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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
Fri May 30 2025
Journal Name
Surabaya Medical Journal
Exploring Dental Students' Perspectives: The Impact of Hybrid Learning in a Post-Pandemic World
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Background: The pandemic crisis prompted the world to adopt unexpected approaches to continue life as normally as possible. The education sector, including professors, students, and the overall teaching system, has been particularly affected. Objective: This study seeks to evaluate the benefits, challenges, and strategies related to COVID-19 from the perspectives of college students, particularly those in higher education in Iraq. Method: The online survey questionnaire was distributed via Google Forms and specifically aimed at undergraduate dental students. Results: A total of 348 students participated in the survey. There was a significant correlation (P > 0.01) between student satisfaction with hybrid learning and their experi

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Publication Date
Mon Mar 07 2022
Journal Name
Journal Of Educational And Psychological Researches
The effect of a counseling program in reducing emotional submission among intermediate school students
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Emotions are part of the personality of the individual and affect many different aspects of the personality, and it is an important element of social and psychological adaptation, especially if it is within the limits of nature, and if the methods used to express them are appropriate and moderate.

Submission is one of the characteristics that express the way an individual relies upon in dealing with others and in dealing with matters of life. An individual who complies with instructions and orders and abides by them, and performs what is required of him without hesitation or delay. Adolescence is an important and accurate stage in the constructive development of an individual and in his psychological and social life.

The

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Publication Date
Mon Jun 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Improvement the corrosion Behavior of Titanium by Nanotubular Oxide in a simulated saliva solution
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Abstract<p>The corrosion behavior of Titanium in a simulated saliva solution was improved by Nanotubular Oxide via electrochemical anodizing treatment using three electrodes cell potentiostat at 37°C. The anodization treatment was achieved in a non-aqueous electrolyte with the following composition: 200mL ethylene glycol containing 0.6g NH4F and 10 ml of deionized water and using different applied directed voltage at 10°C and constant time of anodizing (15 min.). The anodized titanium layer was examined using SEM, and AFM technique.</p><p>The results showed that increasing applied voltage resulted in formation titanium oxide nanotubes with higher corrosion resistance </p> ... Show More
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Publication Date
Tue Sep 24 2024
Journal Name
Arab World English Journal
A Critical Discourse Analysis of Women’s Representation in Maysaloon Hadi’s Novel The Black Eyes
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This study applies a discourse analysis framework to explore the portrayal of women in Maysloon Hadi’s novel (The Black Eyes) (2011), using Critical Discourse Analysis (CDA) and Norman Fairclough’s tri-dimensional model (1989) as the analytical foundation. It investigates the roles and challenges women face in the novel. While there is growing interest in the portrayal of women in literature, Iraqi literature—especially from the perspective of Iraqi women writers remains underexplored. Hadi’s *The Black Eyes* provides a unique case to examine this intersection. Despite the novel’s rich narrative, which offers insight into Iraqi women’s lives, there is a lack of comprehensive CDA to understand how its language constructs

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Publication Date
Mon May 15 2023
Journal Name
International Journal Of Professional Business Review
Is It Possible To Adopt A Budget Of Performance In The Iraqi Government Companies?
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Purpose: The study aims to investigate the extent to which material and non-material requirements are available in applying budgeting programs and performance in Iraqi governmental companies that are not aimed at achieving profits. whose activities are limited to providing services of public interest. This is done by studying the extent to which the requirements of each stage of preparing the programs and performance budget can be met.   Theoretical framework: The process of evaluating financial performance is the main objective of all economic units, whether they are governmental or private economic units. Budgets contribute to the evaluation process by analyzing deviations in the application. The study includes an analytical pres

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Publication Date
Sun Apr 01 2007
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Observations on the ultrastructure of a rat mammary gland treated with harmal and borage
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Background : It had been indentified by histological, histochemical and morphometrical studies that peganum harmala is a mammogenic herb and borage officinalis is a lactogenic one . To complete our investigation about these two herbs , we performed electron microscopical study . Materials and methods : Rats were grouped according to their physiological status into three groups . Each group was subdivided in to three subgroups : one control and two experimental . The two experimental group were treated daily; the 1st one with an aqueous extract of peganum harmala seeds and the 2nd with an aqueous extract of borage officinalis flowers . After two weeks of treatment , mammary glands were employed for electron microscopical study . Resu

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Publication Date
Thu Dec 03 2020
Journal Name
Almaarif University College
The effect of food additives (Monosodium Glutamate-MSG) on human health-A Critical Review
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According to the famous saying of the medieval physician Paracelsus, "There is no substance without poison. Only the dose determines the extent of the toxic effect." Here, the effect of monosodium glutamate (MSG) on human health and the risks to the health of its frequent use in the short term was addressed and the long term was evaluated according to the studies of several researchers specializing in this regard. Monosodium glutamate (MSG) is known as one of the most popular food additives that classified as a flavor enhancer. Parts of the evidence were reviewed from the literature explaining its effect on immune system cells in addition to metabolic disorders by exposing individuals to obesity and what is known as metabolic syndrome, as w

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Publication Date
Thu Feb 07 2019
Journal Name
Iraqi Journal Of Laser
Creating a Conductive Surface of the PMMA by Laser Cladding with DWCNT and MWCNTS
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This work studied the electrical and thermal surface conductivity enhancement of polymethylmethacrylate (PMMA) clouded by double-walled carbon nanotubes (DWCNTs) and multi-walled carbon nanotube (MWCNTs) by using pulsed Nd:YAG laser. Variable input factors are considered as the laser energy (or the relevant power), pulse duration and pulse repetition rate. Results indicated that the DWCNTs increased the PMMA’s surface electrical conductivity from 10-15 S/m to 0.813×103 S/m while the MWCNTs raised it to 0.14×103 S/m. Hence, the DWCNTs achieved an increase of almost 6 times than that for the MWCNTs. Moreover, the former increased the thermal conductivity of the surface by 8 times and the later by 5 times.

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Publication Date
Sun Feb 28 2021
Journal Name
Journal Of Economics And Administrative Sciences
The impact of complexity management on dynamic capabilities: a survey at some private colleges
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This research aims to understand complexity management and its impact on the use of the dynamic capabilities of a sample of private colleges.  Private colleges are currently facing many crises, changes, unrest and high competitive pressures.  Which is sometimes difficult or even impossible to predict.  The recruitment of dynamic capabilities is also one of the challenges facing senior management at private colleges to help them survive and survive.  Thus, the problem of research was (there is a clear insufficiency of interest in Complexity Management and trying to employ it in improving the dynamic capabilities of Colleges that have been discussed?). A group of private colleges was selected as a

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Publication Date
Wed Jun 10 2009
Journal Name
Iraqi Journal Of Laser
The performance of a passively Q-switched Cr:YAG4+ in an end- pumped laser system
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A characteristic study of a passively Q-switched diode pumped solid state laser system is presented in this work. For laser a comparison study for the theoretically calculated results with a simulation results using a software which calculates the Q-switched solid state laser parameters was such as energy, peak power and pulse width were performed. There was a good agreement between our theoretical calculations and the simulation values.

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