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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 Jan 01 2024
Journal Name
Lecture Notes In Electrical Engineering
A Study of the Influence of Steel Brushes in Rail Surface Magnetic Flux Leakage Detection Using Finite Elements Simulation
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Publication Date
Fri Mar 01 2024
Journal Name
Journal Of Applied Spectroscopy
Spectrophotometric Method for Determination of Cu(II) Using a New Schiff Base Ligand
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The Cu(II) was found using a quick and uncomplicated procedure that involved reacting it with a freshly synthesized ligand to create an orange complex that had an absorbance peak of 481.5 nm in an acidic solution. The best conditions for the formation of the complex were studied from the concentration of the ligand, medium, the eff ect of the addition sequence, the eff ect of temperature, and the time of complex formation. The results obtained are scatter plot extending from 0.1–9 ppm and a linear range from 0.1–7 ppm. Relative standard deviation (RSD%) for n = 8 is less than 0.5, recovery % (R%) within acceptable values, correlation coeffi cient (r) equal 0.9986, coeffi cient of determination (r2) equal to 0.9973, and percentage capita

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Publication Date
Fri Feb 08 2019
Journal Name
Journal Of The College Of Education For Women
The House of Illusions A Study in Genet's The Balcony
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The definition of "prostitute" and prostitution is a difficult one and a
question over which the legislators of many lands and nations differed. A
notable feature of prostitution is its epidemic increase at times of war,
revolution and armed commotion, on account of economic, social and
psychological factors generated by such conditions of mortal conflicts. Wars
invariably deprive young wives and lovers of their men folk, resulting in
financial , sexual and emotional frustrations . At no time is the natural
balance between the sexes more seriously disturbed than during wars, when
thousands of men are thrown into one sector of the country and hundreds of
towns and villages are left to women and children only. Lo

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Publication Date
Thu Feb 29 2024
Journal Name
Sabrao Journal Of Breeding And Genetics
LOW-‎COST SOIL ‎MOISTURE SENSORS’ ASSESSMENT FOR THEIR ACCURACY AFTER CALIBRATION THROUGH THE ‎GRAVIMETRIC METHOD
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The existing study aimed to assess four soil moisture sensors’ capacitive (WH51 and SKU: S EN0193) and resistive (Yl69 and IC Station) abilities, which are affordable and medium-priced for their accuracy in six common soil types in the central region of Iraq. The readings’ calibration for the soil moisture sensor devices continued through two gravimetric methods. The first depended on the protocols’ database, while the second was the traditional calibration method. The second method recorded the lowest analysis error compared with the first. The moderate-cost sensor WH51 showed the lowest standard error (SE), MAD , and RMSE and the highest R² in both methods. The performance accuracy of WH51 was close to readings shown by the manufac

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Publication Date
Sat Sep 30 2023
Journal Name
Al–bahith Al–a'alami
Satirical Television Programs and Their Impact on the Image of Iraqi Politicians
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This research delves into the role of satirical television programs in shaping the image of Iraqi politicians. The research problem is summarized in the main question: How does satire featured in television programs influence the portrayal of Iraqi politicians? This research adopts a descriptive approach and employs a survey methodology. The primary data collection tool is a questionnaire, complemented by observation and measurement techniques. The study draws upon the framework of cultural cultivation theory as a guiding theoretical foundation. A total of 430 questionnaires were disseminated among respondents who regularly watch satirical programs, selected through a multi-stage random sampling procedure.
Th

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Publication Date
Wed Jun 28 2023
Journal Name
Al–bahith Al–a'alami
The Role of Ethnographic Programs on Documentary Channels in Enhancing Audience Knowledge
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This research investigates the engagement of the Iraqi audience with ethnographic programs and their impact on knowledge enhancement and intellectual perspectives. A questionnaire consisting of closed-ended questions was designed and administered to a purposive sample of 400 participants who exclusively follow ethnographic programs and documentary channels. The data were transcribed and subjected to statistical analysis using the SPSS software to ensure reliability and test hypotheses. The findings revealed that Al Jazeera Documentary Channel had the highest viewership percentage among respondents for ethnographic programs, while DW (Deutsche Welle) had the lowest viewership percentage. This suggests that Al Jazee

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Publication Date
Wed Mar 01 2023
Journal Name
Shift
Construction Safety Personnel Qualifications: The Impact of Education, Experience, and Certificate Programs
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Publication Date
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
Research and Development Programs Effectiveness in the Central Library of Baghdad University
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Research and Development Programs Effectiveness in the Central Library of Baghdad University

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Publication Date
Mon Oct 13 2025
Journal Name
Al–bahith Al–a'alami
The role of witchery and astrology programs in spreading illusion and myth
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« The emergence of satellite channels has led to fundamental changes in the supposed role of television, making it a center of culture and an important tributary to social upbringing and influencing the attitudes and values of individuals and in making public opinion regarding various issues, some television programs target ordinary people at home by virtue of the nature of their subjects, where there is a large audience of viewers, who consume and absorb what is offered to them from the cultural production of those satellite channels that play with the aspirations of groups of society to find metaphysical or magic solutions to their social problems or psychological delusions. The media, through its various messages, contributes to brin

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Publication Date
Sat Jan 02 2021
Journal Name
Journal Of The College Of Languages (jcl)
The comparative method in Maupassant’s (A woman’s Life): Le système comparatif dans Une vie de Maupassant
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The comparative method plays a major role in Maupassant’s novel (A woman’s Life).This is due to a good theme choice and smooth writing style characterized by simplicity, spontaneity and brevity.

The author uses the comparative method in the introduction of his novel where he compares the monastery’s closed world to the open world of the countryside of La Normandie, which represents the dream life of the heroine Jeanne.

The present paper is an attempt to answer the question regarding the importance of applying the comparative method in the novel (A Woman’s Life) by Maupassant. The paper stresses the fact that the novelist employs the comparative method in his book for certain features .One of these features is the

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