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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
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
A Cognitive Linguistic Study of UP and DOWN in Iraqi Arabic
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This study is an attempt to investigate the conceptual metaphor of UP and DOWN commonly used in Iraqi community. Some of the metaphorical expressions in Iraqi colloquial Arabicarewidely used by Iraqi speakers in everyday language. Ithas been analyzed by following the cognitive theory of metaphor (Lakoff& Johnson,1980).The study indicates that the Iraqi speakerexperiences more of the metaphorical expressions of UP and DOWN to referto many of the abstract concepts that shape his/her impression of everyday life situations.

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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
A stylistic study of proisepoeme and congratulation from Hafiz Ibrahim's collection
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A stylistic study in the poetry of Hafiz Ibrahim, praise be to God, Lord of the worlds, and prayers and peace be upon his best messengers, and the seal of his prophets, Muhammad and his good and pure family, and after ...
The poet Hafez Ibrahim is considered one of the well-known poets in the modern era, and his language was distinguished by sobriety, eloquence in expressions, and beautiful meanings And he had my journey in the study of his poetry a stylistic study, and the research came with an introduction in which the concept of stylistics was briefly explained, since it was studied by many researchers, then divided the research into three topics: I studied in the first the construction of the poem, and I stood at the most importan

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Publication Date
Thu Feb 07 2013
Journal Name
Iraqi Journal Of Medical Science
A study of serum magnesium and calcium levels in missed abortion
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Publication Date
Mon Sep 04 2017
Journal Name
Journal Of College Of Education For Women
Tagmemic Analysis of English and Arabic Praise Poetry: A Contrastive Study
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This research provides a new method to study praise poetry that can be used as a course to teach English and Arabic to students in the College of Education. This research answers two questions: Is it possible to examine praise poetry as a tagmeme? Is this analysis of great help in teaching English and Arabic to students in the College of Education? The data that will be chosen for the purpose of analysis are two of Shakespeare's sonnets and two of AL Mulik's poems. The sonnets selected for this purpose are 17 and 18. AL Mulik's poems selected for the same purpose are 8 and 9. Each line in both English and Arabic data is numbered by the researcher herself. Then, those lines are grouped into sentences to facilitat

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Publication Date
Sun Sep 07 2008
Journal Name
Baghdad Science Journal
A Study of some biochemical parameters in patients with - thalassemia
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Serum levels of iron,copper,ceruloplasmin and transferrine were estimated in three groups of patients with ?- thalassemia: 24 patients have splenectomy thalassemia major, 29 patients have non splenectomy thalassemia major and 19 patients have thalassemia intermedia , data were compared to normal and pathological controls (anemia and minor). There were significant increase in trace element levels in all studied groups of pateints as compared to normal and pathological controls. Also there were a significant increase in ceruloplasmin levels,While the result revealed that there were a significant decrease in transferrine levels in all groups of patients studied as compared to normal and pathological controls. The result also indicate that the

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Publication Date
Thu Sep 30 2021
Journal Name
Rigeo
A Stylistic Study of Vocative Particles in Selected English Literary Texts
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A vocative expression can be defined as an expression of direct address where the participant identity is set forth explicitly within a sentence. This study aims at showing how the vocative particles are used in literally texts, namely in the short story “The Garden Party" written by Kathryn Mansfield and identifying the forms of these vocative particles as used by the characters along with the functions of these vocative particles. For the analysis of vocative forms, the researcher used Quirk and Greenbaum (1973) model. Functionally, the data were analyzed based on Quirk et al. (1985) model. However, the results of this study shows that the characters in “The Garden Party” short story used various forms of vocative particles and

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Publication Date
Thu Dec 15 2022
Journal Name
Arab World English Journal
Genre-Based Analysis of Selected Political Debates: A Discourse Analysis Study
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The researchers of the present study have conducted a genre analysis of two political debates between American presidential nominees in the 2016 and 2020 elections. The current study seeks to analyze the cognitive construction of political debates to evaluate the typical moves and strategies politicians use to express their communicative intentions and to reveal the language manifestations of those moves and strategies. To achieve the study’s aims, the researchers adopt Bhatia’s (1993) framework of cognitive construction supported by van Emeren’s (2010) pragma-dialectic framework. The study demonstrates that both presidents adhere to this genre structuring to further their political agendas. For a positive and promising image

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Publication Date
Mon Feb 10 2025
Journal Name
International Linguistics Research
A Semiotic Study of Reduplicative Words in Selected American Slang Expressions
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This study explores the semiotic aspects of American slang, specifically focusing on the phenomenon of reduplicative expressions in informal speech. Despite the extensive research on American slang, limited attention has been given to the cultural and mythical meanings embedded within reduplicative expressions. To address this gap, the study investigates how these expressions convey denotative, connotative, and mythical meanings within casual American discourse. The objectives of the study include: 1. To what extent does Barthes’ semiotic model hold potential for application in this study? 2. How are reduplicative slang expressions widely used in everyday American life? 3. To what extent do qualitative and quantitative methods hav

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Publication Date
Fri Jun 29 2018
Journal Name
Journal Of The College Of Education For Women
Tagmemic Analysis of English and Arabic Praise Poetry: A Contrastive Study
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 This research provides a new method to study praise poetry that can be used as a course to teach English and Arabic to students in the College of Education. This research answers two questions:

  1. Is it possible to examine praise poetry as a tagmeme?
  2. Is this analysis of great help in teaching English and Arabic to students in the College of Education?

           The data that will be chosen for the purpose of analysis are two of Shakespeare's sonnets and two of AL Mulik's poems. The sonnets selected for this purpose are 17 and 18. AL Mulik's poems selected for the same purpose are 8 and 9.

   &nbs

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Publication Date
Tue Aug 30 2022
Journal Name
International Journal Of Research In Social Sciences & Humanities. E-issn
Black poetess, White poems: Phillis Wheatley A Case Study of Hybridity
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