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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 Jun 04 2022
Journal Name
Al–bahith Al–a'alami
Iraq's Image in the British Press An analytical study of the Guardian and The Daily Telegraph for 1 / 1- 31/3/2019: Research extracted from a master's thesis
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The topic of the research dealt with the image of Iraq in the British press based on a sample of the newspapers (The Guardian and the Daily Telegraph), which are among the most important and largest newspapers in the United Kingdom and the world, because of its active role in guiding local and international public opinion towards important issues and events, Since these two newspapers are interested in the accuracy of sensitive political topics, the message aimed at knowing the media image that these two newspapers painted about Iraq in the period that was limited to the first quarter of 2019, and also to know the nature of the contents promoted by these newspapers about the Iraqi reality, The method of content analysis was used as an ap

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Publication Date
Wed Dec 15 2021
Journal Name
Al-academy
Simulation of myths in industrial product design "the seven eyes amulet as a model"
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The research is to identify the legend of the seven eyes amulet of Babylonian origin and the representations it carried of the link between the Babylonian past and the Islamic present presented in the design works of the promoted products, preserving its impact in the souls as a way to avoid the act of envy, and from this was the research problem that I want to get answers to, which That is (How was the legend of the seven-eyes amulet represented in the design of industrial products?), making its goal to identify how that legend was represented within the design work of marketed industrial products, and in order to reach the answer, the research presented many concepts starting with the legend in its various forms in industrial products.

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Publication Date
Sat Jun 30 2018
Journal Name
College Of Islamic Sciences
Narrative narration in the poetry of Mohammed Abdul Muttalib   (Top poem as a model)
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Poets of the age since ancient times to recount the events of their adventures in a fun story style in which the elements of the story of personalities, time and place, and we do not mean this modern art technique (poetic story) as it is now, but was aimed at the pleasures of the other receiving because it is the rule of the quality of literary output, Other times the narrative of events inspired by his broad imagination and this mixing indicates the story's involvement with Arabic poetry to be (poetic story) and this depends entirely on addressing the poet to the recipient, and requires in this narrative to be familiar with the elements of influence and suspense in the other or turned into a monotonous and dull narrative Influential, un

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Publication Date
Tue May 16 2023
Journal Name
Political Sciences Journal
The Dens of Extremism and Terrorism in Syrian Camps (Al-Hol as a model)
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After the defeat of the military terrorist organization "ISIS" and the fall of the throne of its alleged state in the Iraqi city of Nineveh, in Syrian Baghouz, and the end of its control over the land, the Syrian camps, especially "Al-Hol" camp, emerge as an incubator for the ideology of the terrorist organization "ISIS" and a vital base for its consolidation and dissemination, which includes (68,000- 73,000) people. During the years following the military defeat of (ISIS), the camp witnesses the spread of extremist ideas widely at the hands of its residents, including the families of the organizations dead's, extremist detainees, and those who deal with it, taking advantage of the deterioration of the environmental, se

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Publication Date
Tue Mar 15 2022
Journal Name
Al-academy
Transformations of the body from traditional expression to subjectivity : Marina Abramivic as a model.
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The way artists deal with body in their artistic works has had so many forms and methods, whether as an object for their drawings or as a material to create live artistic performances that relate to the idea of correspondence and interaction between different artistic categories such as: drama, dance, and painting as it is the case of the artist Marina Abramovic who has always used her body as an artistic unit to generate meaning and to perform her lively shows.
To go deeper into her career, our work was divided into 3 sections:
The first section was devoted to follow the main artistic stages that her body had gone through, starting with paintings she performed using concepts based on acting, simulation and nudity and ending wi

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Publication Date
Tue Jun 14 2022
Journal Name
Al-academy
The genealogy of rough discourse in contemporary theatre (YES, GODOT play) as a model
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The research is exposed to the concept of rough discourse in contemporary theater with a critical reading that takes the genealogical work as a starting point in deconstructing the references of rough discourse and pursuing its paths in the civilization and cultural framework and how it identifies aesthetically within the theatrical field and the extents of its procedural treatments in order to reveal it and clarify its limits and representations, as the research included the first chapter. (methodological framework), the second chapter (theoretical framework), which included two sections, the first took place under the title (rough dramatization), while the second topic took place under the title (rough drama), and the second chapter re

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Publication Date
Mon Jul 01 2019
Journal Name
Journal Of Engineering
The Characters of the Form in the Vernacular Architecture A comparative study of the form's characters of facades of individual houses and commercial buildings in the City of Baghdad after 2003–Zayoona district as a case study
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The characters of facades' form of the Iraqi building after 2003 have been changed, it has been described by many names. The problem of the research is that what are the features of the characters of the form in the façades of the buildings in Baghdad city after 2003? Are the façade of the individual houses or the commercial buildings is the heaviest in the visual weight? The research aims to answer those questions by choosing the vernacular architecture as a measurement tool. It is the informal image of the architecture, which is built by people informally and spontaneously, without official control and legislation to be organized. This is smellier to what has happened in Baghdad, after 2003 according to previous stud

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Publication Date
Sat Feb 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
A comparison of the Semiparametric Estimators model smoothing methods different using
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In this paper, we made comparison among different parametric ,nonparametric and semiparametric estimators for partial linear regression model users parametric represented by ols and nonparametric methods represented by cubic smoothing spline estimator and Nadaraya-Watson estimator, we study three nonparametric regression models and samples sizes  n=40,60,100,variances used σ2=0.5,1,1.5 the results  for the first model show that N.W estimator for partial linear regression model(PLM) is the best followed the cubic smoothing spline estimator for (PLM),and the results of the second and the third model show that the best estimator is C.S.S.followed by N.W estimator for (PLM) ,the

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Publication Date
Fri Oct 28 2022
Journal Name
Political Sciences Journal
A future view for the political systems of the Arab Gulf states After normalization ... the United Arab Emirates as a case study
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The dangers of (Israel's) integration with Arab countries in the middle east region will threaten the Arab security structure dimension, which the latter makes the Arab regional system vulnerable for distortion due to its nominal and symbolic value which is far from the Arab self and questioning with its effectiveness in comparing with the real capabilities to Arab countries in achieving the common targets. So, how to assess the different problems that began to hit the structure of the Arab regional system? and how to pledge an allegiance after putting forward what is known as the American Deal of the Century for the administration of former US President Donald Trump for making another step toward normalization with (Israel)?. The reveal

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Publication Date
Sat Jun 01 2019
Journal Name
Al-nahrain Journal Of Science
THREE DIMENSIONAL EXPLICIT MODEL FOR COMETARY TAIL IONSINTERACTIONSWITH SOLAR WIND
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The different interactions between cometary tail and solar wind ions are studied in the present paper based on three-dimensional Lax explicit method. The model used in this research is based on the continuity equations describing the cometary tail-solar wind interactions. Three dimensional system was considered in this paper. Simulation of the physical system was achieved using computer code written using Matlab 7.0. The parameters studied here assumed Halley comet type and include the particle density , the particles velocity v, the magnetic field strength B, dynamic pressure p and internal energy E. The results of the present research showed that the interaction near the cometary nucleus is mainly affected by the new ions added to the

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