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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
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
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
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 Mar 06 2022
Journal Name
Al–bahith Al–a'alami
Semiotic criteria for analyzing religious symbols in press reports Qantara news site as a model
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The report includes a group of symbols that are employed within a framework that gives a language of greater impact. This research discusses the problem of the semiotic employment of religious symbols in press reports published in the electronic press across two levels: Reading to perceive the visual message in its abstract form, and the second for re-understanding and interpretation, as this level gives semantics to reveal the implicit level of media messages through a set of semiotic criteria on which it was based to cut texts to reach the process of understanding and interpretation.

The report includes a group of symbols that are employed within a framework that gives a language of greater impact. This research discusses the p

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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
Thu Jun 20 2019
Journal Name
Baghdad Science Journal
A Comparative Analysis of the Zernike Moments for Single Object Retrieval
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Zernike Moments has been popularly used in many shape-based image retrieval studies due to its powerful shape representation. However its strength and weaknesses have not been clearly highlighted in the previous studies. Thus, its powerful shape representation could not be fully utilized. In this paper, a method to fully capture the shape representation properties of Zernike Moments is implemented and tested on a single object for binary and grey level images. The proposed method works by determining the boundary of the shape object and then resizing the object shape to the boundary of the image. Three case studies were made. Case 1 is the Zernike Moments implementation on the original shape object image. In Case 2, the centroid of the s

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Publication Date
Wed May 15 2024
Journal Name
International Journal Of Religion
The Theory of Quantity in Measures and Scales a Comparative Jurisprudential Study
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Every body has a size and mass that distinguishes it from others and makes it different from others. Some of these bodies are huge and large in size, and some are small and light in weight. Among these masses and bodies are some that are dealt with by their size and weight, each according to its quantity, weight, and cheapness. This is why they created quantities by which these weights and quantities could be estimated, so they used measures and weights for that. Objectives: The research aims to know some measures and weights, such as the wife’s maintenance, the amount of zakat, etc.I found it to be a widely spread topic, and widely used in the folds of jurisprudence. During my reading of jurisprudence books, I found jurists using many qu

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Publication Date
Thu Jun 01 2017
Journal Name
كلية التربية للبنات
The rights of orphans in the Old Testament and Islam, a Comparative Study
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Allah Almighty has aggrandized the position of orphans and elevated their status in the society and has given the graces for those who sponsor the orphan and care for and protecting them, even those who rub their heads. The divine care is manifested in the verses of the Holy Bible and the Holy Quran. Therefore, the whole world cared for the orphan, and called for the rights of the orphans in the conferences and the channels. But all that was little effort that does not meet what the orphan need and some were only ink on paper that were not applied. All that mentioned above is necessary in dealing with the study (the rights of orphans in the Old Testament and Islam, a Comparative Study). The study was divided into a Preface and four inquirie

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Publication Date
Tue Mar 28 2023
Journal Name
International Journal Of Dentistry
The Effect of Different Obturation Techniques in Primary Teeth on the Apical Microleakage using Endoflas: A Comparative In Vitro Study
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Objectives. This study was carried out to quantitatively evaluate and compare the sealing ability of Endoflas by using differentobturation techniques. Materials and Methods. After 42 extracted primary maxillary incisors and canines were decoronated, theircanals were instrumented with K files of size ranging from #15 to #50. In accordance with the obturation technique, the sampleswere divided into three experimental groups, namely, group I: endodontic pressure syringe, group II: modified disposable syringe,and group III: reamer technique, and two control groups. Dye extraction method was used for leakage evaluation. Data wereanalyzed using one-way ANOVA and Dunnett’s T3 post hoc tests. The level of significance was set at p<0:05. Results.

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Publication Date
Mon Jan 02 2017
Journal Name
Al-academy
Style and the jump in industrial product design - a comparative study
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Find cares studying ways in the development of industrial products and designs: the way the progressive development (how typical) and root development (jump design), was the aim of the research: to determine the effectiveness of the pattern and the jump in the development of designs and industrial products. After a process of analysis of a sample of research and two models of contemporary household electrical appliances, it was reached a set of findings and conclusions including:1-leaping designs changed a lot of entrenched perceptions of the user on how the product works and its use and the size and shape of the product, revealing him about the possibilities of sophisticated relationships with the product, while keeping the typical desi

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