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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
Sun Jul 04 2021
Journal Name
Journal Of Interdisciplinary Mathematics
Comparison the solutions for some kinds of differential equations using iterative methods
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This manuscript presents several applications for solving special kinds of ordinary and partial differential equations using iteration methods such as Adomian decomposition method (ADM), Variation iterative method (VIM) and Taylor series method. These methods can be applied as well as to solve nonperturbed problems and 3rd order parabolic PDEs with variable coefficient. Moreover, we compare the results using ADM, VIM and Taylor series method. These methods are a commination of the two initial conditions.

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
Using the plastic wastes in fabrication of composite materials for different applications
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This study suggests using the recycled plastic waste to prepare the polymer matrix composite (PMCs) to use in different applications. Composite materials were prepared by mixing the polyester resin (UP) with plastic waste, two types of plastic waste were used in this work included polyethylene-terephthalate (PET) and Polyvinyl chloride (PVC) with varies weight fractions (0, 5, 10, 15, 20 and 25 %) added as a filler in flakes form. Charpy impact test was performed on the prepared samples to calculate the values of impact strength (I.S). Flexural and hardness tests were carried out to calculate the values of flexural strength and hardness. Acoustic insulation and optical microscope tests were carried out. In general, it is found that UP/PV

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Publication Date
Sat Dec 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Finding the best estimation of generalized for failure rates by using Simulation
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The statistical distributions study aimed to obtain on best descriptions  of variable sets phenomena, which each of them got one behavior of that distributions .  The estimation operations study for that distributions considered of important things which could n't canceled in variable behavior study, as result  this research came as trial for reaching to best method for information distribution estimation which is generalized linear failure rate distribution, throughout studying the theoretical sides by depending on statistical posteriori methods  like greatest ability, minimum squares method and Mixing method (suggested method).        

The research

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Publication Date
Thu Apr 01 2010
Journal Name
Journal Of Educational And Psychological Researches
The Effect of Using Computer in program BasedStudying for Student in Jordan
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This study aimed at investigating the effect of using computer in
Efficiency of Training Programme of Science Teachers in Ajloun District in
Jordan.
1- What is the effect of using computer in program for the two groups
2- ( the experimental and control group ) .
3- Are there any statistics different in the effect of using computer
program for the two groups ?
4- Are there any statistics (comparison ) or different of the effect of the
effect of using computer program refer to the sex (male or female )?
The community of the study consisted of all the science student in
educational directorate of Ajloun district for the academic year 2009 –
2010, they are (120) ( male and female) . The sample of the study<

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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Social responsibility and its role in enhancing the quality of services: an analytical study of the views of a sample of employees in the Directorate of Electricity Distribution Nineveh / Center
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The current research aims to diagnose the role of social responsibility as a contributing factor in enhancing the quality of services provided by the public sector in Iraq, where the research sought to demonstrate the relationship and impact of social responsibility dimensions (economic, legal, moral, and human) on the sector Services related to the electric field in Nineveh governorate because of its importance and its direct relationship with the citizen especially after the end of military operations in the destruction of the electricity sector by a large percentage in the city of Mosul. Nineveh Electricity Distribution Directorate / Center was chosen as a research community including (administrators and staff) of the research

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Publication Date
Thu Dec 31 2015
Journal Name
International Visible Conference On Educational Studies & Applied Linguistics 2016
A New Perspective About Masculinity and the Issue of Identity in Ernest Hemingway's The Old Man and The Sea and Michael Ondaatje's in The Skin of a lion
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A New Perspective About Masculinity and the Issue of Identity in Ernest Hemingway's The Old Man and The Sea and Michael Ondaatje's in The Skin of a lion

Publication Date
Sun Oct 15 2023
Journal Name
Sumer 3
Assessment of the Salivary level of Sphingosine kinases-1 in periodontitis and its correlation with periodontal parameters
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One of the key molecules in the conversion of sphingosine to sphingosine-1- phosphate is SPHK-1, also known as Sphingosine Kinase 1 (SPHK-1). Sphingosine-1-phosphate (S1P) is a lipid that acts as a signaling molecule and plays an essential role in inflammatory and immunomodulatory responses. S1P has recently been identified as a mediator and a biomarker in inflammatory bone diseases such as osteoporosis and inflammatory osteolysis based on the biological effects of S1P in osteoclastic and osteoblastic cells and immune cells. According to recent research, S1P may play a role in the pathogenesis of periodontitis, an inflammatory bone-destructive condition. This study assesses the salivary level SPHK-1 in periodontitis and its correlat

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Publication Date
Thu Mar 19 2015
Journal Name
Al-academy
Theatrical Visual System between the Cultural Identity and Globalization Culture Iraqi Theatre as Case Study: فرحان عمران موسى
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It seems that the features of the theatrical discourse , since its early establishment by the Greeks, were cultural features specifically confined to that society. Such features determined the direction of the theatrical discourse for this state instead of that state. There could be some sort of similarity among those features , nevertheless they remained within the general humanitarian framework . What achieved relatedness were those features and particularities that distinguished the theatrical community. Such features and particularities vary from one show to another. This is what we call " Local Specificity" .The Iraqi theatrical memory has always emphasized the concept of Experimentation through originality and renewal since the arr

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Crossref
Publication Date
Fri Mar 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Study the random walking of the ISX60 market index For the Iraq Stock Exchange
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This paper aimed to test random walking through the ISX60 market index for the ability to judge market efficiency at a weak level. The study used Serial Correlation Test, the Runs Test, the Variance Ratio Test, as well as the Rescaled Range Test.The population of the study represents of Iraq Stock Exchange. The study concluded accepting the hypothesis of the study that the returns of the ISX60 market index in the Iraqi market for securities does not follow the random walking in general and as a result the Iraq market for securities is inefficient within the weak level of efficiency and the study recommended need a supervisors work in the Iraqi market for securities to activate all means a which will work to communication with information

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Publication Date
Thu Dec 01 2016
Journal Name
المجلة العربية للعلوم و نشر الأبحاث
Assessment of Carbonate Rocks , Western Desert of Iraq as Dimension Stones for Building
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