B nanocomposite catalyst consist mainly of SiO2 (quartz) and Fe2O3 (hematite) crystallites. B.G dye degradation is estimated to discover the catalytic action of Fe- B synthesized surface in the presence of UVC light and hydrogen peroxide. B.G dye solution with 10 ppm primary concentration is reduced by 99.9% under the later parameter 2ml H2O2, pH= 7, temperature =25°C within 10 min. It is clear that pH of the solution affects the photo- catalytic degradation

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Using the molecular methods in detection of antibiotics resistance genes in bacteria of Typhoi (Salmonella typhi): Batool A. Shihab|Sahira Y. Rwayah|Ashna J. Faik
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This study was carried out for direct detection of typhi and some of its multidrug resistance genes(tem,capt,gyrA&sul2)which encode for resistance to (Ampicillin, Chloramphenicol,Ciprofioxacin,Co-trimoxazole)by using Polymerase Chain Reaction technique .(71)blood samples for people suffering from typhoid fever symptoms depending on the clinical examination and (25)for control were collected. The results investigation for flic gene which encode for flagellin protein indicated that only (19)with percentage of (26,76%)gave appositive results while all control had a negative ones. Investigation for antibiotic resistance drug in samples which show positive results for flic gene showed that there is a multidrug for all antibiotics with (94.7

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Publication Date
Sun Jan 01 2023
Journal Name
International Journal Of Economics And Finance Studies
THE ROLE OF TARGET COST MANAGEMENT APPROACH IN REDUCING COSTS FOR THE ACHIEVEMENT OF COMPETITIVE ADVANTAGE AS A MEDIATOR: AN APPLIED STUDY OF THE IRAQI ELECTRICAL INDUSTRY
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Publication Date
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
Optimum conditions for ascorbic acid determination in three Iraqi citrus using HPLC technique
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A high-performance liquid chromatography method was employed for the quantitative determination of ascorbic acid (AA) which called vitamin C in three types of Iraqi citrus (orange mandarin and aurantium ) and to establish this goal , evaluation of ascorbic acid degradation is so important due to its significant criticality when exposure to ordinary atmospheric conditions. The chromatographic analysis of AA was carried out after their sequential elution with KH2PO4 ( as mobile phase) by reverse-phase HPLC technique with C8 column and UV detection at 214 nm. .Bad resolutions was appeared clearly for C8 column , so another alternative condition were carried out to improve the resolution by replacement of C8 by C18 column .Statistical treat

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Publication Date
Sun Mar 30 2008
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Quantitative Analysis of the Mixing of Three Solids Different in Density by an Air Fluidized Bed
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Three cohesionless free flowing materials of different density were mixed in an air fluidized bed to study the mixing process by calculating performance of mixing index according to Rose equation (1959) and to study the effect of four variables (air velocity, mixing time, particle size of trace component and concentration of trace component) on the mixing index and as well as on mixing performance. It was found that mixing index increases with increasing the air velocity, mixing time and concentration of trace component until the optimum value. Mixing index depends on the magnitude of difference in particle size The first set of experiments (salt then sand then cast iron) give higher mixing index and better performance of mixing than the

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Publication Date
Tue Jun 01 2021
Journal Name
Political Sciences Journal
The economic dimensions of the railway link between Iraq and Kuwait and the role of national alternatives (Faw port and the dry canal as a model(
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   Decision-makers in each country work to define a list of internal and external interests, goals and threats to their countries according to the nature of their awareness of these interests, goals and threats. 

  Hence, Iraq is not an exception to this rule, and the process of evaluating its interests and the objectives of its foreign policy is subject to the pattern of awareness of decision-makers and the influencing forces in defining its basic interests, which often witness some kind of difference in defining them, evaluating their importance and determining the size of the threats they face. And among these interests and threats that have witnessed a difference in the assessment of their

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of The College Of Education For Women
Data-Driven Approach for Teaching Arabic as a Foreign Language: Eygpt
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Corpus linguistics is a methodology in studying language through corpus-based research. It differs from a traditional approach in studying a language (prescriptive approach) in its insistence on the systematic study of authentic examples of language in use (descriptive approach).A “corpus” is a large body of machine-readable structurally collected naturally occurring linguistic data, either written texts or a transcription of recorded speech, which can be used as a starting-point of linguistic description or as a means of verifying hypotheses about a language.  In the past decade, interest has grown tremendously in the use of language corpora for language education. The ways in which corpora have been employed in language pedago

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Publication Date
Fri Dec 30 2011
Journal Name
Al-kindy College Medical Journal
Postprandial Hyperglycemia as a Significant Risk Factor for Coronary Heart Disease
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Background: The highest concentrations of
blood glucose during the day are usually found
postprandialy. Postprandial hyperglycemia (PPH)
is likely to promote or aggravate fasting
hyperglycemia. Evidence in recent years suggests
that PPH may play an important role in functional
& structural disturbances in different body organs
particularly the cardiovascular system.
Objective: To evaluate the effect of (PPH) as a
risk factor for coronary Heart disease in Type 2
diabetic patients.
Methods: Sixty-three type2 diabetic patients
were included in this study. All have controlled
fasting blood glucose, with HbA1c correlation.
They were all followed for five months period
(from May to October 2008)

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