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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 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
Thu Jun 12 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Photogrammetric analysis of facial soft tissue profile of Iraqi adults sample with Class II div.1 and Class III malocclusion: (A comparative study)
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Background: The purposes of this study were to determine the photogrammetric soft tissue facial profile measurements for Iraqi adults sample with class II div.1 and class III malocclusion using standardized photographic techniques and to verify the existence of possible gender differences. Materials & methods: Seventy five Iraqi adult subjects, 50 class II div.1 malocclusion (24 males and 26 females), 25 class III malocclusion (14 males and 11 females), with an age range from 18-25 years. Each individual was subjected to clinical examination and digital standardized right side photographic records were taken in the natural head position. The photographs were analyzed using AutoCAD program 2007 to measure the distances and angles used in t

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Publication Date
Thu Nov 03 2022
Journal Name
Res Militaris
Prose of Sons of Imam Ali Al-Rida (Peace Be Upon Them): A Study Regarding the Structure of the Image and Its Implications - Simile as a Model
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Praise be to God, Lord of the Worlds, and prayers and peace be upon the most honorable of creation, Muhammad, whom God sent as a mercy to the worlds, and his pure God and his faithful companions. The Islamic heritage was replete with texts issued from among the pure infallibility, which constituted a prominent teacher that takes the student to stop there in search of its goals, purposes and beauty. The choice was made from those texts that were issued by the imams of Muslims in the Abbasid era, namely Imam Muhammad al-Jawad, his son Imam Ali al-Hadi and his grandson Imam Hassan Zaki al-Askari. (Peace be upon them), and scholars have called them (sons of satisfaction), and researchers have shed light on these texts from rhetorical, artistic

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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
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
Fri Sep 15 2023
Journal Name
Bionatura
A comparison of VCAM-1 and ICAM-1 as atherosclerosis risk factors in patients with systemic lupus erythematosus from Iraq
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All major organs may be impacted by the connective disease systemic lupus erythematosus, a separate risk factor for coronary artery disease (CAD). Adhesion molecules like intercellular adhesion molecules (ICAM) and vascular cell adhesion molecules (VCAM) can detect endothelial damage and dysfunction, which appear to play a crucial role. This study investigated whether people with SLE had elevated subclinical and clinical atherosclerosis risk factors. Traditional CAD risk factors such as smoking, hypertension, and hyperlipidemia cannot entirely explain this elevation. It is thought that immunological dysfunction also increases CAD risk in SLE patients. The study aimed to assess early endothelial changes in SLE Iraqi female patients w

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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
Wed Sep 27 2023
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Assessing the reliability of serum macrophage migration inhibitory factor as a marker for diabetic nephropathy prediction in type 2 diabetes patients and the effect of ACE inhibitors on its level
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Abstract Diabetic nephropathy (DN) is a prevalent chronic microvascular diabetic complication. As inflammation plays a vital role in the development and progress of DN the macrophages migration inhibitory factor (MIF), a proinflammatory multifunctional cytokine approved to play a critical function in inflammatory responses in various pathologic situations like DN. This study aimed To assess serum levels of MIF in a sample of Iraqi diabetic patients with nephropathy supporting its validity as a marker for predicting nephropathy in T2DM patients. In addition, to evaluate the nephroprotective effect of angiotensin-converting enzyme (ACE) inhibitors in terms of their influence on MIF levels. This is a case-control study involving ninety

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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
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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