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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
Sun Jun 26 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of banking effort tests in the face of monetary credit risk and its impact on the profits and adequacy of the bank’s capital : / a case study of Sumer Commercial Bank for the period from 2015 to 2020
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The research seeks to identify the proposed scenarios to predict and ward off monetary credit risks that the bank is exposed to in the future, using the banking stress tests model, and showing their impact on capital adequacy and profitability ratio,To achieve this purpose, Sumer Commercial Bank was taken as a case study, and mathematical equations were used to extract the results. Low percentage of profits and returns, strictness in the process of granting credit and financing operations in order to reduce credit risks.

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
Effect of Ferocene Concentration on the Percent Conversion and Molecular Weight of Poly(Methyl Methacrylate) Homopolymers
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This research is addressing the effect of different ferrocene concentration (0.00, 2.15x10-3, 4.30x10-3, 8.60x10-3, and 12.9x10-3) on the bulk free radical polymerization of methyl methacrylate monomer in benzene using benzoyl peroxide as initiator. The polymerization was conducted at 60º C under free oxygen atmosphere. The resulting polymers were characterized by FTIR. The results were compared with the presence and absence of ferrocene at 10% conversion. The %conversion was 3.04% with no ferrocene present in the polymerization medium and its increase to 9.06 with a first lowest ferrocene concentration added, i.e. 2.15 x10-3mol/l. This was positively reflected on the poly(methyl methacrylate) molecular weight measured by viscosity techniq

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Publication Date
Fri Jan 01 2021
Journal Name
Ecology, Environment And Conservation
A qualitative study of Periphytic algae attached to thesurface of river boats in the Tigris River in AlAadhamiya, Baghdad, Iraq
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A seasonal study of periphytic algae attached to the surface of river boats was conducted in Tigris river in Al Aadhamiya site for the period from October 2016 to May 2017. A total of 107 taxa of periphytic algae were identified belonging to the four classes of algae. The periphytic algae community dominated by Bacillariophyceae was (60.7%) followed by Chlorophyceae (20.5%) and Cyanophyceae (17.7%) Chrysophyceae was constituted (0.9%) of the total number. During the whole period of study filamentous taxa such as Oscillatoria amphibian, Phormidium spp., Spirulinagigantean, Cladophoreglomerata and Melosira roeseana remained the dominant colonizer which may be reflect the ability of this species to grow multiplies under different environmental

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of a novel coating material on the microleakage of glass hybrid restoration in primary teeth – An in vitro study
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Background: Glass ionomer restorations are widely employed in the field of pediatric dentistry. There is a constant demand for a durable restoration that remains functional until exfoliation. This study aimed to measure and compare the effect of a novel coating material (EQUIA Forte Coat) on the microleakage of glass hybrid restoration (EQUIA Forte HT) in primary teeth. Material and method: Thirty cavitated (class-II) primary molars were allocated randomly into two groups based on the coat application; uncoated (control) and coated group (experimental). Cavities were prepared by the use of a ceramic bur (CeraBur) and restored with EQUIA Forte HT with or without applying a protective coat (EQUIA Forte Coat). Samples went through the

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Publication Date
Wed Mar 15 2023
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of a novel coating material on the microleakage of glass hybrid restoration in primary teeth – An in vitro study
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Background: Glass ionomer restorations are widely employed in the field of pediatric dentistry. There is a constant demand for a durable restoration that remains functional until exfoliation. This study aimed to measure and compare the effect of a novel coating material (EQUIA Forte Coat) on the microleakage of glass hybrid restoration (EQUIA Forte HT) in primary teeth. Material and method: Thirty cavitated (class-II) primary molars were allocated randomly into two groups based on the coat application; uncoated (control) and coated group (experimental). Cavities were prepared by the use of a ceramic bur (CeraBur) and restored with EQUIA Forte HT with or without applying a protective coat (EQUIA Forte Coat). Samples went through the therm

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Publication Date
Mon Jun 30 2025
Journal Name
International Journal Of Sustainable Development And Planning
The Role of Sustainable Environmental Indicators in Urban Happiness: A Study of Al-Amir Neighborhood in Al-Najaf City, Iraq
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Publication Date
Wed Feb 21 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Perceptions of Senior Pharmacy Students Towards the Impact of Artificial Intelligence on University Education and Scientific Writing: A Qualitative Study
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Background: The roles of AI in the academic community continue to grow, especially in the enhancement of learning outcomes and the improvement of writing quality and efficiency. Objectives: To explore in depth the experience of senior pharmacy students in using artificial intelligence for academic purposes. Methods: This qualitative study included face-to-face individual interviews with senior pharmacy students from March to May 2023 using a pre-planned interview guide of open-ended questions. All interviews were audio-recorded. Thematic analysis was used to analyze the data. Results: The results were obtained from 15 in-depth face-to-face interviews with senior pharmacy students (5th and 4th years). Eight participants were male, an

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Publication Date
Wed Feb 21 2024
Journal Name
Al-rafidain Journal Of Medical Sciences ( Issn 2789-3219 )
Perceptions of Senior Pharmacy Students Towards the Impact of Artificial Intelligence on University Education and Scientific Writing: A Qualitative Study
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Background: The roles of AI in the academic community continue to grow, especially in the enhancement of learning outcomes and the improvement of writing quality and efficiency. Objectives: To explore in depth the experience of senior pharmacy students in using artificial intelligence for academic purposes. Methods: This qualitative study included face-to-face individual interviews with senior pharmacy students from March to May 2023 using a pre-planned interview guide of open-ended questions. All interviews were audio-recorded. Thematic analysis was used to analyze the data. Results: The results were obtained from 15 in-depth face-to-face interviews with senior pharmacy students (5th and 4th years). Eight participants were male, and seven

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Publication Date
Mon May 01 2023
Journal Name
Environmental Nanotechnology, Monitoring & Management
A review study summarizes the main characterization techniques of nano-composite photocatalysts and their applications in photodegradation of organic pollutants
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Publication Date
Mon Feb 01 2021
Journal Name
Journal Of Physics: Conference Series
Experimental Analysis for the Influence of Ignition Time on Combustion Characteristics of a Free Piston Engine Linear Generator
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Abstract<p>Free Piston Engine Linear Generator (FPELG) is a modern engine and promising power generation engine. It has many advantages compared to conventional engines such as less friction, few numbers of parts, and high thermal efficiency. The cycle-to-cycle variation one of the big challenges of the FPELG because it is influence on the stability and output power of the engine. Therefore, in this study, the effect of ignition time on combustion characteristics is investigated. The single-cylinder FPELG with spark ignition (SI) combustion type by using compressed natural gas (CNG) fuel type was set to run. LabVIEW is used to run the engine and control of input parameters. All experimental data</p> ... Show More
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