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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
Fri Sep 24 2021
Journal Name
Applied Sciences
The Impact of Calcitriol on Orthodontic Tooth Movement: A Cumulative Systematic Review and Meta-Analysis
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A cumulative review with a systematic approach aimed to provide a comparison of studies’ investigating the possible impact of the active form of vitamin D3, calcitriol (CTL), on the tooth movement caused by orthodontic forces (OTM) by evaluating the quality of evidence, based on collating current data from animal model studies, in vivo cell culture studies, and human clinical trials. Methods: A strict systematic review protocol was applied following the application of the International Prospective Register of Systematic Reviews (PROSPERO). A structured search strategy, including main keywords, was defined during detailed search with the application of electronic database systems: Medline/Pubmed, EMBASE, Scopus, Web of Science, and

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Publication Date
Fri Jun 20 2025
Journal Name
Baghdad Science Journal
The Role of Fear and Predator Dependent Refuge on a Stage Structure Prey-Predator System
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The present paper investigates the role of fear and predator dependent refuge in the prey-predator system. The system describes the interaction between prey and a stage structure of predator that incorporates Holling II functional response. The predator splits into two compartments immature (juvenile) and mature (adult). The mature predators can hunt and reproduce but this capability is not found in the immature predators, the immature depend on their parents. The growth rate of prey decreases due to the existence of mature predators. The existence, uniqueness, and boundedness of the solution of the system are investigated. Three equilibrium points of the system are determined. The local stability of the system is studied. The global stabil

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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of Engineering
The Design and Simulation of a Novel Optical Adder Depending on Optical Tri-state Gates
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Essential approaches involving photons are among the most common uses of parallel optical computation due to their recent invention, ease of production, and low cost. As a result, most researchers have concentrated their efforts on it. The Basic Arithmetic Unit BAU is built using a three-step approach that uses optical gates with three states to configure the circuitry for addition, subtraction, and multiplication. This is a new optical computing method based on the usage of a radix of (2): a binary number with a signed-digit (BSD) system that includes the numbers -1, 0, and 1. Light with horizontal polarization (LHP) (↔), light with no intensity (LNI) (⥀), and light with vertical polarization (LVP) (↨) is represen

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Publication Date
Sun Sep 30 2018
Journal Name
Scientific Journal Of Silesian University Of Technology. Series Transport
Measuring the relative importance of applying engineering solutions to urban traffic intersections: a planning perspective
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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
A Critical Stylistic Analysis of the Ideological Positioning in Some Selected Poems by John Donne
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This paper deals with the ideological positioning of the English poet John Donne in a selected poems of his i.e Holy Sonnet X, as regards the theme of death found therein. The researchers adopt an emerging branch of stylistics, called Critical Stylistics, as proposed by Jeffries (2010) in order to uncover the ideologies of the author regarding the topic concerned and how linguistic choices are used to slant ideas. The model is comprised of ten tools of analysis which, upon being applied to the selected data, have shown how the poet exploits language resources in order to pass his ideology and influence his readers. In this paper, the workings of only one tool are presented as applied to a certain portion of the data.

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Publication Date
Tue Dec 09 2025
Journal Name
International Journal Of Arabic-english Studies
Spatial Excavation of Psyche and Family Dynamics in Stephen Karam's The Humans: A Psychogeographical Reading
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The American playwright Stephen Karam explores the human psyche and relationships in The Humans (2016) by employing the spatial operations of the props on the stage. The play presents the gathering of the Blake family in their daughter and her boyfriend's new apartment on a Thanksgiving dinner. The article examines how the description of the details of the place reflects the characters' fear, pain, trauma, relationships and secrets. It aims to show how the characters' psychologies are depicted through the physical setting of the dark apartment and its menacing atmosphere. The study follows the theory of place in approaching the text. It tries to analyze the relationship between the place and the characters and how it develops a type

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Publication Date
Thu Jun 12 2025
Journal Name
Al-adab Journal
Deconstructing the Archetypal Mirror of Godot in Ali Abdul-Nabi Al-Zaidi’s “A Second Death”
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لطالما كان انتظار الملأ للخلاص والتي ترتبط بشكل اساسي بال "منتظر" او ال "مخلص" جزءا من الوعي الجمعي الذي تطور ليكون مرتبطا بالنمط البدائي والذي بدوره أصبح مرآةً تنعكس على اساسها فرص الانسان نحو النجاة. في مسرح القرن العشرين, لم تنفك فكرة الانتظار ان ترتبط بمسرحية صاموئيل بيكيت العبثية " في انتظار غودو" كونها مثالا رمزيا بالرغم من انه تجسيد شخصية "غودو" وقعت تحت وطأة الكثير من عمليات التحوير والتغيير في اطاره

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Publication Date
Mon Oct 01 2018
Journal Name
Arpn Journal Of Engineering And Applied Sciences
Achieving a theoretical approximation characterize the stopping power of heavy ion in D-T plasma
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The dependence of the energy losses or the stopping power for the ion contribution in D- T hot plasma fuels upon the corresponding energies and the related penetrating factorare arrive by using by a theoretical approximation models. In this work we reach a compatible agreement between our results and the corresponding experimental results.

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Publication Date
Mon Feb 14 2022
Journal Name
Journal Of Educational And Psychological Researches
The Linguistic and Conceptual Equivalence of Conner’s Revised Scales When Applied on a Sudanese Sample
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This study investigates the Linguistic and Conceptual equivalence of Conner’s Revised Scales when applied on a Sudanese sample. Sudanese parents and teachers completed behavior-rating scales on a stratified sample of 200 children. These instruments were based on Conner’s parent -48 and teacher-28 questionnaires. Following a reliable translation into Sudanese Arabic the test-retest reliability of the items and the internal consistency of the original Conner’s' revised scales were explored. The associations between scale scores and between parents and teachers scores were also examined. Both instruments displayed good reliability and the original Conners scales had satisfactory internal consistency. The inter-correlation sugg

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Publication Date
Wed Dec 01 2021
Journal Name
Journal Of Arts Faculty Of Baghdad University
The Discourse of Christian Minority in Saad Hana's Novel "Abducted in Iraq": A Critical Perspective.
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