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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
Sun Mar 06 2022
Journal Name
Al–bahith Al–a'alami
THE ETHICAL RESPONSIBILITY OF THE COMMUNICATOR IN PRESS INSTITUTIONS TO CONSOLIDATE THE VALUES OF TOLERANCE: A Study of the Communicator in the Newspapers (Al-Zaman, Al-Sabah, Al-Mada) For the period: 1/5/2020 to 1/10/2020
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This research deals with the role that the media can play in spreading awareness, culture and sound behavior among members of society, due to its ability to reach the largest number of individuals; its wide spread within society; and the moral responsibility of the media in consolidating the components of civil peace. The media works on forming intellectual convictions and behavioral attitudes by publishing opinions and ideas, introducing them to people's awareness and enhancing them in the practice of their daily lives, he was its media medium. Sociologists and psychologists confirm that the media. The significance of the research comes due to the broadening of violence and sectarian fighting; the absence of a culture of civil social pe

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Publication Date
Mon Jun 30 2025
Journal Name
Medical Journal Of Babylon
Assessment of Six Polymorphic Variants as Genetic Risks for Coronary Artery Disease: A Case–Control Study
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Abstract<sec> <title>Background:

Coronary artery disease (CAD) is the leading cause of death worldwide. Certain genetic polymorphisms play an important role in this multifactorial disease, being linked with increased risk of early onset CAD.

Objective:

To assess six genetic polymorphisms and clinical risk factors in relation to early onset nondiabetic Iraqi Arab CAD patients compared to controls.

Materials and Methods:

This case–contro

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Publication Date
Sun Jun 01 2014
Journal Name
Alustath Journal For Human And Social Sciences
Obstacles to the application of electronic management in university libraries: the universities of Baghdad and Al-Mustansiriya as a model.
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The research aims to identify the obstacles facing the application of electronic management in our university libraries, including the central library of the University of Baghdad and the central library of Al-Mustansiriya University, the research sample, as they are among the main libraries that used electronic technologies in managing some of their work and in providing their services, and they have a website via the Internet. The research relied on the case study method to identify the obstacles by visiting the two libraries, interviewing their managers and employees responsible for the departments, and answering inquiries about the obstacles that prevent the application of electronic management in order to identify them and find appropr

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Publication Date
Sun Oct 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Mackenzie role model dimensions in the quality of service, "a Prospective study of the views of a sample of Iraqi banks managers
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The organizational integration forms a necessity according to McKinsey model, especially for service organizations. In the context of various service sector developments, importance adoption of compact mechanisms by these organizations to upgrade their services has increased and senior management must be more aware of environmental, competitive and developmental requirements. It gets more important when it shows in an organization seeking at excellence of making services within its policies and strategies. Subject organizational integration dimensions (strategy, structure, systems, style, staff, shared values, and skills) are effective components in directing behaviors of employees and organization. This motivated both researcher

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Publication Date
Tue Apr 18 2023
Journal Name
Al–bahith Al–a'alami
Media policy and its impact on the level of objectivity in the Iraqi media : A study from the communicators’ point of view in the Iraqi medi outlets for the period from (1/5/2021 to 1/9/2021)
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The research aims to reveal the impact of media policy in Iraqi media outlets on the level of objectivity in these outlets. A study from the communicators’ point of view where the researcher used a survey method on the communicators in media outlets to reveal the extent of media policies knowledge as well as the pressures exerted by this policy on communicators in media outlets. It also reveals the extent of their commitment to objectivity, neutrality in dealing with information and the way used to transfer it.
The research sample included (179) respondents from communicators in a range of Media outlets such as (Press, Radio, and Television), The researcher was careful with the diversity of the sample, and

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of The College Of Languages (jcl)
The Intellectual as an Alien: A Study of Henry James's The Beast in the Jungle and James Joyce's "A Painful Case"
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This research paper studies the alienation of the intellectuals in the modern novel through the study of two alienated characters, John Marcher in Henry James's The Beast in the Jungle, and Mr. Duffy in James's Joyce's "A Painful Case." As a result of the complexity of life in the industrial societies, the individuals, especially the intellectual ones, feel themselves unable to integrate into social life; they fear society and feel that it endangers their individuality and independence. Thus, these characters live on the fringe of the societ

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Publication Date
Wed Sep 01 2010
Journal Name
Al-khwarizmi Engineering Journal
A Study of the Effect of Kaolin as a Fuel Oil Additive on the Corrosion Inhibition of Fireside Superheater Boiler Tubes
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The objective of the present study is to determine the effect of Kaolin as a fuel oil additive to minimize the fireside corrosion of superheater boiler tubes of ASTM designation (A213-T22) by increasing the melting point of the formed slag on the outside tubes surface, through the formation of new compounds with protective properties to the metal surface. The study included measuring corrosion rates at different temperatures with and without additive use with various periods of time, through crucible test method and weight loss technique.

      A mathematical model represents the relation between corrosion rate and the studied variables, is obtained using statistical regression analysis. Using this model,

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Publication Date
Fri Oct 28 2022
Journal Name
Political Sciences Journal
Applications of contemporary feminist theory and its role in international relations (Singapore as a Model)
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Since the emergence of the science of international relations as an independent academic scientific field,  various theories and trends have appeared and have tried to understand and explain the international reality and give a clear picture of what is happening within the international system of interactions and influences and the search for tools for stability and peace in international relations. Among these theories is the feminist theory, which is a new intellectual trend on the level of international relations theories,  which tried to give an explanation of what is happening in world politics and in international relations in particular. The main issue that feminist theory is concerned with is the lack of women’s subordination

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Publication Date
Tue Apr 02 2019
Journal Name
Journal Of Environmental Health Science And Engineering
Adsorptive performance of a mixture of three nonliving algae classes for nickel remediation in synthesized wastewater
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Publication Date
Tue Sep 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Salivary mucoepidermoid carcinoma, auclair vs brandwein grading system: A histopathological comparative study
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Background: The grading systems of salivary mucoepidermoid carcinoma depend on different histologic and morphologic features. The aim of this study was to compare between Auclair and Brandwein systems according to their histologic criteria, and the type of cell predominant. Materials and Methods: Twenty-one case included hematoxylin-eosin (H&E) stained tissue slides that were diagnosed as MEC, originally categorized into low and high grade type regardless of the grading system, have meticulously undergone histopathologic review. The sample was graded according to criteria owing to Auclair and Brandwein methods. The predominant type of cells was determined by microscopic examination according to grade of tumor. Results: Regarding the

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