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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 Dec 15 2018
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative evaluation of the radiographic density of GuttaFlow® 2 in different obturation techniques using Spiral Computed Tomography
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Background: Ideal root canal obturation depends on many factors; one of them is good sealing of root canal without pores. The aim of this study was to determine the radiographic density of GuttaFlow® 2 with different obturation techniques using spiral computed tomography. Materials and Methods: Forty palatal roots of permanent maxillary first molar were used in this study. Following working length determination, root canal was prepared using rotary PROTAPER universal system. They were randomly divided into four groups of 10 roots each, the groups are Conventional lateral condensation with Apexit Plus sealer, Conventional lateral condensation with GuttaFlow® 2 as a sealer, Soft Core Regular with GuttaFlow® 2 as a sealer and singl

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Publication Date
Fri May 01 2020
Journal Name
مجلة بحوث الشرق الأوسط
دراسة مقارنة لمستوى التمکین الإداری بین مشرفی التربیة الریاضیة (الاختصاص والفنی) لمدیریات التربیة فی محافظة بغداد A Comparative Study of the Level of Administrative Empowerment between the Physical Education Supervisors (Specialization and Technical) of Education Directorate in Baghdad Governorate
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Publication Date
Sat Jun 04 2022
Journal Name
Al–bahith Al–a'alami
Digital public relations and its role in prioritizing the masses: An analytical study of the United Nations website : (A paper extracted from a PhD dissertation)
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This paper aims to identify how the United Nations works through its website in prioritizing audiences towards international issues، by identifying the digital PR mechanisms used in digital PR contents in prioritizing audiences towards the international issues they deal with. To achieve the objectives of this paper, the researcher used the survey method and content analysis tool with a view to identifying the ranking of international issues on the website of health، peace and security، humanitarian assistance، human rights، women، migrants، refugees and displaced persons، economic development، United Nations affairs، culture and education، environment and climate، sustainable development, and law and crime prevention. One of

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Publication Date
Mon Apr 01 2024
Journal Name
Egyptian Journal Of Immunology
The role of C-reactive protein, procalcitonin, interleukin-6 and neutrophil / lymphocyte ratio as a laboratory biomarker in COVID-19
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Biomarkers such as Interleukin-6 (IL-6), Procalcitonin (PCT), C-reactive protein (CRP) and Neutrophil-Lymphocyte Ratio (NLR) have a role in the pathogenesis of severe coronavirus disease 2019 (COVID-19). The aim of this study was to explore the differences between serum levels of such biomarkers in severe and non-severe COVID-19 cases and compare them with normal people and to evaluate the sociodemographic variables and chronic diseases effect on the severity of COVID-19. The study included 160 subjects, divided into two groups, a case group of 80 patients, and a control group of 80 normal persons. The case group was divided into two subgroups: 40 severe COVID-19 patients and 40 patients with non-severe disease. Blood IL-6 was asses

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Publication Date
Wed Feb 12 2025
Journal Name
Chemchemtech
A REVIEW OF ANALYTICAL METHODS FOR THE ANALYSIS OF PHARMACEUTICALS IN ENVIRONMENTAL SAMPLES
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One of the main causes for concern is the widespread presence of pharmaceuticals in the environment, which may be harmful to living things. They are often referred to as emerging chemical pollutants in water bodies because they are either still unregulated or undergoing regulation. Pharmaceutical pollution of the environment may have detrimental effects on ecosystem viability, human health, and water quality. In this study, the amount of remaining pharmaceutical compounds in environmental waters was determined using a straightforward review. Pharmaceutical production and consumption have increased due to medical advancements, leading to concerns about their environmental impact and potential harm to living things due to their increa

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Publication Date
Wed Oct 17 2018
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison of Bayes Estimators for the parameter of Rayleigh Distribution with Simulation
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   A comparison of double informative and non- informative priors assumed for the parameter of Rayleigh distribution is considered. Three different sets of double priors are included, for a single unknown parameter of Rayleigh distribution. We have assumed three double priors: the square root inverted gamma (SRIG) - the natural conjugate family of priors distribution, the square root inverted gamma – the non-informative distribution, and the natural conjugate family of priors - the non-informative distribution as double priors .The data is generating form three cases from Rayleigh distribution for different samples sizes (small, medium, and large). And Bayes estimators for the parameter is derived under a squared erro

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Publication Date
Tue Jul 11 2023
Journal Name
Journal Of Educational And Psychological Researches
Domestic Violence and Extremism among the Young: A Field Study in the Madain Region
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Young people represent the power and cornerstone of societies and their superiority is linked to their well-being. Their empowerment is as essential as the heart to the body, if it is corrupt, then the whole body is corrupt, and vice versa. The exposure to extremism and pressure from their families leads to violent acts and crimes for obtaining money through unknown organized bodies. This will drive them to fail in their life in an attempt to fulfill their most basic needs, which they have been deprived of by their families, the government, and other institutions. Therefore, governments should provide job opportunities for young people and provide entertainment centers, sports clubs, and family education centers that raise awareness of s

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Publication Date
Sun Oct 02 2016
Journal Name
Journal Of Educational And Psychological Researches
Teaching Problems facing the first three class teachers in the city of Buraimi
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The present study aimed to identify teaching problems which facing the teachers for first three grades classes, and if these problems different according to some variables teacher qualification, experience period, class grade). The study sample consist of (137 )

 female teachers who teach the first three grades in Braimy city in Oman, teachers spread in five government schools. Both researchers developed questionnaire to measure problems faced by the mentioned teachers, consist of 50 questions distributed into 4 dimensions (teacher, students, the curriculum, the evaluations), Also researchers checked questionnaire validity and stability. The results indicate to: The most common probl

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Publication Date
Mon Jan 01 2024
Journal Name
Communications In Mathematical Biology And Neuroscience
The contribution of amensalism and parasitism in the three-species ecological system's dynamic
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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Influence of Organizational Power on the Achievement of Entrepreneurship for Business Organizations An Analytical Study of the Views of a Sample of Managers in the Iraqi Ministry of Education
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This research aims to study the influence of organizational power on the achievement of entrepreneurship for business organizations. It is an analytical study of the views of a sample of managers in the Iraqi Ministry of Education. The research highlights the contribution that can be made from the knowledge of the theory of business organizations in achieving organizational success. The organizational power of the organization contributes to achieving entrepreneurship in the business environment and achieving a competitive position in the work environment. The research dealt with two variables: the first is the independent variable, the organizational power in its dimensions (Expend Power, Structural Power, Prestige Power). And t

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