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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 21 2015
Journal Name
Al-mustansiriyah Journal Of Science
A comparative Study of Adiponectin and Oxidative Stress (malondialdehyde and peroxynitrite) levels in Iraqi Patients with Acromegaly
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The aim of this study is to find a relationship between oxidative stress and adiponectin in Iraqi patients with acromegaly. The present study included 30 patients with acromegaly disease attending at Al-Yarmuk teaching hospital , and 30 healthy individuals as a control group.The two groups with ages ranging (30-55) years. The results revealed a highly significant elevation in all parameters (GH,IGF-1 , adiponectin , malondialdehyde , and peroxynitrite ) levels in sera of patients when compared with healthy control .It can be concluded that oxidative stress (malondialdehyde and peroxynitrite ) may be valuable in detecting of endocrine diseases like acromegaly .

Publication Date
Mon Feb 01 2016
Journal Name
Al-mustansiriyah Journal Of Science
A comparative Study of Adiponectin and Oxidative Stress (malondialdehyde and peroxynitrite) levels in Iraqi Patients with Acromegaly
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The aim of this study is to find a relationship between oxidative stress and adiponectin in Iraqi patients with acromegaly. The present study included 30 patients with acromegaly disease attending at Al-Yarmuk teaching hospital , and 30 healthy individuals as a control group.The two groups with ages ranging (30-55) years. The results revealed a highly significant elevation in all parameters (GH,IGF-1 , adiponectin , malondialdehyde , and peroxynitrite ) levels in sera of patients when compared with healthy control .It can be concluded that oxidative stress (malondialdehyde and peroxynitrite ) may be valuable in detecting of endocrine diseases like acromegaly .

Publication Date
Wed Mar 13 2019
Journal Name
Al-khwarizmi Engineering Journal
Transient Behavior Analysis for Solar Energy Storage in PCM-CFM Material Using Equivalent Heat Capacity Method as Storage Model
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A paraffin wax and copper foam matrix were used as a thermal energy storage material in the double passes air solar chimney (SC) collector to get ventilation effect through daytime and after sunset. Air SC collector was installed in the south wall of an insulated test room and tested with different working angles (30o, 45o and 60o). Different SC types were used; single pass, double passes flat plate collector and double pass thermal energy storage box collector (TESB). A computational model based on the finite volume method for transient tw dimensional domains was carried out to describe the heat transfer and storage in the thermal energy storage material of collector. Also, equivalent specific heat metho

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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
The grammatical approach to explain Bant Souad's poem (Explanation of Ibn Hisham as a model) a . M . Dr. Abdul Hamid Hamad shehatha Mustansiriya University Faculty of Basic Education the department of Arabic language
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This study is concerned with shedding light on the grammatical method of Ibn Hisham Al-Ansari (761 AH), in his explanation of Bant Souad’s poem by the poet Kaab bin Zuhair, and I included a brief description of Ibn Hisham’s life with a number of explanations of this poem, then clarified the most important features of this method The grammar represented by his reliance on hearing and presenting it to analogy with mention of types of analogy, as well as his attribution of opinions to their owners with weighting, selection and balancing, and his attention to reasoning and a number of grammatical ailments, and his approach is also distinguished by following the method of fractal.

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
Reasons for Lying in Kindergarten Children from the Kindergarten Teachers’ Point of View: A Comparative Study between Males and Females: سجلاء فائق هاشم , كلثوم عبد عون ردام
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Lying is considered a dangerous tendency among children if it has become a habit. It results in many social problems, such as child’s loss of confidence, lack of others’ respect to him, and his lack of respect to the desired values ​​of the society, such as honesty and trust. Consequently, he will be led to a deviation when he becomes old; especially if the child’s socially unaccepted behavior has not been directed. The research, thus, aims to examine the causes of lying in the most important stage of children’s life; that is, between (4-6) years. Such an aim helps to know about the individual reasons of lying among males and females from teachers’ perspectives. To meet the objective of the study, a number of (128) children

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Publication Date
Fri Jul 28 2023
Journal Name
The Journal Of Physical Chemistry A
Tubular Magnetic Shielding Scan (TMSS): A New Technique for Molecular Space Exploration. (i) The Case of Aromaticity of Benzene and [<i>n</i>]Paracyclophanes
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Both traditional and novel techniques were employed in this work for magnetic shielding evaluation to shed new light on the magnetic and aromaticity properties of benzene and 12 [n]paracyclophanes with n = 3–14. Density functional theory (DFT) with the B3LYP functional and all-electron Jorge-ATZP and x2c-TZVPPall-s basis sets was utilized for geometry optimization and magnetic shielding calculations, respectively. Additionally, the 6-311+G(d,p) basis set was incorporated for the purpose of comparing the magnetic shielding results. In addition to traditional evaluations such as NICS/NICSzz-Scan, and 2D-3D σiso(r)/σzz(r) maps, two new techniques were implemented: bendable grids (BGs) and cylindrical grids (CGs) of ghost atoms (Bqs). BGs a

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Publication Date
Thu Dec 31 2020
Journal Name
Pollution Research Journal
ANALYSIS OF THE HYDRAULIC CHARACTERISTICS OF AL MAHAWIL STREAM USING HECRAS: A FIELD STUDY
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A water resources management for earthen canal/stream is introduced through creating a combination procedure between a field study and the scientific analytical concepts that distinguish the hydraulic problems on this type of stream with using the facilities that are available in HECRAS software; aiming to point the solutions of these problems. Al Mahawil stream is an earthen canal which is subjected to periodic changes in cross sections due to scour, deposition, and incorrect periodic dredging processes due to growth of the Ceratophyllum plants and weeds on the bed and banks of the stream; which affect the characteristics of the flow. This research aims to present a strategy of water resources management through a field study that conducte

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Publication Date
Sun Mar 30 2008
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Quantitative Analysis of the Mixing of Three Solids Different in Density by an Air Fluidized Bed
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Three cohesionless free flowing materials of different density were mixed in an air fluidized bed to study the mixing process by calculating performance of mixing index according to Rose equation (1959) and to study the effect of four variables (air velocity, mixing time, particle size of trace component and concentration of trace component) on the mixing index and as well as on mixing performance. It was found that mixing index increases with increasing the air velocity, mixing time and concentration of trace component until the optimum value. Mixing index depends on the magnitude of difference in particle size The first set of experiments (salt then sand then cast iron) give higher mixing index and better performance of mixing than the

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Publication Date
Tue Jun 01 2010
Journal Name
Journal Of The College Of Languages (jcl)
Nature as a holy book
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Nature and natural beauty have always been the source of inspiration for poets and mystics.  For them, nature is one of the most recurrent and celebrated themes. It is a significant symbol of the beauty, righteousness and freshness they are looking for. For religious and mystical poets, it is a reference to God, his beauty, and splendour. Comparing it with the scripture, Thomas Ryan, a Catholic priest and a mystical writer, says ''The Bible is the 'small book', the world of nature is the 'big book'. Both reveal the Creator.''1

     For Muslim mystics, God does exist everywhere as the Qur'an states:   ''Wherever (Whithersoever)  you turn, there is God's face” (Chapter (Surah): 2

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Publication Date
Sun Aug 06 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Computer Analysis Of A simplified Eye Model
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  Computer analysis of simple eye model is performed in the present work by using the Zemax optical design software 2000E . The most important optical parameters of the eye were calculated such as the effective focal length (EFL) , the image spot size at the retina and found to be in a reasonable agreement with the values needed for the laser retinal treatment .The present eye model leads to an effective wavelength and we found the image spot diagram at the surface of the retina and the wavefront error which are provided at zero field angle. This gives a good evidence of the validity of the model in one hand, and can be used to determine the compatibility of any optical design intended for visual applications. By using the pulse fre

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