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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
Tue Dec 20 2011
Journal Name
المؤتمر الدولي الثالث للاحصائيين العرب
Use a form ARX(p,q) to estimate time series for the Iraqi Economy
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Due to the lack of statistical researches in studying with existing (p) of Exogenous Input variables, and there contributed in time series phenomenon as a cause, yielding (q) of Output variables as a result in time series field, to form conceptual idea similar to the Classical Linear Regression that studies the relationship between dependent variable with explanatory variables. So highlight the importance of providing such research to a full analysis of this kind of phenomena important in consumer price inflation in Iraq. Were taken several variables influence and with a direct connection to the phenomenon and analyzed after treating the problem of outliers existence in the observations by (EM) approach, and expand the sample size (n=36) to

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Publication Date
Wed Mar 01 2023
Journal Name
Iraqi Journal Of Physics
Design and Construction of a Dust Detection System using Infrared Laser: The Case of Dust Storms in Baghdad in the Summer 2022
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Iraq suffers from serious pollution with harmful particles that have important direct and indirect effects on human activities and human health. In this research, a system for detecting pollutants in the air was designed and manufactured using infrared laser technology. This system was used to detect the presence of pollutants in the dust storms that swept the city of Baghdad which could have a negative impact on human health and living organisms.

The designed detection system based on the use of infrared laser (IR) with a wavelength of 1064 nm was used for the purposes of detecting pollutants based on the scattering of the laser beam from these pollutants. The system was aligned to obtain the best signal for the scattered rays, w

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Publication Date
Thu Oct 18 2018
Journal Name
European Journal Of Organic Chemistry
PdII-Mediated Oxidative Amination for Access to a 9-Azabicyclo[4.2.1]nonane Compound Library and Anatoxin-a
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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison Between the Methods Estimate Nonparametric and Semiparametric Transfer Function Model in Time Series Using Simulation
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Publication Date
Thu Sep 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Different Methods of Canine Retraction- Part 1
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Background: This review aimed at explaining different methods of canine retraction along the archwire. Methods: Searching for different methods of canine retraction using fixed orthodontic appliances was carried out using different databases, including PubMed Central, Science Direct, Wiley Online Library, the Cochrane Library, Textbooks, Google Scholar, Research Gate, and hand searching from 1930 till February 2022. Results: After excluding the duplicate articles, papers describing the methods of canine retraction along the archwires were included. The most commonly used methods are NiTi closed coil spring and elastic chain. Conclusions: Various methods of canine retraction along the archwires were explained in detail regarding their adv

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Publication Date
Sun Mar 28 2021
Journal Name
Journal Of The College Of Education For Women
The Stories of Proverbs in the Holy Qur’an, Prophet’s Hadith, and Arabs’ Sayings: A Literary Study: مسلم عبيد فندي الرشيدي
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The Arab realized that proverbs and their stories had a great literary and linguistic significance, accordingly, they collected them from their sources and wrote them down. Thus, researchers went in studying them in different directions. The aim of the present research is thus to study the stories of proverbs in the Holy Qur’an, Prophet’s hadiths, and in the sayings of Arabs. Such a study helps to show the extent of the relevance of their stories to the proverbs, their literary values, the points of convergence between them and what they highlight, and the extent of their proximity to reality. It further helps to determine the factors that contributed to the transformation of Quranic verses, Prophet’s hadiths, and some phrases of s

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Publication Date
Mon Apr 06 2020
Journal Name
Asian Journal Of Civil Engineering
Integrated project delivery (IPD) method with BIM to improve the project performance: a case study in the Republic of Iraq
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Publication Date
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
''The use of factor analysis to identify the leading factors to high blood pressure.''A field study in Baghdad hospitals
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Abstract :

    In view of the fact that high blood pressure is one of the serious human diseases that a person can get without having to feel them, which is caused by many reasons therefore it became necessary to do research in this subject and to express these many factors by specific causes through studying it using (factor analysis).

  So the researcher got to the five factors that explains only 71% of the total variation in this phenomenon is the subject of the research, where ((overweight)) and ((alcohol in abundance)) and ((smoking)) and ((lack of exercise)) are the reasons that influential the most in the incidence of this disease.

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Publication Date
Sun Mar 28 2021
Journal Name
Journal Of The College Of Education For Women
Judicial Legislations and the Tribal Claims System in the Royal Period: A Documentary Study: احمد عبدالواحد عبد النبي
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The present research tackles a number of historical facts and incidents with a purely legal dimension in an important stage in the contemporary history of Iraq, especially the era of the British occupation. This resulted in innumerable social, political and legal problems, particularily the judicial legislation problems in Iraq. These legislations included a set of civil laws and in force governmental procedures that will be discussed historically by examining documents issued by the Ministries of Justice and Interior Affairs in the governments of monarchy for the period from 1921-to-1958. The data of the present paper relied on the Iraqi Library and Archives, (hence DKW). The study adopted the narrative historical methodology when inves

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Publication Date
Tue Jun 20 2023
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
The PharmD Students’ Beliefs, Perceptions, and Challenges Regarding their First Year in the PharmD Program: A Qualitative Study
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Background: The beliefs of pharmacy students in their curriculum may be critical to the success of medical education and the development of global health competences. Objective: To assess the beliefs, attitudes, and obstacles of PharmD students at the College of Pharmacy, University of Baghdad, during their first year in the newly adopted PharmD program. Method: In-depth qualitative interviews were conducted using flexible probing approaches. A sample of fourth-year PharmD students from the University of Baghdad's College of Pharmacy was selected using a purposive sampling method. The gathered data was analyzed using a thematic content analysis approach. Results: 40% of participants applied for the program because they believed it w

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