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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
Thu Jun 18 2020
Journal Name
Rimak International Journal Of Humanities And Social Sciences
STRESS IN ENGLISH AND ARABIC: A CONTRASTIVE STUDY
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DBN Rashid, Rimak International Journal of Humanities and Social Sciences, 2020

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Publication Date
Sat Apr 01 2017
Journal Name
Al–bahith Al–a'alami
Quranic Words Referring to Lies A Media Study
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This research aims to invest qur›anic words referring to lie in media language. The researcher has chosen a set of qur›anic words functioning as «lie».
It is an attempt to review the media language which is used to make use of repetition of terms and templated which make it weak and ineffective language. The use of qur›anic texts and terms according to the semantic field for each topic will give this media language an opportunity for growth, development and stability.
This researcher identifies a number of words to study them in the light of their lexical meaning using the Dictionary of Language Standards by Ibn Fares as it focuses on the general meaning of the root language. He also uses the Dictionary of the Basis of Rhe

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Publication Date
Fri Jun 30 2023
Journal Name
Samarra Journal Of Pure And Applied Science
Preclinical Oral Histology Research: A Retrospective Review Study
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A retrospective study is conducted to identify factors that improve prospective animal studies; contribute to the optimization of animal protection from all unnecessary and preventable damage. Preclinical oral histology research from 2010-2020 is evaluated and 64 studies were reviewed relating to two interventions: bone trauma and surgical incision. The harm-benefit analysis is featured in this study through the application of the recent form of Bateson's Cube. Depending on its three axes, we can assess animal suffering, the likelihood of benefit, and the importance of research. The total number of animals used in the research is 2685. Rats, 51.6%, and rabbits, 48.4%, are the most commonly used animals. Research related to bone healing acco

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Publication Date
Mon Jul 25 2022
Journal Name
Studies In Pragmatics And Discourse Analysis
Negation in American Discourse: A Socio-Cognitive Study
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The present study cognitive aims to investigate the negation phenomenon in American political discourse under Critical Discourse Analysis (CDA) principles. The research sample includes two speeches given by Clinton and Trump in their election campaigns in 2016. Since the nature of the study follows the social-cognitive approach, the researcher adopted two models of analysis to achieve the study’s objectives: First, the theoretical framework of MST (developed by Fauconnier (1994), Fauconnier and Sweetser (1996) to examine meaning construction resulting from building different levels of negative mental spaces by two different genders the selected speeches. Second, pragmatic model to examine the role of gender from the functional per

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Publication Date
Thu Jun 01 2006
Journal Name
Journal Of The College Of Languages (jcl)
Demonstratives in English and Arabic : A Contrastive Study
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This paper studies the demonstratives as deictic expressions in Standard Arabic and English by outlining their phonological, syntactic and semantic properties in the two languages. On the basis of the outcome of this outline, a contrastive study of the linguistic properties of this group of deictic expressions in the two languages is conducted next. The aim is to find out what generalizations could be made from the results of this contrastive study.

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Publication Date
Sun Dec 01 2024
Journal Name
كلية التربية للبنات
Strategic Maneuvering in Commercial Advertisement: A Pragmatic Study
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This study deals with strategic maneuvering in advertisement from a pragmatic point of view found in some commercial advertisements in order to investigate and analyze the pragmatic devices that are used in the strategic maneuvering and stages. The study attempts to shed light on the most fuzzy areas in advertisements that is probably how the language of advertisements employed by advertisers to affect consumers positively. The primary goal of strategic maneuvering is to discover how the pragmatic devices have persuasive techniques that are used to gain a competitive advantage and more sales. This study is a contribution to the field of research in the language used in advertising. In this research, the effectiveness of strategic man

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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Professional Nursing
Incivility among nursing faculty: A multi-country study
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Publication Date
Wed Jun 13 2012
Journal Name
Journal Of Kerbala University
Thermo physical behaviour of binary and ternary systems for cyclohexanol with some Ketones at three temperature
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Publication Date
Wed Dec 01 2010
Journal Name
Al-khwarizmi Engineering Journal
Prediction of Equilibrium Mixing Index and Optimum Mixing Time for Three solid materials in Fluidized Column
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     Equilibrium and rate of mixing of free flowing solid materials are found using gas fluidized bed. The solid materials were sand (size 0.7 mm), sugar (size0.7 mm) and 15% cast iron used as a tracer. The fluidizing gas was air with velocity ranged from 0.45-0.65 m/s while the mixing time was up to 10 minutes. The mixing index for each experiment was calculated by averaging the results of 10 samples taken from different radial and axial positions in fluidized QVF column 150 mm ID and 900 mm height.

     The experimental results were used in solving a mathematical model of mixing rate and mixing index at an equilibrium proposed by Rose. The results show that mixing index increases with inc

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Publication Date
Fri Sep 30 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Ijarah and lease ending with ownership and its implications for the bank's profits: A case study in the Emirates Islamic Bank and Emirates NBD
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The formula of Ijarah and Ijarah ending with ownership is one of the investment formulas in Islamic banks, so this research has shed light on it in order to benefit from the experiences of the research sample banks, This research aims to find a reliable way for Iraqi Islamic banks, namely (leasing and leasing ending with ownership) in order to invest their money without usurious interests, The problem of the research emerges through the lack of awareness of the Iraqi Islamic banks to work with different Islamic financing formulas and their inability to invest their money through the adoption of their administrations for different formulas, including the leasing, and this is reflected in the decrease and fluctuation of its profits, Theref

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