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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 Mar 06 2018
Journal Name
Bulletin Of Chemical Reaction Engineering & Catalysis
The Impact of Hydrogen Peroxide as An Oxidant for Solvent-free Liquid Phase Oxidation of Benzyl Alcohol using Au-Pd Supported Carbon and Titanium Catalysts
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The solvent free oxidation of benzyl alcohol was conducted employing Au and Pd supported catalysts, while utilizing hydrogen peroxide 35% (H2O2) as the oxidant, H2O2 is  very cheap, mild, and an environment friendly reagent, which produced water as the only by-product. Various proportions of Au-Pd catalysts on carbon and titanium oxide activated as supports were synthesized through the use of sol immobilization catalyst synthesis technique. Characterization of the synthesized catalysts was performed using X-Ray Diffraction (XRD), Brunauer-Emmett-Teller (BET), Field Emission Scanning Electron Microscopy (FESEM), and Transmission Electron Microscopy (TEM). It was found that the synthesized Au-Pd/ activated carbon catalyst was  benef

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Publication Date
Wed Aug 30 2023
Journal Name
Al-kindy College Medical Journal
The Impact of using the Internet and Social Media on Sleep in a group of Secondary School Students from Baghdad
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Background: Insufficient sleep due to excessive media use is linked to decrease physical activity, poor nutrition, obesity, and decreased overall health-related quality of life.

Objectives: To assess the effect of using the internet and social media on the sleep of 4th-stage secondary school students.

Subjects and Methods: Cross-sectional study with the analytic element; for 500 secondary school students, obtained by choosing two schools randomly from each of the six educational directorates, by using a structured questionnaire.

Result: Secondary scho

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Publication Date
Mon Aug 01 2011
Journal Name
Journal Of Engineering
PROPERTIES OF HARDENED CONCRETE USING CRUSHED CLAY BRICK AS AGGREGATES
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This paper provides the result of an investigation to use of crushed clay brick as
aggregates in producing concrete. Eight different crushed clay brick aggregate concretes were
used in this investigation. Compressive strength, splitting tensile strength and pulse velocity of
crushed clay brick aggregates concrete were determined and compare to natural aggregate
concrete. The compressive strength of crushed clay brick aggregates concretes were always
lower than the compressive strength of natural aggregates concrete regardless the age of
concrete, but the crushed clay brick aggregates concrete showed better performance as the age of
concrete increases and average reduction in compressive strength were 33.5% at the age

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Preparation of polymer thin film using as NH3 gas Sensor
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Polyaniline organic Semiconductor polymer thin films have been prepared by oxidative polymerization at room temperature, this polymer was deposited on glass substrate with thickness 900nm, FTIR spectra was tested , the structural,optical and electrical properties were studied through XRD ,UV-Vis ,IR measurements ,the results was appeared that polymer thin film sensing to NH3 gas.

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Publication Date
Fri Apr 30 2021
Journal Name
Egyptian Journal Of Chemistry
Indirect Spectrophotometric Determination of Mebendazole Using NBromosuccinimide as An Oxidant and Tartarazine Dye as Analytical Reagent
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A simple indirect spectrophotometric method for determination of mebendazol in pure and pharmaceutical formulation was presented in this study. UV-Visible spectrophotometry using the optimal conditions was developed for determination of mebendazole in pure drug and different preparation samples. The method is based on the oxidation of drug by nbromosuccinimide with hydrochloric acid and the left amount of oxidizing agent was determined by the reaction with tartarazine and the absorbance was measured at 428 nm. Calibration curves were linear in the range of 5 to 30 µg.mL-1 with molar absorptivity 8437.2 L.mol-1 .cm-1 . The limits of detection and quantification were determined and found to be 0.7770 µg.mL-1 and 2.3400 µg.mL-1 respec

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Publication Date
Sun Apr 25 2021
Journal Name
Egyptian Journal Of Chemistry
Indirect spectrophotometric determination of Mebendazole using n-bromosuccinimide as an oxidant and tartarazine dye as analytical reagent
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Publication Date
Wed Mar 30 2016
Journal Name
College Of Islamic Sciences
The link of destination Using the evidence Analytical Fundamental Study
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This paper seeks to study the link between the fundamentalist evidence based on the observance of governance and interests and the ranks of the three legitimate purposes (necessary, need and detailed). The researcher followed the descriptive-analytical approach. The study reached important results, including that the measurement relates to the three ranks, but predominantly attached to measure the meaning of the need and the need, and the measurement of the semi-formal and semi-predominance improvement. Reclamation is considered by the majority of scholars to be authentic if it is related to the necessity and the need, and that it is not acceptable to improve only by a witness who recommends it. The excuses relate to Hajji and Tahini, no

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Publication Date
Sun Jan 01 2023
Journal Name
International Conference Of Computational Methods In Sciences And Engineering Iccmse 2021
Penetration of charged particles in ZnO using energy loss function model
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In this paper, we propose an approach to estimate the induced potential, which is generated by swift heavy ions traversing a ZnO thin film, via an energy loss function (ELF). This induced potential is related to the projectile charge density, ρq(k) and is described by the extended Drude dielectric function. At zero momentum transfer, the resulting ELF exhibits good agreement with the previously reported results. The ELF, obtained by the extended Drude model, displays a realistic behavior over the Bethe ridge. It is observed that the induced potential relies on the heavy ion velocity and charge state q. Further, the numerical results show that the induced potential for neutral H, as projectile, dominates when the heavy ion velocity is less

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Publication Date
Sat Jan 01 2022
Journal Name
Methods And Objects Of Chemical Analysis
Spectrophotometric Analysis of Quaternary Drug Mixtures using Artificial Neural network model
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A Novel artificial neural network (ANN) model was constructed for calibration of a multivariate model for simultaneously quantitative analysis of the quaternary mixture composed of carbamazepine, carvedilol, diazepam, and furosemide. An eighty-four mixing formula where prepared and analyzed spectrophotometrically. Each analyte was formulated in six samples at different concentrations thus twentyfour samples for the four analytes were tested. A neural network of 10 hidden neurons was capable to fit data 100%. The suggested model can be applied for the quantitative chemical analysis for the proposed quaternary mixture.

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Publication Date
Tue Sep 06 2022
Journal Name
Methods And Objects Of Chemical Analysis
Spectrophotometric Analysis of Quaternary Drug Mixtures using Artificial Neural network model
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A Novel artificial neural network (ANN) model was constructed for calibration of a multivariate model for simultaneously quantitative analysis of the quaternary mixture composed of carbamazepine, carvedilol, diazepam, and furosemide. An eighty-four mixing formula where prepared and analyzed spectrophotometrically. Each analyte was formulated in six samples at different concentrations thus twenty four samples for the four analytes were tested. A neural network of 10 hidden neurons was capable to fit data 100%. The suggested model can be applied for the quantitative chemical analysis for the proposed quaternary mixture.

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