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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 Oct 06 2024
Journal Name
Ukrainian Journal Of Nephrology And Dialysis
Effect of Lactobacillus supernatant on swarming-related gene expression in Proteus mirabilis isolated from urinary tract infections
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Proteus mirabilis isolates have been intensively researched for their capacity to cause urinary tract infections (UTIs) and their swarming motility, although little is known about this phenomenon. Probiotic Lactobacillus species, which are beneficial bacteria, are being studied worldwide as therapeutic and preventative agents against bacterial infections. This study investigated Lactobacillus supernatants as a potential new treatment against Proteus mirabilis. In addition to testing their antimicrobial and anti-swarming activities, the research also aimed to understand the genetic mechanisms behind the observed phenotypic changes. Methods. A total of 150 urine specimens were collected from UTI patients at various hospitals in Baghdad. Dire

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Publication Date
Mon Jul 01 2024
Journal Name
Iop Conference Series: Earth And Environmental Science
Assessment of Two Extraction Methods LLE and QUEChERS to Determine Pesticides Residues in Vegetables by Gas Chromatography
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Abstract<p>The extraction of pesticides is a critical and urgent issue in the preparation for and determination of pesticide residues. The lack of a quick, easy, and successful extraction process is the most critical and challenging problem, even if diagnostic tools have improved and pesticide residues have been better understood. This study contrasted the QuEChERS method, which uses gas chromatography with a flame ionization detector, with the LLE method, which uses liquid-liquid extraction, in order to extract pyridaben from cucumbers and spiromesifen from tomatoes. The GC-FID device was employed to ascertain the spiromesifen LOD and LOQ, which were 0.002 μg mL<sup>-1</sup> and 0.00</p> ... Show More
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Publication Date
Fri Jan 01 2021
Journal Name
Chemosphere
Impact of anaerobically digested silver and copper oxide nanoparticles in biosolids on soil characteristics and bacterial community
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Publication Date
Thu Jul 06 2017
Journal Name
Al-mustansiriyah Journal Of Science
Physiological and histological effects of (zinc and iron) oxide nanoparticles on some fertility parameters in female mice
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Nowadays nanoparticles have widespread application in various industriesbecause of their special and unique features, there are many studies in sideeffects of nanomaterial. This study done by 40 white female mice withevery other day intraperitoneally injection of low and high doses of both ofZnO kg of body weight) and FeOnanoparticles (5 and 40 mg/kg). After a 15 days period, the mice weresacrificed and blood samples were collected for hormone analysis, andtissue samples for morphometric studies.Statistical Analysis shows significant differences in LH, Estrogen,Progesterone hormone levels between groups, while there are insignificantdifferences in Follicle stimulating hormone (FSH) level between thegroups compared with its level in

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Publication Date
Thu Apr 21 2022
Journal Name
Journal Of Ecological Engineering
Simultaneous Adsorption of Ternary Antibiotics (Levofloxacin, Meropenem, and Tetracycline) by SunFlower Husk Coated with Copper Oxide Nanoparticles
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In this study, a new adsorbent derived from sunflower husk powder and coated in CuO nanoparticles (CSFH) was investigated to evaluate the simultaneous adsorption of Levofloxacin (LEV), Meropenem (MER), and Tetracycline (TEC) from an aqueous solution. Significant improvements in the adsorption capacity of the sunflower husk were identified after the powder particles had been coated in CuO nanoparticles. Kinetic data were correlated using a pseudo-second-order model, and was successful for the three antibiotics. Moreover, high compatibility was identified between the LEV, MER, and TEC, isotherm data, and the Langmuir model, which produced a better fit to suit the isotherm curves. In addition, the spontaneous and exothermic nature of the adsor

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Publication Date
Sat Dec 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Oxidative Desulfurization of Simulated Diesel Fuel by Synthesized Tin Oxide Nano-Catalysts Support on Reduced Graphene Oxide
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   The modified Hummers method was applied to prepare graphene oxide (GO) from the graphite powder. Tin oxide nanoparticles with different loading (10-20 wt.%) supported on reduced graphene oxide were synthesized to evaluate the oxidative desulfurization efficiency. The catalyst was synthesized by the incipient wetness impregnation (IWI) technique. Different analysis methods like FT-IR, XRD, FESEM, AFM, and Brunauer-Emmett-Teller (BET) were utilized to characterize graphene oxide and catalysts. The XRD analysis showed that the average crystal size of graphene oxide was 6.05 nm. In addition, the FESEM results showed high metal oxide dispersions on the rGO. The EDX analysis shows the weight ratio of Sn is close to its theoretical weight.

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
Thickness and gamma-ray effect on physical properties of CdO thin films grown by pulsed laser deposition
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Polycrystalline Cadmium Oxide (CdO) thin films were prepared
using pulsed laser deposition onto glass substrates at room
temperature with different thicknesses of (300, 350 and 400)nm,
these films were irradiated with cesium-137(Cs-137) radiation. The
thickness and irradiation effects on structural and optical properties
were studied. It is observed by XRD results that films are
polycrystalline before and after irradiation, with cubic structure and
show preferential growth along (111) and (200) directions. The
crystallite sizes increases with increasing of thickness, and decreases
with gamma radiation, which are found to be within the range
(23.84-4.52) nm and (41.44-4.974)nm before and after irradiation for

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Publication Date
Thu Feb 01 2024
Journal Name
Journal Of Engineering
Performance Evaluation of Two Stages Parallel Flow Indirect Evaporative Cooling with Aspen Pads in Baghdad Climate Conditions
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This study delves into the realm of advanced cooling techniques by examining the performance of a two-stage parallel flow indirect evaporative cooling system enhanced with aspen pads in the challenging climate of Baghdad. The objective was to achieve average air dry bulb temperatures (43 oC) below the ambient wet bulb temperatures (24.95 oC) with an average relative humidity of 23%, aiming for unparalleled cooling efficiency. The research experiment was carried out in the urban environment of Baghdad, characterized by high temperature conditions. The investigation focused on the potential of the two-stage parallel flow setup, combined with the cooling capability of aspen pads, to surpass the limitat

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Publication Date
Sat Jan 01 2022
Journal Name
Materials Today: Proceedings
Evaluation on processing parameter's effects on some mechanical properties of pure magnesium bulk prepared by powder metallurgy
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Publication Date
Wed Oct 11 2023
Journal Name
Al-khwarizmi Engineering Journal
Baghdad's University Solar Power Potentials: An Exploration with PVsyst and Helioscope at Al-Khwarizmi College of Engineering
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Globally, buildings use about 40% of energy. Many elements, such as the physical properties of the structure, the efficiency of the cooling and heating systems, the activity of the occupants, and the building’s sustainability, affect the energy consumption of a building. It is really difficult to predict how much energy a building will need. To improve the building’s sustainability and create sustainable energy sources to reduce carbon dioxide emissions from fossil fuel combustion, estimating the building's energy use is necessary. This paper explains the energy consumed in the lecture building of the Al-Khwarizmi College of Engineering, University of Baghdad (UOB), Baghdad, Iraq. The weather data and the building construction informati

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