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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 Mar 06 2022
Journal Name
Al–bahith Al–a'alami
DEPENDENCE OF MEDIA OFFICES ON THE CABINET'S WEBSITE AS A SOURCE OF INFORMATION
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     The research aimed to identify the extent to which the media offices in the ministries depend on the website of the Iraqi Council of Ministers as a source of information. Such goal includes a set of sub-goals: Knowing the reasons for media offices' reliance on the information provided by the Cabinet's website; and revealing the benefit derived from relying on the Cabinet's website.

The researcher used the survey method to screen and comprehend the extent to which the media offices in the ministries depend on the website of the Iraqi Council of Ministers as a source of information.

The mechanism of comprehensive account of the limits of research wa

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Publication Date
Tue Jan 12 2021
Journal Name
Pollution Research
DETERMINATION OF ANILINE IN WASTEWATER BY CLOUDPOINT EXTRACTION FOLLOWED BY HPLC USING 8-HYDROXYQUINOLINE AS A DERIVATIZATION AGENT
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A procedure, depending on the derivatization and determination of aniline was depicted andvalidated in this study. 8-hydroxyquinoline (8-HQ) was used as the derivatizing agent for thedetermination of aniline. An optimization study was performed for the derivatization reaction, i.e.,the diazonium coupling reaction, the optimum parameters were as follows: 22 mM of hydrochloricacid, 54mM of sodium hydroxide, and 1.8mM of sodium nitrate. The optimization study of themethod of cloud point extraction (CPE) revealed that the extraction solvent was 0.5 ml of Triton X-100, the optimum temperature was 90 °C, and the incubation time was 25 min. The linearity,correlation coefficients, molar absorptivities, and limits of detection were improved using t

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Publication Date
Wed Nov 01 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation and characterization of Posaconazole as a Nano-micelles using d-α-Tocopheryl polyethylene glycol 1000 succinate (TPGS)
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It is important to note that Posaconazole (POCZ) is a newly developed extended-spectrum triazole that belongs to BCS class II and has a solubility of less than 1µg/ml. In patients with a weakened immune system, POCZ has been shown to be effective as an antifungal treatment for invasive infections caused by candida and aspergillus species. The nano-micelles technique can be used to increase POCZ solubility. In order to increase their apparent solubility in water, nano-micelles are made by combining macromolecules that self-assemble into ordered structures capable of entrapping hydrophobic drug molecules in the interior domain. Dispersed colloidal systems, of which nano-micelles are a subset, are a large and diverse group. Composed of a p

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
A study of some atomic properties for He-like selected ions
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The atomic properties have been studied for He-like ions (He atom, Li+, Be2+ and B3+ions). These properties included, the atomic form factor f(S), electron density at the nucleus , nuclear magnetic shielding constant and diamagnetic susceptibility ,which are very important in the study of physical properties of the atoms and ions. For these purpose two types of the wave functions applied are used, the Hartree-Fock (HF) waves function (uncorrelated) and the Configuration interaction (CI) wave function (correlated). All the results and the behaviors obtained in this work have been discussed, interpreted and compared with those previously obtained.

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
A Factorial Study for separation anxiety in students, of Baghdad City
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A Factorial Study for separation anxiety in students, of Baghdad City

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Publication Date
Sat Jan 05 2019
Journal Name
Iraqi Journal Of Physics
Characterization of (SnO2)1-x(TiO2:CuO)x films as NH3 gas sensor
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Tin dioxide (SnO2) were mixed with (TiO2 and CuO) with concentration ratio (50, 60, 70, 80 and 90) wt% films deposited on single crystal Si and glass substrates at (523 K) by spray pyrolysis technique from aqueous solutions containing tin (II) dichloride Dihydrate (SnCl2, 2H2O), dehydrate copper chloride (CuCl2.2H2O) and Titanium(III) chloride (TiCl3) with molarities (0.2 M). The results of electrical properties and analysis of gas sensing properties of films are presented in this report. Hall measurement showed that films were n-type converted to p- type as titanium and copper oxide added at (50) % ratio. The D.C conductivity measurements referred that there are two mechanisms responsible about the conductivity, hence it possess two act

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Publication Date
Tue May 07 2019
Journal Name
Proteomics
Proteomic Analysis of Stromal and Epithelial Cell Communications in Human Endometrial Cancer Using a Unique 3D Co‐Culture Model
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Abstract<p>Epithelial and stromal communications are essential for normal uterine functions and their dysregulation contributes to the pathogenesis of many diseases including infertility, endometriosis, and cancer. Although many studies have highlighted the advantages of culturing cells in 3D compared to the conventional 2D culture system, one of the major limitations of these systems is the lack of incorporation of cells from non‐epithelial lineages. In an effort to develop a culture system incorporating both stromal and epithelial cells, 3D endometrial cancer spheroids are developed by co‐culturing endometrial stromal cells with cancerous epithelial cells. The spheroids developed by this method are phenot</p> ... Show More
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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
The Use of Light Text in Arab TV Shows (The Voice TV Program) -A Model
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The research tackles an important subject, namely, the light text and how it works well in the Arab television programs. The methodological framework of the research     presents the research problem stated in the following question: How can the text be used and what is its impact in the Arab TV programs? The importance of this research is that it deals with the subject of light text and its impact on Arab television programs.

This study is useful to the workers and scholars in the field of lighting as well as the goal of the research in (studying of the employment of light text in Arab television programs).

The limits of research were manifested in the study of the light text and how to make use of it

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Publication Date
Sat Aug 01 2020
Journal Name
Key Engineering Materials
Compressive Strength Performance of Reactive Powder Concrete Using Different Types of Materials as a Partial Replacement of Fine Aggregate
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Reactive Powder Concrete (RPC) can be incorporate as a one of the most important and progressive concrete technology. It is a special type of ultra-high strength concrete (UHSC) that’s exclude the coarse aggregate from its constitutive materials. In this research an experimental study had been carried out to investigate the effect of using three types of materials (porcelain aggregate) and others sustainable materials (glass waste and granular activated carbon) as a partial replacement of fine aggregate. Four percentages had considered (0, 10, 15 and 20) % to achieve better understanding for the influence of these materials upon the compressive strength of RPC. Four curing ages had included in this study, these are; 7, 28, 60 and

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Publication Date
Sat Aug 01 2020
Journal Name
Key Engineering Materials
Compressive Strength Performance of Reactive Powder Concrete Using Different Types of Materials as a Partial Replacement of Fine Aggregate
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Reactive Powder Concrete (RPC) can be incorporate as a one of the most important and progressive concrete technology. It is a special type of ultra-high strength concrete (UHSC) that’s exclude the coarse aggregate from its constitutive materials. In this research an experimental study had been carried out to investigate the effect of using three types of materials (porcelain aggregate) and others sustainable materials (glass waste and granular activated carbon) as a partial replacement of fine aggregate. Four percentages had considered (0, 10, 15 and 20) % to achieve better understanding for the influence of these materials upon the compressive strength of RPC. Four curing ages had included in this study, these are; 7, 28, 60 and

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