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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 15 2024
Journal Name
Journal Of Legal Sciences
Criminal Protection of Human Genome “Human Gene Editing as a Model”
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Lawful protection of the human gene conceded a moral concern regarding the future of existence human. After the discovery of the human genetic map, scientific experiments and research related to the human gene increased, negative applications of genetic engineering  in particular that violate essential human rights,  the right to human dignity to be specific. These practices represent actual challenges to the existence and diversity of current and future generations. Therefore, the presence of legal rules at the domestic and global levels is an absolute necessity to prohibit these threats and determine civil and criminal accountability for those who infringe any laws related to this issue.

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Publication Date
Wed Dec 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
Openness Management by Figures as a Model of Integrity and Transparency
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Competitive advantage is a substantial  strategic objective for organizations. It requires high levels in the quality of products and services provided to customers, continuous improvement of costing , care for creativity and innovative employees, and speed unique to the marketing and financial engineering, and business re-engineering processes. The situation in this area, requires actors to attract and develop human resources, including help in proper implementation of the strategic tasks that targeted by those institutions. According to the opinions and viewpoints of management scholars, the competitive advantage resource is the most important issue for organizations in the third millennium, which can be a

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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
Thu Dec 15 2022
Journal Name
Al-academy
Evaluating the education quality in the College of Fine Arts "Design Department as a model"
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Education quality evaluation is one of the objectives of education quality. The evaluation includes assessing the education standards and academic program outcomes to develop intellectual, scientific and practical concepts for the educational structure. It considers the determination of the rates of the number of accepted students and graduates. The research focuses on "what are the levels of education quality according to the evaluation mechanisms in the design department" to enhance the quality system and the objectives of theoretical and applied education.
It is identifying the levels of education quality and evaluating it according to the numbers and rates of graduate students of the design department branches for morning and ev

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Publication Date
Thu May 14 2020
Journal Name
Journal Of Planner And Development
Visual Pollution and its Impact on the Aesthetics: The Town of Eizariya as a Model
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This study seeks to shed light on the aspects of visual pollution and its impact on the aesthetics of the town of Al-Eizariya known to suffer from the phenomenon. In order to identify the real causes of the problem which develops in various forms and patterns, threatening not only the aesthetic appearance of the towns, but also causes the emergence of new problems and phenomena that will have negative repercussions on the population. The researcher uses the analytical descriptive method to analyze the phenomenon of visual pollution in terms of reality, development, manifestations and spread and uses photos which document the visual pollution and its impact on the aesthetics of the known. The study concluded the existence of a strong rela

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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 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 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
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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