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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
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
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
Sat Oct 03 2020
Journal Name
International Journal Of Pharmaceutical Research
Serum Afamin As A Novel Biomarker for NonAlcoholic Fatty Liver Disease as A Complication of Hypothyroidism in Iraqi Patients.
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Afamin, which is a human plasma glycoprotein, a putative multifunctional transporter of hydrophobic molecules and a marker for metabolic syndrome. Afamin concentration have been proposed to have a significant role as a predictor of metabolic disorders. Since NAFLD is associated with metabolic risk factors, e.g., dyslipidemia, insulin resistance and visceral obesity, it is considered as the hepatic manifestation of the metabolic syndrome. The objective of this study is to determine Afamin levels in hypothyroid patients with and without fatty liver disease and compare the results with controls. Also to study the relationship of Afamin level with the Anthropometric and Clinical Features (Age, Gender, BMI and Duration of Hypothyroidism) , Serum

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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
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
Mon Nov 19 2018
Journal Name
Al–bahith Al–a'alami
Analytical Study of Cartoon picture AL-Mada Newspaper is a model
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The researcher studies and explains the content of some pictures that are published in al-Mada newspaper. The research is important as it deals with a topic that has a relation with visual culture and its role to transfer the press letter to the audience. The researcher finds that cartoonist exposed the security services through important people who have a major role in state policy and reveals the level of corruption and the weak treatments for this phenomenon and its reflection on the whole society and individuals. In addition to that, cartoonists try to encourage the public for going on the peaceful demonstrations since it is a good tool to make pressure on the government to punish the corrupts.

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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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Publication Date
Sat Feb 03 2018
Journal Name
Al- Utroha Journal
Grice’s Maxims in British and American Conversation: A Comparative Study.
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DBN Rashid, Al- Utroha Journal, 2018

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Publication Date
Tue Aug 07 2018
Journal Name
Oral And Maxillofacial Surgery
Mandibular war injuries caused by bullets and shell fragments: a comparative study
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Publication Date
Tue Aug 07 2018
Journal Name
Oral And Maxillofacial Surgery
Mandibular war injuries caused by bullets and shell fragments: a comparative study
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