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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
Thu Dec 15 2022
Journal Name
Al-academy
The functional diversity of the directorial vision in the political theater cinema as a model
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It is very necessary for the political theater to be within the space of every theatrical performance, so that the theater carries the diverse and enlightened values and cultures of this world. political theatre. In the first chapter, the researcher dealt with (the methodological framework), which includes the research problem identified by the researcher with the following question (the functional diversity of the directorial vision in the political theater)
Importance, purpose, limits and seal by defining terminology.
In the second chapter, the researcher dealt with the theoretical framework on two topics, the first (transformations of directorial vision in theatrical performance) and the second topic (aesthetic experiences i

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Publication Date
Fri Aug 01 2025
Journal Name
Al-academy
The effectiveness of media in Iraqi theatre performances, the play (The Pawns) as a model
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أن الثورة الرقمية أصبحت اليوم واقع حتمي نعيشه من حيث القت بظلالها على مختلف جوانب الحياة، ولم يخل المسرح من هذا التأثير وخاصة في ظهور ملامح ما بعد الحداثة بكل ما تحملهُ من رؤى فكرية وفلسفية وجمالية، مع ذلك التطور التكنولوجي في هذا السياق يسعى المسرحيون والمخرجون والممثلون الى تأسيس علاقات فاعلة مع شبكات الانترنيت والوسائط الرقمية مما ظهر العديد من المواقع المهتمة بالمسرح. من هنا ظهرت اهمية الربط بين الث

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Publication Date
Sat Jun 04 2022
Journal Name
Al–bahith Al–a'alami
Iraq's Image in the British Press An analytical study of the Guardian and The Daily Telegraph for 1 / 1- 31/3/2019: Research extracted from a master's thesis
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The topic of the research dealt with the image of Iraq in the British press based on a sample of the newspapers (The Guardian and the Daily Telegraph), which are among the most important and largest newspapers in the United Kingdom and the world, because of its active role in guiding local and international public opinion towards important issues and events, Since these two newspapers are interested in the accuracy of sensitive political topics, the message aimed at knowing the media image that these two newspapers painted about Iraq in the period that was limited to the first quarter of 2019, and also to know the nature of the contents promoted by these newspapers about the Iraqi reality, The method of content analysis was used as an ap

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Publication Date
Mon Jun 03 2024
Journal Name
Functional Foods In Health And Disease
A comparative study of the effect of extracts extracted from Ocimum basilicum leaves using organic extract and essential oil
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Background: Medicinal plants that possess antimicrobial and antioxidant properties have garnered significant attention for their role in maintaining food quality, improving safety, and impeding spoilage. They also can aid in controlling food contamination risks and augmenting the nutritional value of foods. Objective: The study aimed to obtain botanical extracts possessing antimicrobial capabilities and use them to inhibit the growth of molds and yeasts. Additionally, these extracts are aimed at prolonging product shelf life by harnessing their antioxidant attributes. Methods: Several microorganisms, including E. coli and Pseudomonas, were subjected to testing. Ethanolic alcohol, chloroform, and essential oil extracts were prepared;

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Publication Date
Sun Jan 01 2012
Journal Name
مجلة واسط للعلوم والطب
Study of nuclear characters to some 164, 166, 168 68 Er isotopes by using the interacting boson model IBM-1
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The aim of this study is to show the concepts of nuclear shape and the geometrical picture to the even-even nuclei of 164,166,168E isotopes in the context of the Interacting boson Model IBM-1. The energy spectra were calculated and the effective charge values (eB) of the electromagnetic transition strength were obtained and used to calculate the B(E2) values of the electromagnetic transitions and the quadrupole moment Q of 2+ -states. The Hamiltonian parameters were calculated by taking in account the properties of these nuclei. Comparison were made with the available experimental data and included in tables. The geometrical picture of these nuclei were looked at by calculating the deformation which were represented by the potentia

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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
COMPARATIVE STUDY BETWEEN A NOVEL DETERMINISTIC TEST FOR MERSENNE PRIMES AND THE WELL-KNOWN PRIMALITY TESTS
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In this article, a new deterministic primality test for Mersenne primes is presented. It also includes a comparative study between well-known primality tests in order to identify the best test. Moreover, new modifications are suggested in order to eliminate pseudoprimes. The study covers random primes such as Mersenne primes and Proth primes. Finally, these tests are arranged from the best to the worst according to strength, speed, and effectiveness based on the results obtained through programs prepared and operated by Mathematica, and the results are presented through tables and graphs.

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Publication Date
Tue Feb 01 2022
Journal Name
Int. J. Nonlinear Anal. Appl.
Computer-based plagiarism detection techniques: A comparative study
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Plagiarism is becoming more of a problem in academics. It’s made worse by the ease with which a wide range of resources can be found on the internet, as well as the ease with which they can be copied and pasted. It is academic theft since the perpetrator has ”taken” and presented the work of others as his or her own. Manual detection of plagiarism by a human being is difficult, imprecise, and time-consuming because it is difficult for anyone to compare their work to current data. Plagiarism is a big problem in higher education, and it can happen on any topic. Plagiarism detection has been studied in many scientific articles, and methods for recognition have been created utilizing the Plagiarism analysis, Authorship identification, and

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Publication Date
Tue Aug 02 2022
Journal Name
Journal Of Legal Sciences
Judicial Precedent and Its Controls – A Comparative Study
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Judicial jurisprudence is one of the important legal solutions to address the shortcomings of legislation. Throughout its long history, human societies have known many cases in which the judge finds himself facing a legislative vacuum in addition to civil legal texts that are difficult for the judge to implement due to ambiguity or contradiction, which requires diligence. To rule on resolving disputes before him in order not to deny justice, but the judge in his jurisprudence was not absolute, but rather bound by certain controls represented by observing the wisdom of legislation on the one hand and taking into account the nature of the texts on the other side, and from here this research came to shed light on the jurisprudence and its cont

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Publication Date
Wed Oct 26 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) diphenol
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New series of 4,4'-((2-(Aryl)-1H-benzo[d]imidazole1,3(2H)-diyl)bis(methylene))Diphenol(3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hy

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Publication Date
Wed Oct 05 2022
Journal Name
Research Journal Of Chemistry And Environment
Synthesis, Antioxidant ability and Docking study for new 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) diphenol
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New series of 4, 4'-((2-(Aryl)-1H-benzo [d] imidazole-1, 3 (2H)-diyl) bis (methylene)) Diphenol (3a-g) was successfully synthesized from cyclization of the reduction product of bis Schiff bases (2) with aryl aldehydes bearing phenolic hydroxyl in the presence of acetic acid. The structure of these compounds was identified from FT-IR, 1H NMR, 13C NMR and EIMs. The Antioxidant capability was screened by DPPH and FRAP assays. Both assays showed antioxidant capability more than BHT as well. Compounds 3b and 3c showed antioxidant capacity slightly less than ascorbic acid. The docking study for theses compound was carried out as III DNA polymerase inhibitor. The results of docking demonstrated that the increase in hinderances around phenolic hydr

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