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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 Dec 18 2017
Journal Name
Al-khwarizmi Engineering Journal
Fabrication and Characterization of Tri Metal Oxides by Chemical Spray Pyrolysis Technique as a Gas Sensor
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In this research tri metal oxides were fabricated by simple chemical spray pyrolysis technique from (Sn(NO3)2.20 H2O, Zn(NO3)2.6 H2O, Cd(NO3)2.4 H2O) salts at concentration 0.1M with mixing weight ratio 50:50 were fabricated on silicon substrate n-type (111). (with & without the presence of grooves by the following diemensions (20μm width, 7.5μm depth) with thickness was about ( 0.1 ±0.05 µm) using water soluble as precursors at a substrate temperature 550 ºC±5, with spray distance (15 cm) and their gas sensing properties toward H2S gas at different concentrations (10,50,100,500 ppmv) in air were investigated at room te

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Publication Date
Mon Jan 01 2018
Journal Name
Al-dhad Book Store And Publishing
Calculus part 1
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This book includes three main chapters: 1. Functions & Their Derivatives. 2. Minimum, Maximum and Inflection points. 3. Partial Derivative. In addition to many examples and exercises for the purpose of acquiring the student's ability to think correctly in solving mathematical questions.

Publication Date
Sat Feb 07 2026
Journal Name
Al.qadisiya Journal For The Sciences Of Physical Education
The Influence of Using Special Exercises with Weights to Develop Moments of Force to Some of the Striking Shoulder and Arm Muscles and Accuracy of the Skill of the Smash and Rectum in Volleyball
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This research is an attempt to develop exercise with weights to strengthen some of the striking muscles in the shoulder and arm and to develop the accuracy of the smash and rectum skills. The importance of this paper lies in the study of moments of force to achieve the ability to control muscular work and to explore the impact of physical and skill exercises with weights to develop moments of force for some muscles. The experimental method on a sample of players, selected according to the intentional method, including ( 9) advanced players representing Air Force Club participating in the Premier League for season 2011-2012. It is concluded that the exercises proposed have their effective impact on developing the variables of moments force f

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Publication Date
Fri May 16 2025
Journal Name
Tikrit Journal Of Engineering Sciences
Comparative Study of Activated Carbon and Silver Nanoparticle-Loaded Activated Carbon Derived from Tea Waste for Removal of Tetracycline from Aqueous Solution
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The present work elucidates the utilization of activated carbon (AC) and activated carbon loaded with silver nanoparticles (AgNPs-AC) to remove tetracycline (TC) from synthetically polluted water. The activated carbon was prepared from tea residue and loaded with silver nanoparticles. Scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and Brunauer-Emmett-Teller (BET) were used to characterize the activated carbon (AC) and silver nanoparticles-loaded activated carbon (AgNPs-AC). The impact of various parameters on the adsorption effectiveness of TC was examined. These variables were the initial adsorbate concentration (Co), solution acidity (pH), adsorption time (t), and dosag

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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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