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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 Oct 01 2016
Journal Name
Al–bahith Al–a'alami
Semiotics of Joseph Curtis… A Study in Perspective and Concept
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Joseph Curtis wrote in his book (Introduction to Semiotics narrative and rhetoric) on the development of a semiotic project in exploring the meaning of communion. The book is rich in theoretical and analytical benefits both in the approach of texts and in the pursuit of letters in search of mechanisms of scriptural and scriptural generation and mechanics in narrative production, especially as the book offers exercises that help to assess the distance separating the narrative spread from the sin of the text, for the semiotics, Refers to the theoretical developments of the science of relations, through the combination of conventional definitions and the representative and comparative limitations, to provide an approach to the application o

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Publication Date
Wed Dec 14 2022
Journal Name
Journal Of The College Of Languages (jcl)
A Pragma-Stylistic Study of Misdirection in Selected Detective Novels
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The analysis of detective novels has taken different aspects. The linguistic analysis of them, for example, has tackled the linguistic systems of morphology, phonology, syntax, semantics, and pragmatics. In line with the linguistic analysis, this study explores the various pragmatic and stylistic devices realized through detective novels for the purpose of misdirecting and deceiving the reader. The problem is that when readers try to reach to the truth, they face difficulties. They might not reach to the right solution or infer wrong conclusions because writers use some techniques to hide the truth and mislead them. This study aims at examining these techniques and devices; namely, Grice's Maxims and ambiguity as pragmatic devices on the

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Publication Date
Thu Apr 30 2020
Journal Name
The Asian Esp Journal
A Linguistic Study of ''and'' (و) in Arabic and English.
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The conjunctive ''and'' and its Arabic counterpart ''و'' are discourse markers that express certain meanings and presuppose the presence of other elements in discourse. They are indispensable aids to both the text writers and readers. The present study aims to show that such cohesive ties help the writer to organize his main argument and communicate his ideas vividly and smoothly. They also serve as explicit signals that help readers unfold text and follow its threads as realized in the progression of context. The researcher has utilized the Quirk Model of Semantic Implication for data analysis. A total of 42 (22 for English and 20 for Arabic) political texts selected from different elite newspapers in both Arabic and English for the analy

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Publication Date
Sat Apr 06 2019
Journal Name
International Journal Of English Linguistics
A Morpho- Syntactic study of Contemporary Science Fiction Short Stories
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The aim of the present study is to research two morphological processes: acronym and compounding (phrasal compounds/ circumlocution) and one syntactic category which are 'existential sentences' in science fiction short stories. The present paper identifies different types and rates of existential sentences. In this respect , 'bare existential and locative’ read the high percentages and may be contrasted with other classifications of English existential sentences which have a verb other than 'be' and a definite expression. 'Phrasal compounds' vary in rates as they constitute notable percentage for those that involve 'lexical means and lexical relations' followed by 'prepositional compounds' , 'conjunctional compounds' , and those invo

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Publication Date
Thu Mar 31 2022
Journal Name
Journal Of The College Of Education For Women
A Pragmatic Study of Identity Representation in American Political Speeches
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Identity is an influential and flexible concept in social sciences and political studies. The basic sense of identity is looking for uniqueness. In one sense, it is a sign of identification with those we assume they are similar to us or at least in some significant ways they are so. Globalization, migration, modern technologies, media and political conflicts are argued to have a crucial effect on identity representation in terms of the political perspectives specifically in the United States of America. This paper endeavors to investigate how American politicians represent their identities in speeches delivered in different periods of time namely from 2015 to 2018 in terms of the pragmatic paradigm. Three randomly selected speeches by fa

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Publication Date
Thu Apr 23 2020
Journal Name
International Journal Of Innovation, Creativity And Change
A PRAGATIC STUDY OF APOLOGY STRATEGIES IN ONLINE ENGLISH LETTERS
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DBN Rashid, International Journal of Innovation, Creativity and Change, 2020

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Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Cleaner Production
A study of biogas production from date palm fruit wastes
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Publication Date
Sun Dec 30 2012
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Removal of Nickel Ions Using A Biosorbent Bed (Laminaria saccharina) Algae
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The present study aims to remove nickel ions from solution of the simulated wastewater using (Laminaria saccharina) algae as a biosorbent material. Effects of experimental parameters such as temperature at (20 - 40) C⁰, pH at (3 - 7) at time (10 - 120) min on the removal efficiency were studied.
Box-Wilson method was adopted to obtain a relationship between the above three experimental parameters and removal percentage of the nickel ions. The experimental data were fitted to second order polynomial model, and the optimum conditions for the removal process of nickel ions were obtained.
The highest removal percentage of nickel ions obtained was 98.8 %, at best operating conditions (Temperature 35 C⁰, pH 5 and Time 10 min).

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Publication Date
Fri Mar 31 2017
Journal Name
Journal Of Engineering
Aerodynamic Characteristics of a Rectangular Wing Using Non-LinearVortex Ring Method
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The aerodynamic characteristics of general three-dimensional rectangular wings are considered using non-linear interaction between two-dimensional viscous-inviscid panel method and vortex ring method. The potential flow of a two-dimensional airfoil by the pioneering Hess & Smith method was used with viscous laminar, transition and turbulent boundary layer to solve flow about complex configuration of airfoils including stalling effect. Viterna method was used to extend the aerodynamic characteristics of the specified airfoil to high angles of attacks. A modified vortex ring method was used to find the circulation values along span wise direction of the wing and then interacted with sectional circulation obtained by Kutta-Joukowsky the

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Publication Date
Sun Apr 30 2017
Journal Name
Journal Of Engineering
Implementation of a Proposed Load-Shedding System Using Altera DE2 FPGA
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A load-shedding controller suitable for small to medium size loads is designed and implemented based on preprogrammed priorities and power consumption for individual loads. The main controller decides if a particular load can be switched ON or not according to the amount of available power generation, load consumption and loads priorities. When themaximum allowed power consumption is reached and the user want to deliver power to additional load, the controller will decide if this particular load should be denied receiving power if its priority is low. Otherwise, it can be granted to receive power if its priority is high and in this case lower priority loads are automatically switched OFF in order not to overload the power generation. The

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