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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 Dec 30 2022
Journal Name
Journal Of The College Of Education For Women
The Death Scene in the "Ayniyah" Poems of Abi Thuayib Al-Huthali and Suda bint Shamardal: A Contrastive Study
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This study is an objective literary study of the poems of Abu Dhu'ayb Al-Hudhali and Su'da Bint Al-Shamrdal. It aims to shed light on the philosophy of death in the poems, and the way this philosophy is treated by both poets. Thus, the main prominent poetic images have been addressed and the outstanding ones have been singled out. The study further investigates the intertextuality with other poetic verses and Quranic verses and reviews the deviation in their semantic, syntactic, and phonetic types. The study adopts the historical approach to examine the occasion of the poems by referring to several historical sources that indicate the seniority. It also adopts the and descriptive-analytical approach represented by the use of content anal

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Publication Date
Sat Jan 01 2022
Journal Name
Communications In Mathematical Biology And Neuroscience
Chaos in the three-species Sokol-Howell food chain system with fear
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Publication Date
Sun Oct 07 2012
Journal Name
Journal Of Educational And Psychological Researches
The Participation of the Students of the Colleges of Education in the Iraqi Universities in Literacy and Adult Education in Iraq. The Students of the Departments of Holy Quran and Islamic Education (A model)
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The study focuses on the problem that Iraq is approaching an increasing rate of literacy;the available data refers to a rate of (18% -19%). In addition to the fact that the generalcurrent role of the programs directed to literacy is not actually effective enough to limit the expansion of this rate.

The importance of this study highlights the fact that the Iraqi universities are an important tributary among the tributaries of human development, especially in spreading the education of the voluntary work in literacy field and confirming the connection between the students and their society and their role in solving one of the prominent challenges that face the development, i.e., literacy.

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Publication Date
Mon Apr 03 2023
Journal Name
Journal Of Educational And Psychological Researches
The predictive Ability of Admission Criteria and Student Performance Level in Master Programs in College of Education at Sultan Qaboos University
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Abstract

Most universities in the world are largely committed to creating credible and transparent admission standards that provide justice in admission and have the ability to predict students' performance in their chosen programs. Hence, this study aimed to reveal the predictive ability of the acceptance criteria for the level of performance of master's students in the College of Education at Sultan Qaboos University. Quantitative data were collected from (115) students' admission documents for those accepted in the postgraduate programs for the academic year 2019-2020, and GPA data was collected from students’ transcripts for the fall semester of 2019. Qualitative data were also collected from the interviews

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Publication Date
Tue Feb 01 2022
Journal Name
Journal Of Engineering
Numerical analysis of a concrete foundation under a combination of a dynamic and a seismic load
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Improving in assembling technology has provided machines of higher evaluation with better resistances and managed behavior. This machinery led to remarkably higher dynamic forces and therefore higher stresses. In this paper, a dynamic investigation of rectangular machine diesel and gas engines foundation at the top surface of one-layer dry sand with various states (i.e., loose, medium and dense) was carried out. The dynamic investigation is performed numerically by utilizing limited component programming, PLAXIS 3D. The soil is accepted as flexible totally plastic material submits to Mohr-Coulomb yield basis. A harmonic load is applied at the foundation with amplitude of 10 kPa at a frequency of (10, 15 and 20) HZ and se

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Publication Date
Sun Oct 15 2023
Journal Name
Sumer 3
Treatment of shallow and deep white spot lesions with three different mouthwashes evaluated by laser fluorescence (an in vitro study)
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This research aims to find how three different types of mouthwashes affect the depth of artificial white spot lesions. Teeth with various depths of white spot lesions were immersed in either splat mouthwash, Biorepair mouthwash, Sensodyne mouthwash, or artificial saliva (control)twice daily for one minute for 4 weeks and 8 weeks at 37°C. After this immersion procedure, lesion depth was measured using a diagnosed pen score. A one-way analysis of variance, Dunnett T3 and Tukey's post hoc α = .05 were used to analyze the testing data. Splat mouthwash enhanced the WSL remineralization and made the lowest ΔF compared with other mouthwashes in shallow and deep enamel after 4 and 8 weeks of treatment. In the repair groups, after 4 weeks

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The Use of Principal Components Analysis in the Formation of a Sustainable Human Development Index for Arab Countries
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This study aims to derive a sustainable human development index for the Arab countries by using the principal components analysis, which can help in reducing the number of data in the case of multiple variables.  This can be relied upon in the interpretation and tracking sustainable human development in the Arab countries in the view of the multiplicity of sustainable human development indicators and its huge data, beside the heterogeneity of countries in a range of characteristics associated with indicators of sustainable human development such as area, population, and economic activity. The study attempted to use the available data to the selected Arab countries for the recent years. This study concluded that a single inde

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Publication Date
Fri Nov 11 2022
Journal Name
Al-mansour Journal
Text Cryptography Based on Three Different Keys
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Secure information transmission over the internet is becoming an important requirement in data communication. These days, authenticity, secrecy, and confidentiality are the most important concerns in securing data communication. For that reason, information hiding methods are used, such as Cryptography, Steganography and Watermarking methods, to secure data transmission, where cryptography method is used to encrypt the information in an unreadable form. At the same time, steganography covers the information within images, audio or video. Finally, watermarking is used to protect information from intruders. This paper proposed a new cryptography method by using thre

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Publication Date
Sat Jan 25 2025
Journal Name
Al-mansour Journal
The Multi-Period Probabilistic Inventory Model Applied at the General Company for Leather Industries
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In this research, the multi-period probabilistic inventory model will be applied to the stores of raw materials used in the leather industry at the General Company for Leather Industries. The raw materials are:Natural leather includes cowhide, whether imported or local, buffalo leather, lamb leather, goat skin, chamois (raw materials made from natural leather), polished leather (raw materials made from natural leather), artificial leather (skai), supplements which include: (cuffs - Clocks - hands - pockets), and threads.This model was built after testing and determining the distribution of demand during the supply period (waiting period) for each material and completely independently from the rest of the materials, as none of the above mate

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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of The College Of Languages (jcl)
A study of some of the of the Verbs’ Arabic Roots in the stories of Osman Ceviksoy Like a Voice in The Dark.: Osman Çeviksoy'un "Karanlıkta Ses Gibi" Başlıklı Öykü Kitabında Arapça Kökenli Türkçe Fillerin İncelenmesi
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Due to the Geographical links, language is one of the multiple affects among Arabs and Turks. As the different studies demonstrate, Turkish contains many words derived from other languages, yet Arabic remains the language that has great affects on Turkish. Unlike Turkish language, Arabic is a derivative language that requires no suffixes. Thus, Arabic verbs are tuned into Turkish verbs by adding auxiliary verbs. The present study traces some of the Turkish compound words of Arabic roots with an explanation that shows the Auxiliary added to form the Turkish verb as found in the stories of Otman Chevek Sawy’s Like A voice in the Dark. The conclusion sums up the findings of the study illustrated by numbers.

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