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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 Dec 01 2018
Journal Name
Acta Facultatis Medicae Naissensis
The Factors Influencing the Risk of Perforation in Patients with Peptic Ulcers: A Cross-Sectional Study from Central Iraq
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Abstract<p>The aim of this study was to evaluate the risk factors that influence the perforation, regardless of the presence of H. pylori infection, in a sample of Iraqi patients with peptic ulcers, admitted to Al-Kindy Teaching Hospital. A total of 90 patients who had perforated peptic ulcer participated in this study. The diagnosis was based on history, clinical examination, laboratory and radiological investigations and was confirmed intraoperatively. A number of probable risk factors for perforation were investigated. Eighty participants were males and 10 were females (male to female ratio 8:1). About 42.2% of patients were in their fifth decade of life. Forty-nine (54.4%) patients were asymptomatic be</p> ... Show More
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Publication Date
Sun Sep 03 2017
Journal Name
Baghdad Science Journal
Kinetic and Mechanistic Studies for the Gas-phase Reaction of Ozone with 2, 3-Dimethyl-2-Butene and 1, 3-Butadiene
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The reactions of ozone with 2,3-Dimethyl-2-Butene (CH3)2C=C(CH3)2 and 1,3-Butadiene CH2=CHCH=CH2 have been investigated under atmospheric conditions at 298±3K in air using both relative and absolute rate techniques, and the measured rate coefficients are found to be in good agreement in both techniques used. The obtained results show the addition of ozone to the double bond in these compounds and how it acts as function of the methyl group substituent situated on the double bond. The yields of all the main products have been determined using FTIR and GC-FID and the product studies of these reactions establish a very good idea for the decomposition pathways for the primary formed compounds (ozonides) and give a good information for the effe

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The Use of Principal Components Analysis in the Formation of a Sustainable Human Development Index for Arab Countries
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This study aims to derive a sustainable human development index for the Arab countries by using the principal components analysis, which can help in reducing the number of data in the case of multiple variables.  This can be relied upon in the interpretation and tracking sustainable human development in the Arab countries in the view of the multiplicity of sustainable human development indicators and its huge data, beside the heterogeneity of countries in a range of characteristics associated with indicators of sustainable human development such as area, population, and economic activity. The study attempted to use the available data to the selected Arab countries for the recent years. This study concluded that a single inde

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
Lying in Arthur Miller's The Crucible: A Pragmatic Study: هديل محمود إبراهيم , جمعه قادر حسين
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Lying is a controversial issue as it is closely related to one's intended meaning to achieve certain pragmatic functions. The use of lying in literary works is closely related to the characters’ pragmatic functions as in the case of Miller's The Crucible where it is used as a deceptive complex phenomenon that cannot be observed out of context. That is, the use of lying as a deceptive phenomenon represents a violation to Grices's Maxims. Thus, the study aims to qualitatively examine the kinds of maxims being violated, the kinds of violations conducted, the strategies followed in the violations, and the pragmatic functions behind such violations across the different categories of lies. To this end, the (30) extracts fou

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Publication Date
Sat Apr 01 2017
Journal Name
Al–bahith Al–a'alami
Palestinian Media Elite Attitudes towards Recording Cinemas in Addressing the Internal Situations: A Field Study
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The follower of the history of cinema in the world notes that cinema started recording one and these films are varied in their subjects, while the life of man was the material of these films to be in a creative artistic style.
If the Palestinian films produced by Palestinian directors do not have an impact on the local, Arab and international levels, this is due to the weakness in several technical fields or with the intention to make them bad or negligence of those who produce these films.
This research deals with the role played by Palestinian films in dealing with the internal situation from the point of view of the Palestinian media elite in terms of their exposure to films and the motives of this exposure and the expectation

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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
What Bukhari shortened to a bug in its attribution: (Applied study in the correct mosque)
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This study aims to show some of Imam Al-Bukhari's criticism of the Hadith from the Metn side, and part of his methodology in dealing with the correct hadiths that are tainted by a bug. This research focuses on what Imam Al-Bukhari summarized in his Sahih illusion of the narrator in his attribution, or uniqueness of the narrator, or to suggest a novel. We find that Bukhari sometimes abbreviates the hadeeth, and does not bring it out completely in his Sahih. He is satisfied with the abbreviated position but has done so because of a bug in it. The Bukhari usually does not declare his intention but knows this through tracking, inspection, and research of the correct hadiths.

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Publication Date
Sat Jun 24 2023
Journal Name
Arab World English Journal
Humor in The Stand-Up Comedy You Wanna Hear Something Crazy?: A Universal Pragmatic Study
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Humor is an interesting phenomenon that has been studied widely, yet it is considered a universal trait that cannot be an old subject for a study. This study is conducted to investigate humor from a universal pragmatic lens in a stand-up comedy show, namely, You Wanna Hear Something Crazy?. It aims to study humor as a coin with two sides, the production side and the understanding side. To achieve the aim of the study, the researchers use an eclectic contains Grice’s CP model (1975) and Habermas’s UP model (1979, 1984, 1987, 1998). The study has noted that while using the observance and the non-observance of the cooperative maxims to produce humor, the universal validity claims of truth, sincerity, and normative rightness for rea

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Jalal AL-deen ALhanafi and his educational effect on the IRAQI society - A historical study
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Sheikh Hanafi was born in one of the popular shops of Baghdad with interlocking social relations, and had a profound impact this camp where his talents in the first Venco loving to Mahalah and Baghdad and was born with this development since his days looked forward to the folklore and folk. In the middle of his youth, including authoring loves the heritage of folk legacies began in motion, from Baghdad, books, articles, research has brought him wide acclaim were not possible without the seriousness and diligence, independence and self-Asamath that mushroom on them
The trip was one of his tools in the scientific fame has gone to many Eastern and Asian countries and visited religious and literary institutes and delivered the lectures an

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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Comparing the Impact Strength and Transverse Flexure Strength of Three Different Dentures Base Materials
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Publication Date
Sun May 01 2016
Journal Name
Journal Of Engineering
Three-Dimensional Finite Element Simulation of the Buried Pipe Problem in Geogrid Reinforced Soil
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Buried pipeline systems are commonly used to transport water, sewage, natural oil/gas and other materials. The beneficial of using geogrid reinforcement is to increase the bearing capacity of the soil and decrease the load transfer to the underground structures.

This paper deals with simulation of the buried pipe problem numerically by finite elements method using the newest version of PLAXIS-3D software. Rajkumar and Ilamaruthi's study, 2008 has been selected to be reanalyzed as 3D problem because it is containing all the properties needed by the program such as the modulus of elasticity, Poisson's ratio, angle of internal friction. It was found that the results

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