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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
Wed Oct 09 2019
Journal Name
International Journal Of Drug Delivery Technology
The comparative study among the MRSAcin, Nisin A and vancomycin, on biofilm formation by Methicillin resistance Staphylococcus aureus isolated from food sources.
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Biofilms formation by pathogens microbial Control considered important in medical research because it is the hazarded virulence factor leading to becoming difficult to treat because of its high resistance to antimicrobials. Glycopeptide antibiotic a (Vancomycin) and the commercial bacteriocin (Nisin A) were used to comparative with purification bacteriocin (MRSAcin) against MRSA biofilm. One hundred food samples were collected from Baghdad markets from July 2016 to September 2016, including (cheese, yogurt, raw milk, fried meat, grilled meat, and beef burger). All samples were cultures; S. aureus was confirmation by macroscopic culture and microscopic examination, in addition to biochemical tests. Methicillin resistance S. asureus (

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Publication Date
Wed Dec 15 2021
Journal Name
Al-academy
The communicative education of fine arts in the COVID-19 crisis and its manifestations in the modernization of the works of the Iraqi painter "Nabil Ali as a model"
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 This study attempts to address the importance of communicative digitization in the field of various arts for the sake of continuity of shopping and aesthetic, artistic and intellectual appreciation of artistic achievements by the recipient on various places of their residence in light of the COVID 19 crisis, and to highlight the importance of the plastic arts of the Iraqi painter exclusively and how it expresses in a contemporary way the environment or life reality in Iraq in light of this crisis. With all its implications affecting the life reality from various aspects and methods of its negative and positive employment. As for the research procedures, the researcher reviewed the research methodology represented by the descriptive ana

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Publication Date
Mon Dec 25 2017
Journal Name
Al-khwarizmi Engineering Journal
A new Cumulative Damage Model for Fatigue Life Prediction under Shot Peening Treatment
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 Abstract

In this paper, fatigue damage accumulation were studied using many methods i.e.Corton-Dalon (CD),Corton-Dalon-Marsh(CDM), new non-linear model and experimental method. The prediction of fatigue lifetimes based on the two classical methods, Corton-Dalon (CD)andCorton-Dalon-Marsh (CDM), are uneconomic and non-conservative respectively. However satisfactory predictions were obtained by applying the proposed non-linear model (present model) for medium carbon steel compared with experimental work. Many shortcomings of the two classical methods are related to their inability to take into account the surface treatment effect as shot peening. It is clear that the new model shows that a much better and cons

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Publication Date
Tue Dec 01 2020
Journal Name
Baghdad Science Journal
Determination of Phosphodiesterase Type 5 Enzyme (PDE-5) Inhibitors and Analogues as Adulterants in Selected Herbal Products using Gas Chromatography–Electron Impact-Mass Spectrometer (GC-EI-MS)
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       Sildenafil, tadalafil, and vardenafil are phosphodiesterase type 5 enzyme (PDE-5) inhibitors used for the treatment of male erectile dysfunction. This present study aims to investigate 55 herbal products indicated for men’s sexual health from the Malaysian market for adulteration of PDE-5 inhibitors and analogues. The screening and identification of 20 PDE-5 inhibitors and analogues in herbal products of various forms (powder, capsules, tablets, and pastels) were conducted using gas chromatography–electron impact-mass spectrometer (GC-EI-MS). The analysis has shown that 19 herbal products were adulterated with PDE-5 inhibitors and analogues. Unique ion fragmentations and the presence of molecular

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Publication Date
Sun Dec 01 2024
Journal Name
Al-kindy College Medical Journal
A Revolutionary Road Map for Obesity Management and Beyond: Tirzepatide as a Dual-Acting Insulinotropic Polypeptide Receptor Agonist
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Tirzepatide is a revolutionary and promising medication with a high impact in the treatment of Obesity and T2DM with their complications. Its efficacy was proven through different trials in achieving favorable weight loss and a significant reduction in glycemic index. It also treated a large diversity of related co-morbidities, including fatty liver, cardiovascular disease, dyslipidemia, and more. Tirzepatide is well tolerated, has a good safety profile, and is highly reliable and suitable for use in a population.

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Publication Date
Wed Feb 22 2023
Journal Name
Iraqi Journal Of Science
A Molecular Investigation of Phytoplasma (Candidatus Phytoplasma) Infecting Arabic Jasmine (Jasminum sambac) in Iraq
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This study was conducted to investigate phytoplasma causing a virescence disease on Arabic jasmine Jasminum sambac based on microscopy and molecular approaches. Samples were collected from symptomatic Arabic jasmine plants grown in nurseries in Baghdad-Iraq. Specimens from infected plants were prepared and Dienes stained for light microscopy examination. Phytoplasma were detected in infected plants by polymerase chain reaction (PCR) using P1/P7 and SecAfor1/SecArev3 Candidatus Phytoplasma specific primer sets. Light microscopy test showed symptomatic Arabic jasmine plants were phytoplasms infected when phloem tissues were stained with a dark blue color. PCR test confirmed the symptomatic plants were phytoplasms infected when SecAfor1/Sec

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
A study of fermi hole for some atomic systems
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the electron correlation effect for inter-shell can be described by evaluating the fermi hole and partial fermi hole for Li atom comparing with Be+ and B+2 ions

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Publication Date
Fri Aug 01 2014
Journal Name
Int. J. Mod. Eng. Res
Exact solutions for MHD flow of a viscoelastic fluid with the fractional Burgers’ model in an annular pipe
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This paper presents an analytical study for the magnetohydrodynamic (MHD) flow of a generalized Burgers’ fluid in an annular pipe. Closed from solutions for velocity is obtained by using finite Hankel transform and discrete Laplace transform of the sequential fractional derivatives. Finally, the figures are plotted to show the effects of different parameters on the velocity profile.

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Publication Date
Thu Apr 06 2023
Journal Name
International Journal Of Emerging Technologies In Learning (ijet)
The Impact of a Scenario-Based Learning Model in Mathematics Achievement and Mental Motivation for High School Students
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Publication Date
Sat Mar 31 2018
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Study of the Performance of Paraffin Wax as a Phase Change Material in Packed Bed Thermal Energy Storage System
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The present work deals with an experimental investigation of charging and discharging processes in thermal storage system using a phase change material PCM. Paraffin wax was used as the PCM which is formed in spherical capsules and packed in a cylindrical packed column which acted as an energy storage system. Air was used as the heat transfer fluid HTF in thermal storage unit. The effect of flow rate and inlet temperature of HTF on the time of charging and discharging process were studied. The results showed that the faster storage of thermal energy can be made by high flow rate of heat transfer fluid HTF and high inlet temperature of heat transfer fluid. It was found that at 65°C HTF inlet temperature, the melting and solidification pr

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