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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 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
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
Wed Dec 01 2010
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Technical methodology balanced performance as a strategic framework for the economic units operating in the Iraqi industrial sector environment
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facing economic units operating in the environment sector of the Iraqi

industrial many pressures in its seeking to measure and evaluate its performance because of variables, today's corporate environment, as the case which makes looking for a methodology can be adopted to evaluate its performance with a more holistic, rather than being limited to traditional measures that are no longer enough to keep pace with rapid changes in today's corporate environment, which requires that measures of performance are derived from the strategy of unity and commensurate with the specificity of the environment in Iraq. Try searching discussion Ttormwhrat and performance measurement systems to suit the business strategies and directions of change

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Publication Date
Fri Jun 28 2024
Journal Name
Arab World English Journal
Cowboy as a Symbol of Individualism: A Pragmatic Analysis of Red Dead Redemption 2
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As cultures are mainly divided into collectivistic and individualistic, members tend to emphasize, through communication, either their position as part of their group or their independence from the group. This emphasis is manifested in using the pragmatic concepts of positive politeness and negative politeness. The present study looks into the reflection of these two cultures in Rockstar’s renowned video game, Red Dead Redemption 2 (2018). It aims at identifying the two cultures as present in the game and showing their significance to its narrative. It fills the gap in the studies of language used within video games as well as its cultural reflections. The study addresses the following question: What are the positive and negative

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Publication Date
Mon Mar 07 2022
Journal Name
Journal Of Educational And Psychological Researches
Math Word Problems in Mathematics Books for the First Three Grads of the Basic Stage in Palestine (An analytical and Evaluative Study)
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This study aimed at revealing the degree of availability of standards of word problems in mathematics books for the first three grades of the basic stage in Palestine. For this purpose, the researcher prepared an analysis tool and a list of criteria consisting of two areas: linguistic formulation and mathematical content. Every area had seven items. The results of the study showed that the third-grade mathematics book has the highest degree of availability of the standards with 85.75%, and then came the second-grade mathematics book with 83.12%. Finally, the first-grade mathematics book came with 80.13%. In the light of the previous results, the researcher recommended to develop the language of word problems, to take into account their i

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Publication Date
Wed Jul 01 2015
Journal Name
Al–bahith Al–a'alami
Methods of Arab TV Programs Production
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This research investigates the methods of producing Investigative Arabic Television Programs that are able to prove its existence during a short period of time as a form of Television programs on Arab satellite channels growing in number and varied in content. The research aims to present qualitative and quantitative descriptions of the methods used in tackling the topics discussed in the program, and knowing whether they satisfy the conditions and scientific foundations for the research, investigation, analysis, and interpretation. The researcher uses the survey method and uses the tool of content analysis including a set of methodological steps that seek to discover the implied meaning of the research sample represented by the program

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Publication Date
Tue Jan 20 2026
Journal Name
Journal Of Physical Education
A Comparative Study of Mental Alertness Between Inactive and Active Individuals In Baghdad University Students Aged 18 – 22 Years Old
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Publication Date
Tue Feb 26 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Return Variation on Investment as a Function for the Difference of Market Share: An Applied Research on a Sample of Private Banks listed in Iraq Stock Exchange (ISX)
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    The research specified with study the relation  between the market share for the sample research banks and the amount of the achieved revenues from the investment, where the  dominated belief  that there potentiality enhancing the revenue on investment with the increase of the banks shares in their markets after their success in achieving rates of successive growth in their sales of sales and to a suitable achieve  market coverage for their products and they have dissemination and suitable  promotion activity, the  market share represented the competition  for the banks, and the markets pay attention to the  market share as a strategic objective and to maintain them also increasi

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