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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
Thu Mar 30 2023
Journal Name
F1000research
In-depth assessment of Iraqi physicians' adherence to treatment guidelines for different diseases: a qualitative study
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Background: In healthcare settings, specialists from different fields may follow the most well-known, reliable, and easy-to-understand medical guidelines. This study aimed to determine Iraqi physicians' adherence to treatment guidelines, to specify which treatment guidelines are utilized for each disease and identify their barriers to follow the guidelines.

Methods: This was qualitative study including face-to-face and virtual semi-structured interviews with specialist physicians from different disciplines. The interviews were conducted between December 2021 and May 2022 in Kirkuk province, Iraq. The qualitative data generated through i

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Publication Date
Mon May 01 2017
Journal Name
Ieee International Electrical Machines & Drives Conference Ieee (iemdc2017), Miami, Usa
The effect of power converter on the design of a Linear Alternator for use with a Joule Cycle-Free Piston Engine
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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The effect of Layout in measuring customer satisfaction (patients) using (Servicescape) model
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Abstract:

This research aims to identify the impact of the Layout Ghazi al-Hariri hospital for surgery specialist on customer satisfaction (patients) using the model (Servicescape), the problem of the research represented in the extent to which the hospital management design of the service and Layout hospital aesthetic and functional aspects that fit patients for therapeutic and nursing services , and used the developer scale by (Miles et al., 2012) for data collection, which includes the independent variable in (17) items distributed in three dimensions (Facility aesthetics , hospital cleanliness, and the Layout accessibility ) The dependent variable is the satisfaction of customers (pat

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Publication Date
Wed Jun 28 2023
Journal Name
Al–bahith Al–a'alami
Public Attitudes Towards National Issues in Interactive Television Programs
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This research aims to investigate the extent to which the Iraqi audience relies on interactive television programs as a source of information regarding national issues and their resulting impacts. It seeks to identify the types and nature of attitudes developed among the public towards national issues through these programs and determine the prominent topics and issues highlighted to the audience. The researcher employed a field survey as the primary research method, employing a questionnaire for data collection along with scientific observation and the Likert three-point scale to measure attitudes. The study was guided by the media dependency theory. A sample of 520 questionnaires was distributed to residents in

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Publication Date
Thu Aug 07 2025
Journal Name
Modern Sport
An analytical study of some of the deterministic variables of the stage of advancement and its relation to the accuracy of the performance of the skill of high jump correction
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Publication Date
Sun Jan 01 2023
Journal Name
Studies In Systems, Decision And Control
Gap Analysis by Readiness Review Including Online Learning During COVID-19 Pandemic Period for Engineering Programs at the College of Engineering—University of Baghdad
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Publication Date
Thu Dec 13 2018
Journal Name
Al-adab Journal
A Victim of "Love": A Study of Beatrice’s Character in "Rappaccini's Daughter" By Nathanial Hawthorne
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Nathaniel Hawthorne (1804-1864) has been widely known for his special interest in the female characters. In many of his novels, he narrates the conditions, values, and the institutions that surround and control the life of women, leading them to be victims. In “Rappaccini’s Daughter” (1844), the heroine, Beatrice is created to be victimized by her loved ones (her father and lover). This paper focuses on the term “victim,” it shows its aspects through the development of Beatrice’s character. The paper also studies a female character in the male-dominated society, to show the cruelty done to her, and how she is considered to be a second rate person, who is unable to live normally, or at least to save herself from dea

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Publication Date
Mon Oct 01 2018
Journal Name
World Journal Of Pharmacy And Pharmaceutical Sciences
THE ANTIBACTERIAL EFFECT OF FLAXSEED EXTRACT ON SELECTIVE ORAL PATHOGENS - COMPARATIVE IN VITRO STUDY
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Flaxseed from the flax plant (Linum usitatissimum), which has been cultivated for domestic use since prehistoric times. This study aims to investigate presence of antibacterial effect of flaxseed extract against selected oral pathogen in-vitro.

Publication Date
Fri May 25 2018
Journal Name
Open Public Health Journal
Comparative Study on the Clinicopathological Profiles of Breast Cancer Among Iraqi and British Patients
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Background: Breast cancer is the most common cancer in Iraq and the United Kingdom. While the disease is frequently diagnosed among middleaged Iraqi women at advanced stages accounting for the second cause of cancer-related deaths, breast cancer often affects elderly British women yielding the highest survival of all registered malignancies in the UK. Objective: To compare the clinical and pathological profiles of breast cancer among Iraqi and British women; correlating age at diagnosis with the tumor characteristics, receptor-defined biomarkers and phenotype patterns. Methods: This comparative retrospective study included the clinical and pathological characteristics of (1,940) consecutive female patients who were diagnosed with invasive b

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Publication Date
Sun Jun 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A study of the Rate of Sedimentation of Magnesium Hydroxide Obtained from Bittern
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