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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
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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Publication Date
Wed Mar 25 2020
Journal Name
International Journal Of Drug Delivery Technology
Osteocalcin as a Biomarker for Estimation of Infertility for Iraqi Patients
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Objective: The evaluation of serum osteocalcin (OSN) for Iraqi infertile patients to see the effect of osteocalcin insufficiency, which may lead to a decreased level of testosterone production in males that may cause infertility. Methods: Forty two newly diagnosed infertile males age range (24–47) years and thirty two apparently healthy males as controls age range (25–58) years. Serum levels of testosterone (TEST), stimulating follicle hormone (FSH) and luteinizing hormone (LH), prolactin (PROL), osteocalcin OSN, and fasting blood sugar (FBS) were performed in both patients and controls. Estimation of serum OSN by Immulite1000 auto-analyzer, TEST, FSH, LH, PROL, and FBS by Immulite2000 auto-analyzer. Results: Infertile patients

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Publication Date
Sat Dec 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Selecting Optimum Dimensions for a Three-Phase Horizontal Smart Separator for Khor Mor Gas-Condensate Processing Plant
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      The Khor Mor gas-condensate processing plant in Iraq is currently facing operational challenges due to foaming issues in the sweetening tower caused by high-soluble hydrocarbon liquids entering the tower. The root cause of the problem could be liquid carry-over as the separation vessels within the plant fail to remove liquid droplets from the gas phase. This study employs Aspen HYSYS v.11 software to investigate the performance of the industrial three-phase horizontal separator, Bravo #2, located upstream of the Khor Mor sweetening tower, under both current and future operational conditions. The simulation results, regarding the size distribution of liquid droplets in the gas product and the efficiency gas/liquid separation, r

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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
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
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
Tue Nov 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Performance evaluation of policies and programs accordance with guide prepared by a dutch court of audit and the board of supreme audit (case study in wasit state company for textile industries)
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Abstract\

preparation process of performance evaluation in organizations is of extreme importance, and under development in organizations and the opening of markets and technological developments in the industry and heightened competition among industrial organizations imposed systems are built for performance give a clear picture about performance and competition,  And centered research problem in answering the following questions: Is performance evaluation system is available in Wasit State Company for Textile Industries(Research sample ), This research aims to assess the performance of policies and programs in the company, according to guide performance evaluation of programs and policies prepared by the Dutch Cou

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