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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
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Desulphurization of Simulated Oil Using SAPO-11 with CNT's as Adsorbent: A Kinetic Study
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In this study, sulfur was removed from imitation oil using oxidative desulfurization process. Silicoaluminophosphate (SAPO-11) was prepared using the hydrothermal method with a concentration of carbon nanotubes (CNT) of 0% and 7.5% at 190 °C crystallization temperature. The final molar composition of the as-prepared SAPO-11 was Al2O3: 0.93P2O5: 0.414SiO2. 4% MO/SAPO-11 was prepared using impregnation methods. The produced SAPO-11 was described using X-ray diffraction (XRD) and Brunauer-Emmet-Teller (N2 adsorption–desorption isotherms). It was found that the addition of CNT increased the crystallinity of SAPO-11. The results showed that the surface area of SAPO-11 cont

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Publication Date
Tue Jan 10 2023
Journal Name
Linguistics And Translation Studies
Comparative analysis of zoomorphic metaphors of the Russian Arabic language as a method of studying cultural linguistics
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: zonal are included in phraseological units, form metaphorical names for a person, give him various emotional and evaluative characteristics. This article examines the topic of zoomorphic metaphors that characterize a person in the Russian and Arabic languages in the aspect of their comparative analysis, since the comparative analysis of the metaphorical meanings of animalisms is an important method for studying cultural linguistics, since zoomorphic metaphors are a reflection of culture in a language.

Publication Date
Mon Oct 01 2012
Journal Name
Al–bahith Al–a'alami
Skills of Media Marketing of the Public Relations Staff: (University of Baghdad as a Model)
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Departments and offices of public relations and media in any institution or company is the most important departments that reflect the results of their work negatively or positively on their reputation. This goes beyond the trust and credibility that its internal and external audiences will give it. Where such matter requires the staff, working in these departments and offices, to have communication skills that qualify them to do the role of marketing the communication message. Yet, the communication skills of public relations and media staff vary from person to person depending on the communication position. This skill has two criteria: Achieving the communication goal and the speed in achieving it as a number of skills

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Publication Date
Sun Sep 22 2019
Journal Name
Baghdad Science Journal
A Molecular and Biochemical Study for Cholesteryl Ester Transfer Protein (CETP) Taq1B in Iraqi Patients with Hyperlipidemia
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Cholesteryl ester transfer protein gene contains some single nucleotide polymorphisms, which have been associated with serum high-density lipoprotein concentration and other lipoproteins. This study is done for determining of cholesteryl ester transfer protein polymorphism and evaluate its effect on serum lipid profile concentrations in some hyperlipidemic patients compared with healthy subjects in Salah Al-din governorate-Iraq. Blood samples were taken from (90) patients suffering from hyperlipidemia, and (70) samples that were apparently healthy controls.  Serum lipid concentrations were measured by enzymatic assays. The polymorphism was genotyped using polymerase chain reaction restriction fragment length polymorphism analysis.&n

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Publication Date
Sat Nov 01 2025
Journal Name
Russian Journal Of General Chemistry
Synthesis, Antibacterial Activity, and Molecular Docking Study of Some New Azo Derivatives Based on 2(4-Aminophenyl)-5-Substituted 1,3,4-Oxadiazole
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Publication Date
Sat Aug 31 2019
Journal Name
Iraqi Journal Of Physics
A Study of the Spectroscopic Performance of Laser Produced CdTe(x):S(1-x) Plasma
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Abstract

In this work, the plasma parameters (electron temperature (Te), electron density( ne), plasma frequency (fp) and Debye length (λD)) have been studied by using the spectrometer that collect the spectrum of Laser produce CdTe(X):S(1-X) plasma at X=0.5 with different energies. The results of electron temperature for CdTe range 0.758-0.768 eV also the electron density 3.648 1018 – 4.560 1018 cm-3  have been measured under vacuum reaching 2.5 10-2 mbar .Optical properties of CdTe:S were determined through the optical transmission method using ultraviolet visible spectrophotometer within the r

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Publication Date
Wed Apr 01 2015
Journal Name
Al–bahith Al–a'alami
University Youth Attitudes towards Electronic Advertisements and their Relationship to the Behavior of the Consumer A Field Study of a Sample of Students of the College of Mass-Communication / University of Baghdad as a Model
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This research aims at identifying the communicative habits and content reflections on the communication process, especially the young audience which is one of the main group for whom the announcements are made. Because young people face life with passion and aspiration making them respond to each effect used by the media in the design of the advertising using all the effective techniques, attractive methods for young children like depending on drama, technical tricks, music and logos easily to be remembered and responded to the desires of the young in their entertainment. This research also aims at identifying the impact of the internet as a channel of commercial advertising on the purchasing behavior of young people at the universities

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Planner And Development
Spatial analysis of rural services in the district of Fallujah, Zgharit village, as a model
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          The study of services in villages is one of the imperative matters that must   be focused on, because it leads to increased attention, which reduces the differences between the countryside and the urban. The extent of its.

  It is well known that community services need to be reached by a person, unlike the anchor services that reach people, here the population distribution plays an important and prominent role in signing these services, so the dispersed distribution pattern and the gathering pattern appeared in the distribution, thus an effect on the time and distance that the person walked to obtain The services are community-based. Therefore

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Publication Date
Tue Sep 13 2022
Journal Name
وقائع المؤتمر العلمي الدولي التاسع / المجلة الامريكية الدولية للعلوم الانسانية والاجتماعية
The Relationship between Job Satisfaction and Organizational Loyalty among Baghdad University Employees in light of Covid- 19 A Descriptive Analytical Study (University of Baghdad as a model)
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The educational service industry is one of the most negatively affected industries by the spread of the COVID-19 pandemic. Government agencies have taken many measures to slow its spread, and then restrict movement and gatherings and stop recreational activities. Furthermore, the repercussions of the curfew had a significant impact due to the interruption in actual attendance for students and employees, and the severity of the Covid-19 crisis and its (economic, social, security, humanitarian and behavioral) effects on all societies and work sectors is no secret to anyone. Iraq, like other countries, was also affected by the negative impact of Covid-19 pandemic in all fields of institutional work, especially public fields, and specifically t

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Publication Date
Sat Jul 04 2026
Journal Name
Al–bahith Al–a'alami
EMPLOYING TWITTER IN THE U.S. PRESIDENTIAL ELECTION CAMPAIGN IN 2016: U.S. PRESIDENTIAL CANDIDATE DONALD TRUMP’S TWEETS AS A “MODEL”: (A Research Drawn from a Master’s Thesis) (An Analytical Study)
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This study aimed to identify the employment of the social networking platform «Twitter» in the 2016 presidential campaign led by the Republican candidate, Donald Trump; and analyse his tweets through his personal account on «Twitter»  for the period from: 10/ 8/2016 to: 11/ 8/2016 which represents the last month of the election campaign.

The study belongs to the type of descriptive studies using the analytical method through an analysis index that includes sub-categories and other secondary categories. The research has adopted the ordinary unit of information material (tweet) as an analysis unit for this purpose.

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