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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 Feb 28 2021
Journal Name
Journal Of Economics And Administrative Sciences
Availability Assessment of theManaging the Audit Program. According to the Specification Standard (ISO 19011:2018): A case study in Ministry of Construction Housing and General Municipalities
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The research aims to study the reliability of government institutions, including the audit directors, which are one of the most important oversight formations in the Ministry of Construction, Housing and Public Municipalities, on which the responsibility for comprehensive auditing of all the Ministry's (municipalities) formations falls on the Managing the Audit Program according to the specification (ISO 19011: 2018) to improve the audit performance which requires compliance with the application of the audit management system in accordance with the standard Specification (ISO 19011: 2018), depending on the methodology of the case study, and using of checklists, which were chosen ac

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Publication Date
Wed Jun 30 2021
Journal Name
College Of Islamic Sciences
العربية Atheism A study in the most important foundations of atheism, and the most prominent suspicions of its advocates: دراسة في أهمّ مرتكزاته، وأبرز شبهات دُعاته
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Atheism is one of the most dangerous absurd doctrines that have swept the world in the modern era. Its strength lies in the bodies that stand behind it and adopt its ideologies which are accompanied by the tremendous media momentum of the theses of its supporters based on scientific and non-scientific levels. And since the denial of the existence of the Creator is the main focus and central point which the atheists based their view towards the universe, life and man, this humble research came to discuss the claim of the existence of the world by pure chance, and try to explain this scientifically through the theory of natural selection and survival of the fittest developed by the English biologist Charles Darwin. The resea

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Publication Date
Fri Jan 13 2023
Journal Name
Atmosphere
Impact of North African Sand and Dust Storms on the Middle East Using Iraq as an Example: Causes, Sources, and Mitigation
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This study aims to determine the reasons for the increase in the frequency of sand and dust storms in the Middle East and to identify their sources and mitigate them. A set of climatic data from 60 years (1960–2022) was analyzed. Sand storms in Iraq are a silty sand mature arkose composed of 72.7% sand, 25.1% silt, and 2.19% clay; the clay fraction in dust storms constitutes 70%, with a small amount of silt (20.6%) and sand (9.4%). Dust and sand storms (%) are composed of quartz (49.2, 67.1), feldspar (4.9, 20.9), calcite (38, 5), gypsum (4.8, 0.4), dolomite (0.8, 1.0), and heavy minerals (3.2, 6.6). Increasing temperatures in Iraq, by an average of 2 °C for sixty years, have contributed to an increase in the number of dust storm

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Publication Date
Wed Jun 03 2020
Journal Name
Political Sciences Journal
The Muslim Arab Self and the image of the other, religiously and culturally different: a critical analytical study of the causes and forms of political and social intolerance in Iraq
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This research aims to analyze the intellectual and civilizational regression that afflicted Iraqi and Arab society due to political and religious tyranny and internal conflicts, which was reflected in the deterioration of human rights values and the absence of equality and justice in dealing with the other religiously, which affected the reluctance of members of religious groups to interact with their national societies and then migrate to Outside, which contributed to a double loss, in terms of the loss of these societies by productive and effective national competencies, and in terms of distorting the image of Islam. The research stressed that the first treatments of this phenomenon are the consolidation of the values of citize

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
The Historical Value of Dickens’s A Tale of Two Cities
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In "historical" fiction, characters that never really existed, give expression to the impact of historical events on the people who really did live through them. The result is not history, as an accurate record of actual events, but fiction in which an earlier age is rendered through the personal joys and sufferings of characters. This paper
aims at investigating the historical realities presented in Dickens’s A Tale of Two Cities.

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Publication Date
Thu Jan 20 2022
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
The Homomorphism of Cubic bipolar ideals of a KU-semigroup
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The idea of a homomorphism of a cubic set of a KU-semigroup is studied and the concept of the product between two cubic sets is defined. And then, a new cubic bipolar fuzzy set in this structure is discussed, and some important results are achieved. Also, the product of cubic subsets is discussed and some theorems are proved.

Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
A THEORETICAL VISION OF THE METHODOLOGY OF MATCHING AND CONGRUENCE
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Perhaps the issue of media and the press, especially one of the most common topics that people deliberate and deal with permanently and continuously. An issue of such significance has pushed researchers to put the following question, “Is it possible to live without media?”, “Can people ignore the newspaper, radio, TV, or the other communication means?”

The answer is very simple. It is difficult for civilized society to overtake information, or dispense with circulation, at the individual or collective level. Yet, the question of how to make the media and how it determines its content still requires extensive media experience; and knowledge of the social structure and its relations; and ac

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Publication Date
Sun Dec 04 2016
Journal Name
Baghdad Science Journal
Extraction of Iraqi Jasminumsambac (L.)Oil and Study It?s Effect as Antioxidant Agents
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Key words:Jasminumsambac, Volatile oil, Antioxidant.

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Publication Date
Fri Oct 26 2018
Journal Name
Journal Of Planner And Development
Acceptable and Unacceptable Growth of Industrial Agglomeration in Urban Environment. Baghdad as Case Study
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Publication Date
Sun Feb 25 2018
Journal Name
Oriental Journal Of Chemistry
Synthesis and Study of Modified Polyvinyl Alcohol Containing Amino acid moieties as Anticancer Agent
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