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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 Sep 30 2024
Journal Name
Modern Sport
The Effect of Skill Exercises According to the Concentration Technique of Lateral Thinking on Motor Accuracy and Learning the Diving Stop Attack for Students in the Epee Weapon
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لمعرفة مدى تأثير تمرينات مهارية وفق تقنية تركيز للتفكير الجاني على الدقة الحركة وتعلم هجمة الإيقاف  بالغطس للطلاب في سلاح الشيش استخدمت الباحثتان المنهج التجريبي على عينة من طلاب المرحلة الثالثة بكلية التربية البدنية وعلوم الرياضة –جامعة ديالى والتي بلغت (30) طالباً موزعين على مجموعتين التجريبية والضابطة وبعد إكمال اجراءات البحث وتطبيق الاختبارات القبلية وتنفيذ التمرينات والاختبار البعدي ومعالجة الب

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Publication Date
Tue Dec 20 2022
Journal Name
International Journal Of Emerging Technologies In Learning (ijet)
Impact of a Proposed Strategy According to Luria’s Model in Realistic Thinking and Achievement in Mathematics
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The research aims to find the impact of a proposed strategy according to the Luria model on realistic thinking among fifth-class scientific students and their achievement in mathematics. To achieve it, the experimental research method and the quasi-experimental design were used for two equal groups, one of them is a control group taught in traditional way and the other is an experimental one taught according to strategy based on Luria model. The research community represents the students of the fifth scientific class from the General Directorate of Education of Karkh First. The research sample (40) students were deliberately chosen and distributed equally between the two groups after making sure that they were equals in their previo

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Publication Date
Sun Jul 01 2018
Journal Name
Journal Of Global Pharma Technology
Preparation, Characterization and Biological Activity of New Derivatives of 3-Cyclic Oxazepine, 3-Cyclic Lactam and 3- Aminomethyl Imidazo (1, 2-a) Benzthiazol
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In this work a series of fourteen new compounds were synthesized. Compound [1] was formed from the reaction of 2-aminobenzothiazole and p-bromophenacyl bromide. Aldehyde group [2] was obtained from the reaction of compound [1] with pocl3 in presence of DMF and CHCl3 .After that shiff bases have been synthesized from the reaction of compound [2] with different aromatic amine to give new shiff bases [3- 5]. These new shiff bases have been reduced to their corresponding amine [6-8] by means of sodium borohydride. Then reaction of shiff bases [3-5] with phenyl isocyanate gives 3-cyclic lactam derivatives [9-11]. 3-cyclic Oxazepine derivatives [12-14] were obtained by reaction of shiff bases [3-5] with succinic anhydride. These new formed co

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Publication Date
Sun Mar 12 2023
Journal Name
Egyptian Journal Of Chemistry
Studying the Molecular Interactions for Potash Alum with Distilled Water and Aqueous Solution of Ethylene Glycol at Different Temperatures.
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Publication Date
Tue Jan 03 2023
Journal Name
College Of Islamic Sciences
Formulas The command and its style in Surat Al-Ma’idah is a rhetorical fundamentalist study.: The command and its style in Surat Al-Ma’idah is a rhetorical fundamentalist study
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Research Summary :

      Praise be to God, Lord of the Worlds, and prayers and peace be upon the Master of the Messengers, his family and all his companions, then after:

     This is a brief research that contained its two rudders the command and its Style in Surat Al-Ma’idah a fundamental rhetorical study, and the study clarified the meaning of imperative in both;  the Arabic  language and in the terminology of the fundamentalists and rhetoricians in a concise manner, and then indicated the imperative of the command , the true meaning, and the meanings interpretated as an  imperative form. I have mentioned some verses of Surat Al-Ma’idah, so what I have quot

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Publication Date
Tue Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
The Effect of Organizational Creativity in Enhancing Knowledge Management Processes: survey study for a sample of academic staff members at the Technical College of management / Baghdad)
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In many organizations, employees who have high mental skills are the main source of organizational creativity. When a firm does not put creativity as a goal, cannot stand solid against the competition. Nowadays, knowledge is the path to discover the innovation and creativity aspects, This can assist the firm to stand face to face with competition in the market. The importance of this research comes from detecting and knowing the relation between creativity and knowledge to know and detect the influence of organizational creativity on backing the management of knowledge and determine the final results. The problem of research is to trace the role of organizational creativity on knowledge management processes in order to enable the

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Publication Date
Wed Dec 29 2021
Journal Name
Al-khwarizmi Engineering Journal
Comparison of Prediction Programs for Short Wave Circuit Link from Iraq to Test points on Both Earth Hemispheres during Solar Minimum
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This paper compare  the accurecy of HF propagation  prediction programs for  HF circuits links between Iraq and  different points world wide  during August 2018 when  solar cycle 24 (start 2009 end 2020) is at minimun activity and also find out the best communication mode  used. The prediction   programs like Voice of America Coverage Analysis Program (VOACAP) and ITU Recommendation RS 533 (REC533 )  had been used to generat HF circuit link  parameters like Maximum Usable Frequency ( MUF) and Frequency of Transsmision (FOT) .Depending  on the predicted parameters (data)  , real radio contacts had been done using a radio transceiver from Icom  model IC 7100 with 100W RF

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Publication Date
Sun Jan 10 2021
Journal Name
Open Access Macedonian Journal Of Medical Sciences
Comparative Study between Neopterin and Alvarado Score in the Diagnosis of Acute Appendicitis and Its Severity
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BACKGROUND: Acute appendicitis (AA) remains a complex case even for experienced surgeons. Rate of negative appendectomy is 5–40% and delayed intervention result in perforated appendicitis in 5–30% of cases. AIM: The aim of the study was to evaluate NPT as a marker for the diagnosis of AA concerning its severity. And compare the diagnostic value of it with the ALV scoring system. METHODS: One hundred twenty patients presented with signs and symptoms of AA and underwent appendectomy, only 84 patients proved to be AA by histopathological examination, were included in the study. Blood samples for neopterin (NPT) estimation and Alvarado (ALV) score was calculated. Control group consists of 45 healthy individual. RESULTS: NPT levels were s

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Publication Date
Sat Jan 01 2022
Journal Name
Proceeding Of The 1st International Conference On Advanced Research In Pure And Applied Science (icarpas2021): Third Annual Conference Of Al-muthanna University/college Of Science
Efficient approach for solving high order (2+1)D-differential equation
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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Aesthetic Levels in Shape Variables in Spectacular Films the Indian Film (Main Tera Hero) a Model: غسان محسن حمد
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The spectacular film is a type of feature films which has specific elements that contribute in increasing the aesthetics of the shape in its structure. The researcher started studying this type of films by researching the spectacular film concept, the history of its development, who are its most important stars and then tackling the Indian cinema represented by Bollywood, which is considered a school for this type of film. The researcher addressed the most important influential elements that entre in its production as well as studying these elements that contribute to building the shape including the configuration, movements of cameras, lenses, the lighting, colors, costumes etc. and what influence they have in forming a special aestheti

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