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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
Wed May 24 2023
Journal Name
College Of Islamic Sciences
Manifestation, implicitness, and the interaction of Quranic discourse systems - a stylistic study
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Stylistics represents a modern approach in understanding the literary text through the linguistic patterns that form it. The distinctive phenomena that the text includes constitute special features in it. As well as exploring its aesthetic aspects through description and analysis at the same time. The close link between stylistics and linguistics made stylistics occupy a prominent place in modern literary criticism.
In this regard, we do not want to dwell on the different directions of stylistics. Rather, we will prolong the discussion in the study of the style as a (deviation. Aversion) from the original. Because this trend plays on the chord of the paradox between the surface structure and the deep structure, especially when the sur

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Publication Date
Thu Oct 18 2018
Journal Name
International Journal Of Research In Social Sciences And Humanities
A Linguistic study of Presupposition in Rattigan’s play ‘while the sun shines’
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As a kind of linguistic study, the study of presupposition in drama is one of captivating topic to explore, because of the capability of this topic to make people perceive the presupposition differently. Presupposition is one of the most important concepts in linguistics. It refers to the implicit inferences made in communication between people. These inferences are necessary to understand the utterances correctly. The research particularly endeavors to focus on the linguistic constructions that activate presupposition.

Publication Date
Sat Sep 30 2023
Journal Name
Journal Of The College Of Education For Women
A Pragmatic Study of Narcissism in the American Movie Big Eyes (2014)
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Narcissism is a complicated phenomenon that can be reflected in the narcissist’s language. Investigating narcissism in terms of linguistics, and pragmatics in particular, does not seem to have been given its due attention, as this study reveals. Thus, this study is an endeavor to discover how narcissism is reflected in the American movie Big Eyes (2014). It is known for introducing narcissistic behaviors. This paper aims to identify the types, motivations, and pragmatic manifestations of narcissism in the selected movie. Three pragmatic theories are chosen to scrutinize narcissism in the data: Searle’s speech acts (1969), Grice’s maxims breaching (1975), and Culppeper’s impoliteness (1996). To cope with the nature of the

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Publication Date
Tue Dec 30 2014
Journal Name
College Of Islamic Sciences
Approaches to the formation of a contemporary explanatory mindset: Critical inductive study
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The issue of the development of Qur'anic studies for the tasks, and the first thought of minds and multiple understandings, and the most precious ideas, and the alternatives were floated, and varied visions, especially as we live in an era exploding knowledge, and complicate secretions, and scramble his ideas, and to devise intellectual approaches To achieve the witnesses of civilization in the words of the Almighty (to be martyrs on the people) Surat Al - Baqarah / 143 attendance and participation in the achievement and a positive interaction with the participants of humanity and civilization in the light of the meaning (to know) rooms / 13.
Therefore, we must emerge from the one-dimensional view of the Koran to the complex mindset t

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Publication Date
Wed Jan 01 2014
Journal Name
Journal Of The College Of Languages (jcl)
The stylistics of expressive structure in Al-Sayyab's attempt- A textual study
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Our research tends to study the poetic attempt of  Badr Shakir Al-Sayyab and examine it stylistically, and we suggested his mature collection '' Rain song'' as a pattern for our textual analysis of the poet's attempt.

   In the beginning , we confirm that branches of applied structures meet to produce poetry such as narration , drama , cinema , mythology , allegory , various religious and historical texts , previous events , and special cumentary events related to work production. If all above-mentioned was complicated and disregarded throughout a single text , the text writer would not secure positive results that might keep open continuity between him and his readers.

   Therefore , this issue w

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Publication Date
Sun Jan 01 2023
Journal Name
Corporate And Business Strategy Review
The role of learning organizations in crisis management strategy: A case study
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The problem of the paper focused on the role of the learning organization in the crisis management strategy, and the extent of the actual interest in both the learning organization and the crisis management and aimed at diagnosing and analyzing that and surrounding questions. The Statistical Package for the Social Sciences (SPSS) program was used to calculate the results and the correlation coefficient between the two main variables. The methodology was descriptive and analytical. The case study was followed by a questionnaire that was distributed to a sample of 31 teachers. The paper adopted a seven-dimensional model of systemic thinking that encourages questioning, empowerment, provision of advanced technologies, and strategic lea

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Publication Date
Thu Aug 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Analyzing current and future direction of non-oil primary balance: Case Study of Iraq Using Exponential Smoothing model
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In recent years, non-oil primary balance indicator has been given considerable financial important in rentier state. It highly depends on this indicator to afford a clear and proper picture of public finance situation in term of appropriate and sustainability in these countries, due to it excludes the effect of oil- rental from compound of financial accounts which provide sufficient information to economic policy makers of how economy is able to create potential added value and then changes by eliminating one sided shades of economy. In Iraq, since, 2004, the deficit in value of this indicator has increased, due to almost complete dependence on the revenues of the oil to finance the budget and the obvious decline of the non-oil s

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Publication Date
Thu Feb 12 2026
Journal Name
Al–bahith Al–a'alami
News Coverage in the Iraqi Electronic Press for Internal Crises: (An Analytical Study of Al-Zaman and Al-Sabah Electronic Newspapers for the period from 1/ 3/ 2013 to 31/ 3/ 2013)
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The research study focused on the need to clarify the relationship between the Websites of Iraqi Newspapers and their roles in covering the internal crises in Iraq. The selection of Iraqi websites for the newspapers Al-Zaman and Al-Sabah was adopted as one of the most important media with a wide audience; and as a model of hot news and continuous coverage of those sites since 2003 so far. As a result, this necessitated the emergence of new types of methods of editing and writing news stories related to Iraq.

Consequently, the enormous and rapidly changing amount of Iraq news, the process of preparing and creating news has become a complex industry

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
What came as a language in the book to explain Ibn Aqeel on Alfiya Ibn malek
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It is found in the book "Ibn Aqeel: Alfiya Ibn Malek" that there are some linqustical aspected are related to the native tribal speakers like Tamim or Tie or some others. Sometimes in the book he said "some Arabian said without mentioning the name of the tribe.
As weel, he hasn’t mentioned the accent but he does mention the language. In the book, he has brought back the most important and the biqqest Arabian tribes suchas tribes of Hegaz, Tamim, Hatheyal, son of Anber, Tie, Rabia Bin Wael, Bani Katham, Au there, Bani AL Harth, Bani Kalb, Bani Hgim, Zabid, Hamedan, Alia Qais, Bani Ameer and many others. However, the most mentioned tribes were Hegaz and Tami.
Hence, the importance of the book expiain Ibn Aqeel by mentioning these A

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Molecular diagnosis of E.coliO157:H7 Which Isolated from Children with Diarrhea by using Multiplex PCR
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A total of 96 stool samples were collected from children with bloody diarrhea from two hospitals in Baghdad. All samples were surveyed and examined for the presence of the Escherichia coli O157:H7 and differentiate it from other Non -Sorbitol Fermenting Escherichia coli (NSF E. coli). The Bacterial isolates were identifed by using morphological diagnostic methods, Samples were cultured on liquid enrichment medium, incubated at 37C? for 24 hrs, and then cultured on Cefixime Tellurite -Sorbitol MacConkey Agar (CT- SMAC). 32 non-sorbitol fermenting bacterial isolates were obtained of which 11 were identified as Escherichia coli by using traditional biochemical tests and API20E diagnostic system without differentiation between

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