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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
Wed Jan 01 2020
Journal Name
Annals Of Tropical Medicine And Public Health
EFFECT OF EUCALYPTUS AND MYRTUS EXTRACTS IDENTIFICATION BY GAS CHROMATOGRAPHY-MASS SPECTROMETRY ON SOME SPECIES OF CANDIDA AS A MODEL OF MEDICAL PLANTS
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Publication Date
Wed Jun 10 2020
Journal Name
Annals Of Tropical Medicine & Public Health
EFFECT OF EUCALYPTUS AND MYRTUS EXTRACTS IDENTIFICATION BY GAS CHROMATOGRAPHY-MASS SPECTROMETRY ON SOME SPECIES OF CANDIDA AS A MODEL OF MEDICAL PLANTS
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The study showed that all extracts (aqueous, ethanolic and acetonic) of the leaves of Eucalyptus and Myrtus plants had a inhibitory effect on the growth of all types of yeasts studied, acetone extract recorded the highest inhibition of yeastat 100ppm concentration,The inhibition was 35mm, 34mm, 24mm and 20mm for Candida parapsilosis, Candida glabrata, Candida tropicalis and Candida albicans respectively, The experiments above showed the least significant differences at 0.05 level.The results ofE. Cammldulensis ethanolic tincture analysis has shown the presence of 44 biologically active substances. The main Eucalyptus leaves component was: 2-Bicyclo (2-2.1) heptanol (12.37%), Ledol (8.23%),1,2,4- Benzenetriol (8.45%) and that contain spathul

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Publication Date
Thu Aug 01 2019
Journal Name
Transylvanian Review
POSSIBILITY OF APPLICATION THE BALANCED SCORECARD IN THE IRAQI INDUSTRIAL COMPANIES: A PROPOSED MODEL
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POSSIBILITY OF APPLICATION THE BALANCED SCORECARD IN THE IRAQI INDUSTRIAL COMPANIES: A PROPOSED MODEL

Publication Date
Tue Mar 02 2021
Journal Name
Humanitarian And Natural Sciences Journal
THE LINGUISTIC STRUCTURES OF THE HISTORIANS ALYAQOUBI (284 AH / 897 AD) ARE A MODEL
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The research in the linguistic structures of the historians Al-Yaqoubi is considered a model of the important topics in historical studies in general, given its importance in the lives of peoples due to its connotations and meanings that summarize interpretation, clarification, and prolonged speech, as it includes life meanings with many dimensions, these structures have been used in historical incidents Important, and throughout the different ages, as it can be used to support an opinion, solve problems, prove evidence, increase wisdom, and it needs rich life experiences, and a sound language, to use it, and needs a wide absorptive capacity for the recipient, the research included linguistic structures in the achievement of science , Lingu

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Publication Date
Mon Oct 01 2018
Journal Name
International Journal Of Research In Social Sciences And Humanities
THE SOCIAL INTERACTION OF LANGUAGE IN A COMIC SERIES: A SOCIOLINGUISTIC STUDY
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Dell Hymesin 1964coined The Ethnography of Communication in an attempt to explain the ways in which people use the language to interact. It hypothesizes that ethnography is less applicable among participants who have the same sociocultural background. It was proven that all the basic speech components occur whenever there is an interactional situation. The elements of (SPEAKING) schema are closely connected. However, the findings establish the fact that these elements take place effectively among participants who have the same sociocultural background.One of the most outstanding conclusions is the capability of the (SPEAKING) model to analyze not only an interaction between two or more participants, but also any event which consists of a mo

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Publication Date
Thu Aug 16 2018
Journal Name
International Journal Of Research In Social Sciences And Humanities
The Social Interaction of Langauge in a Comic Series: A Sociolinguistic Study
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DBNRAHA Hameed, IJRSSH PUBLICATION, 2018

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Publication Date
Sat Jun 04 2022
Journal Name
Al–bahith Al–a'alami
The relationship of using the social networking site Facebook to the accumulation of social capital: (Survey study for a sample of students from the University of Algiers 3)
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The subject of social capital is of great importance, as it provides an analytical framework for researchers interested in understanding the impact of the Internet on many dimensions of human and social life. And because social networking sites have infiltrated societies and produced new variables at the level of human and social communication, this study came to examine the relationship between the use of the social networking site Facebook and the accumulation of social capital among a sample of University of Algeria 3 students, by researching the variables of intensity of use and patterns of use as independent variables and their relationship to social capital. The results of the field study revealed a strong relationship between the

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Role of External Audit in Limiting Creative Accounting Practices in Light of International Standards from The Point of View of Certified Accountancy Experts in Iraq as a Model
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This research aims to solve a problem in the field of accounting and financial knowledge in the world today, that is, the problem of creative accounting. Especially after the global financial crisis and the collapse of many large companies in the world, people find that they use creative accounting methods to distinguish them from reality, showing the results of their activities and their financial status. This research discusses the concept of creative accounting, the most important methods used in financial statements and its relationship with external auditing, and procedures to limit accounting creativity. This study uses descriptive analysis methods after confirming its theoretical aspects in practice. Using the statistical

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Publication Date
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
Comparative Study of Image Denoising Using Wavelet Transforms and Optimal Threshold and Neighbouring Window
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NeighShrink is an efficient image denoising algorithm based on the discrete wavelet
transform (DWT). Its disadvantage is to use a suboptimal universal threshold and identical
neighbouring window size in all wavelet subbands. Dengwen and Wengang proposed an
improved method, which can determine an optimal threshold and neighbouring window size
for every subband by the Stein’s unbiased risk estimate (SURE). Its denoising performance is
considerably superior to NeighShrink and also outperforms SURE-LET, which is an up-todate
denoising algorithm based on the SURE. In this paper different wavelet transform
families are used with this improved method, the results show that Haar wavelet has the
lowest performance among

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Publication Date
Tue Oct 08 2002
Journal Name
Iraqi Journal Of Laser
Study of Laser Propagation Parameters in the Underdense Plasma Region Using a Two Dimensional Simulation Code
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The propagation of laser beam in the underdense deuterium plasma has been studied via computer simulation using the fluid model. An appropriate computer code “HEATER” has been modified and is used for this purpose. The propagation is taken to be in a cylindrical symmetric medium. Different laser wavelengths (1 = 10.6 m, 2 = 1.06 m, and 3 = 0.53 m) with a Gaussian pulse type and 15 ns pulse widths have been considered. Absorption energy and laser flux have been calculated for different plasma and laser parameters. The absorbed laser energy showed maximum for  = 0.53 m. This high absorbitivity was inferred to the effect of the pondermotive force.

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