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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
Thu Dec 15 2022
Journal Name
Aaps Pharmscitech
Formulation and Characterization of Oleogel as a Topical Carrier of Azithromycin
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This study aims to formulate azithromycin oleogel to locally treat skin infections such as acne vulgaris and skin wound infection. Providing a form of azithromycin that can be administered topically is highly desired to prevent unwanted systemic complications including diarrhea, nausea, and abdominal pain. Additionally, it will avoid first pass metabolism, improves patient acceptance, provides an alternative in nauseated patients, decreases the dose by direct contact with the pathological site, and provides a noninvasive and convenient mode of administration. Furthermore, for treating wound infections, the gel will act as a scaffold biomaterial for wound closure besides its antibacterial effect. Herein, we propose the use of grapeseed oil-b

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Publication Date
Wed Jun 07 2023
Journal Name
Journal Of Educational And Psychological Researches
A Proposed Training Program for School Leaders in the Sultanate of Oman on the Planning Practices of the Kaufman Model in Light of the Needs and Challenges of Reality
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The study aims to build a proposed training program for school leaders in the Sultanate of Oman on the planning practices of the Kaufman model in light of the needs and challenges of reality. It also aims to identify the challenges facing school leaders in practicing the stages of strategic planning. To achieve these objectives, the study adopted the descriptive approach due to its suitability to the nature of the study. A questionnaire was used to collect the needed data. The study sample included (225) individuals from school principals, their assistants and senior teachers in post-basic education in the Sultanate of Oman. After processing the data statistically, the study concluded that the reality of planning practices for school lea

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Publication Date
Sun Nov 01 2015
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Treatment of localized vitiligo with 1% pimecrolimus Cream versus 0.05% clobetasol propionate cream—single, blinded, comparative therapeutic trial
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KE Sharquie, HR Al-Hamamy, AA Noaimi, KA Ali, Journal of Cosmetics, Dermatological Sciences and Applications, 2015 - Cited by 3

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Publication Date
Wed May 31 2023
Journal Name
International Journal Of Advanced Technology And Engineering Exploration
Investigation of phase change characteristics for refrigerant R-134a flow in a double pipe heat exchanger with the use of thermal non-equilibrium model
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Almost all thermal systems utilize some type of heat exchanger. In a lot of cases, evaporators are important for systems like organic Rankine cycle systems. Evaporators give a share in a large portion of the capital cost, and their cost is significantly attached to their size or transfer area. Open-cell metal foams with high porosity are taken into consideration to enhance thermal performance without increase the size of heat exchangers. Numerous researchers have tried to find a representation of the temperature distribution closer to reality due to the different properties between the liquid and solid phases. Evaporation heat transfer in an annular pipe of double pipe heat exchanger (DPHEX) filled with cooper foam is investigated numerical

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Publication Date
Sat Jan 01 2022
Journal Name
Education For Health
Determinants of social accountability for medical schools in Iraq: A qualitative case study
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Publication Date
Sat Jan 01 2011
Journal Name
Journal: Ibn Al-haitham Journal For Pure And Applied Sciences
A Study the effect the direction of the distribution of lighting to improve Images in different lighting by using technique adaptive histogram equalization
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Publication Date
Sat May 28 2022
Journal Name
Egyptian Journal Of Chemistry
Study the kinetics of electrochemical removal of cobalt from aqueous solutions using a Flow-by Fixed Bed Bio-electrochemical Reactor
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Publication Date
Fri Dec 15 2023
Journal Name
Iraqi Journal Of Laser
Study the Impact of Silica Nanoparticles on the Properties of Several Dyes for the Fabrication of a Random Laser Gain Medium
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Random laser gain media is synthesized with different types of dye at the same concentration (1×10-3 M) as an active material and silicon dioxide NPs (silica SiO2) as scatter centers through the Sol-Gel technique. The prepared samples are tested with UV–Vis spectroscopy, Fluorescence Spectroscopy, Field Emission Scanning Electron Microscopy (FESEM), and Energy Dispersive X-ray Diffraction (EDX). The end result demonstrates that doped dyes with silica nanoparticles at a concentration of 0.0016 mol/ml have lower absorbance and higher fluorescence spectra than pure dyes. FESEM scans revealed that the morphology of nanocrystalline silica is clusters of nano-sized spherical particles in the range (25-67) nm. It is con

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Publication Date
Sun Mar 01 2015
Journal Name
Current Research In Microbiology And Biotechnology
Evaluation for the Cytotoxic Effect of Exotoxin A Produced by Pseudomonas aeruginosa on Mice by using Cytogenetic Parameters
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This research was conduct to evaluate the cytotoxic effect of exotoxin A (ETA) produced by Pseudomonas aeruginosa on mice in comparison with (phosphate buffer saline (PBS) as a negative control. The effect of the toxin was measured by employing the cytogenetic analysis which included (the mitotic index (MI), chromosomal aberrations (CAs), micronucleus (MN) and sperm abnormalities) parameters. In order to specify the cytotoxic effect of the toxin, three doses of ETA (125, 250 and 500 ng/ml) were used. Results showed that ETA was found to cause a significant decrease in mitotic index (MI) percentage, while significant increase in micronucleus (MN), chromosomal aberrations (CAs) and sperm abnormalities parameters in compression with control wa

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Publication Date
Fri Oct 01 2021
Journal Name
Saudi Pharmaceutical Journal
Organization factors influencing nurse ability to prevent and detect adverse drug events in public hospitals using a patient safety model
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