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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
Fri Jul 01 2016
Journal Name
Al–bahith Al–a'alami
A Semiotic Approach to the Analysis of the News Story
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This study attempts to provide an approach analysis for the news, depending on the bases and principles which conceptuality semiotic researchers of this field first of them «A. J. Gremas» for the theory of «narrative discourse analysis», to more clarify we tried to apply it on a published press- news, to concludes the most important steps and methods that are necessary to follows gain more understanding of the press- news.

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Publication Date
Wed May 17 2023
Journal Name
College Of Islamic Sciences
A stylistic vision of the objection in the Quranic discourse
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The modern stylistic lesson has become more committed to the scientific limits in which it believed, and more confident in itself, and it is no longer just a scientific procedure that helps other curricula and sciences that preceded it.

Based on this, our modest research ((a stylistic vision of the objection in the Quranic discourse)) arose to explore an artistic rhetorical phenomenon that was included in the Holy Quran text. ; Because analysis is a situation that allows us to see a lot and absorb the stranger more clearly.

And since the horizontal arrangement of the linguistic elements in which stylistically undistinguished elements meet with distinct ones, the other trend has emerged that believes that the stylistic dis

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Publication Date
Wed Mar 30 2022
Journal Name
Iraqi Journal Of Science
Investigation of the Characteristics of CO (1-0) Line Integrated Emission Intensity in Extragalactic Spirals
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This paper aims to deal with the understanding of the properties of the molecular gas hydrogen in the extragalactic spirals sample. It is critical to make observations of CO (J = 1-0) line emission for spiral galaxies, particularly those with an energetic nucleus.  In the sample of spiral galaxies compiled, a carbon monoxide CO (1-0) emission line can be observed. This sample of galaxies' gas kinematics and star-forming should be analyzed statistically utilizing appropriate atomic gas HI, molecular gas H2, infrared (1μm-1000μm), visual (at λblue-optical=4400A0), and radio spectrum (at νradio=1.4 GHz and 5GHz) databases. STATISTICA is software that allows us to perform this statistical analysis. The presence of a high scale of s

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Publication Date
Mon Jan 01 2024
Journal Name
Baghdad Science Journal
Synthesizing and Using Iron Oxide Nanoparticles as Nanocomposite in Cotton Fabrics Nanofinishing
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Metal oxide nanoparticles, including iron oxide, are highly considered as one of the most important species of nanomaterials in a varied range of applications due to their optical, magnetic, and electrical properties. Iron oxides are common compounds, extensive in nature, and easily synthesized in the laboratory. In this paper, iron oxide nanoparticles were prepared by co-precipitation of (Fe+2) and (Fe+3) ions, using iron (II and III) sulfate as precursor material and NH4OH solution as solvent at 90°C. After the synthesis of iron oxide particles, it was characterized using X-ray diffraction (XRD), infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). These tests confirmed the obtaining o

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Publication Date
Thu Mar 05 2026
Journal Name
Al–bahith Al–a'alami
THE ISSUES OF YOUTH IN THE TALK SHOWS IN THE IRAQI SATELLITE CHANNELS:: (An Analytical Study of the Shabab wa Banat Program at Al-Sumaria TV Channel and of the Hala Shabab at Al-Iraqia TV Channel) (A Research Drawn from a Master’s Thesis)
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The purpose of this research is to identify the youth issues in Talk Shows in the Iraqi satellite channels via monitoring a sample of episodes of the Talk Shows  episodes which are concerned and analyzed the youth issues in the Iraqi satellite channels, namely, «Hala Shabab Program» at Al-Iraqia satellite Channel and «Shabab wa Banat Program» at Al-Sumaria satellite Channel by recording and re-watching them again. This research is classified as one of descriptive researches. The survey method was adopted in this study.

For this purpose, the researcher prepared an analysis form. The researcher de

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Publication Date
Fri Jan 01 2021
Journal Name
Brazilian Dental Science
Assessing the level and diagnostic accuracy of osteopontin and oral health status in periodontitis patients with/without Type-2 Diabetes Mellitus
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Publication Date
Fri Jan 01 2021
Journal Name
Brazilian Dental Science
Assessing the level and diagnostic accuracy of osteopontin and oral health status in periodontitis patients with/without Type-2 Diabetes Mellitus
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Publication Date
Wed Dec 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
Investment Trends for Iraqi Industries in Terms of Clean Production (selected model)
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   Industrial Investment according to Clean Productive methods is an important element in the process of rational use of Economic Resources, and the Iraqi industrial sector relied on traditional production methods; the productive activities in this sector did not take into consideration the environmental dimension, which leads to achieving the optimal use of economic resources, so it was necessary to have new investment trends heading with Clean Production. Therefore, the research is based on the hypothesis that "Clean Production contributes to improving the environment and rational use of Natural Resources." Based on the descriptive - inductive analysis methodology that study of Iraqi industries with Clean Production,

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Publication Date
Thu Nov 01 2007
Journal Name
University Of Baghdad
The Psychic Experience and its Effects on the Creative Process: A Study in Selected Poems By Allen Ginsberg and David Gascoyne
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Evidences indicate that human beings were preoccupied with extreme forms of mental and psychic experiences long before they were recorded in literature. Greek myths and legends appear to include symbolizations of delusions, mania, and other bizarre forms of thought and behaviuor. The figure of the mad man or woman is analogous to the wild man, or the imaginary being who appears in various forms throughout western literature and art. Various studies refer to the notion of the wild man as a response to a persistent psychological urge. This urge gives an external expression and a valid form to the impulses of reckless physical self-assertion which is believed to be hidden in all of us, but is normally kept under control. Such impulses were exp

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Publication Date
Thu Mar 05 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Early and delayed effect of 2% chlorhexidine on the shear bond strength of composite restorative material to dentin using a total etch adhesive
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Background: Lack of durability of the bond of the dental adhesive systems to tooth structure is one of the most important problems in tooth colored restorative work. This in vitro study was performed to evaluate the effect of 2% chlorhexidine gluconate(CHX) on dentin bond strength by using total etch adhesive system at twenty-four hours and three months of water storage. Material and methods:A flat dentin surface was prepared for forty sound human maxillary premolar teeth which were acid etched with 36% phosphoric acid gel after being divided randomly into four groups of ten teeth each according to storage time and CHX application, theCHX was applied for 60 seconds before adhesive application for groups I and III which were tested after twe

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