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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 Feb 11 2019
Journal Name
Journal Of Pharmaceutical Sciences And Research
Design of experiments model for optimization of spectrophotometric determination of phenylephrine hydrochloride in pure and pharmaceutical formulations using p-bromanil
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A simple, fast, inexpensive and sensitive method has been proposed to screen and optimize experimental factors that effecting the determination of phenylephrine hydrochloride (PHE.HCl) in pure and pharmaceutical formulations. The method is based on the development of brown-colored charge transfer (CT) complex with p-Bromanil (p-Br) in an alkaline medium (pH=9) with 1.07 min after heating at 80 °C. ‘Design of Experiments’ (DOE) employing ‘Central Composite Face Centered Design’ (CCF) and ‘Response Surface Methodology’ (RSM) were applied as an improvement to traditional ‘One Variable at Time’ (OVAT) approach to evaluate the effects of variations in selected factors (volume of 5×10-3 M p-Br, heating time, and temperature) on

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Publication Date
Sat Dec 24 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Potential Positive Effects using Coenzyme Q10 Supplement as Adjuvant Therapy to Gabapentin for Managing Diabetic Neuropathy
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The most prevalent chronic complication of diabetes mellitus is diabetic neuropathy. The pathogenesis of diabetic neuropathy is exacerbated by hyperglycemia-induced oxidative stress, which causes nerves to deteriorate in a programmed manner. Many clinical trials depend on supplement in an attempt to improve neuropathy symptoms such as (pain & tingling) and patient quality of life, one of them is Coenzyme Q10 which is reported to have an anti-inflammatory and antioxidant effects, and was totally nontoxic and non-reported side effects. This study aimed to evaluate using a Coenzyme Q10 supplement as an adjuvant therapy to gabapentin to improve the clinical symptoms of diabetic neuropathy in relation to its anti-inflammatory and antioxid

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Publication Date
Thu Sep 18 2025
Journal Name
Sustainable Engineering And Innovation
Using fruit fly and dragonfly optimization algorithms to estimate the Fama-MacBeth model
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This research proposes the application of the dragonfly and fruit fly algorithms to enhance estimates generated by the Fama-MacBeth model and compares their performance in this context for the first time. To specifically improve the dragonfly algorithm's effectiveness, three parameter tuning approaches are investigated: manual parameter tuning (MPT), adaptive tuning by methodology (ATY), and a novel technique called adaptive tuning by performance (APT). Additionally, the study evaluates the estimation performance using kernel weighted regression (KWR) and explores how the dragonfly and fruit fly algorithms can be employed to enhance KWR. All methods are tested using data from the Iraq Stock Exchange, based on the Fama-French three-f

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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
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
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
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
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
Tue Dec 09 2025
Journal Name
Discourse And Interaction
A discursive pragmatic study of emotional blackmail in American movies
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This study examines emotional blackmail from a discursive pragmatic standpoint to gain insights into how this psychologically manipulative phenomenon is revealed in the discourse of some American movies. Five extracts from five American movies are purposely selected and analyzed using an eclectic model based on a discursive pragmatic approach to navigate this unexplored study area. The model incorporates Halliday’s (2014) transitivity system, Martin and White’s (2005) attitude system, Forward and Frazier’s (1997) types and tools of emotional blackmail, and Mayfield’s (2010) informal fallacies. The present study is guided by four research questions that identify the types and tools of emotional blackmail employed in the selec

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