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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 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
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
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
Fri Dec 01 2017
Journal Name
British Journal Of Oral And Maxillofacial Surgery
A novel approach for the three-dimensional evaluation of facial asymmetry of unilateral cleft lip and palate patients (UCLP)
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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of Oral Medicine And Oral Surgery
Evaluating dental implant stability using three devices Osstell<sup>®</sup>, Periotest<sup>®</sup>, and AnyCheck<sup>®</sup>: a clinical study
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Introduction: Implant stability is usually measured with resonance frequency analysis (RFA) and damping capacity assessment (DCA). This study aimed to measure primary and secondary stabilities using 3 devices that are based on these methods, namely; RFA (Osstell®) and DCA (Periotest® and AnyCheck®) to assess the correlations of the measurements obtained by these devices and the correlations between implant stability and insertion torque. Material and Methods: This observational prospective study included 35 dental implants. The implant stability was measured using the 3 devices. Mann–Whitney U

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Publication Date
Sun Sep 02 2012
Journal Name
Baghdad Science Journal
Preparation of PVC composite using reinforced Iraqi Bentoniet clay as a filler & study their mechanical and thermal properties
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In this study , Iraqi Bentonite clay was used as a filler for polyvinyl chloride polymer. Bentonite clay was prepared as a powder for some certain particle size ,followed by calcinations process at (300,700,900) OC ,then milled and sieved. The selected sizes were D ~75 µm and D ~150. After that polyvinyl Al-Cohool solution prepared and used as a coated layer covered the Bentonite powder before applied as a filler ,followed by drying , milling and sieving for limited recommend sizes. polyvinyl chloride solutions were prepared and adding of modified Bentonite power at certain quantities were followed .Sheet of these variables on the mechanical and thermal properties of the prepared reinforced particular polyvinyl chloride composite

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Publication Date
Thu Nov 02 2023
Journal Name
Journal Of Engineering
Constructing a Sustainable Roller Compacted Concrete Using Waste Demolished Material as Replacement of Cement: A Review
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Roller Compacted Concrete is a type of concrete that is environmentally friendly and more economical than traditional concrete. Roller Compacted Concrete is typically used for heavy-duty and specialist constructions, such as hydraulic structures and pavements, because of its coarse surface. The main difference between RCC and conventional concrete mixtures is that RCC has a more significant proportion of fine aggregates that allow compaction and tight packing. In recent years, it has been estimated that several million tons of waste demolished material (WDM) produced each year are directed to landfills worldwide without being recycled for disposal. This review aimed to study the literature about creating a Roller-Comp

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Publication Date
Mon Nov 28 2016
Journal Name
Separation Science And Technology
Using sewage sludge as a permeable reactive barrier for remediation of groundwater contaminated with lead and phenol
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Publication Date
Sun May 02 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Value at risk simulation in a fixed return stock portfolio using the Monte Carlo simulation model The concept of a bond portfolio
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This research aims to predict the value of the maximum daily loss that the fixed-return securities portfolio may suffer in Qatar National Bank - Syria, and for this purpose data were collected for risk factors that affect the value of the portfolio represented by the time structure of interest rates in the United States of America over the extended period Between 2017 and 2018, in addition to data related to the composition of the bonds portfolio of Qatar National Bank of Syria in 2017, And then employing Monte Carlo simulation models to predict the maximum loss that may be exposed to this portfolio in the future. The results of the Monte Carlo simulation showed the possibility of decreasing the value at risk in the future due to the dec

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