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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 Dec 01 2021
Journal Name
Baghdad Science Journal
Antimicrobial Effect of Eco- Friendly Silver Nanoparticles Synthesis by Iraqi Date Palm (Phoenix dactylifera) on Gram-Negative Biofilm-Forming Bacteria
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Date palm silver nanoparticles are a green synthesis method used as antibacterial agents. Today,
there is a considerable interest in it because it is safe, nontoxic, low costly and ecofriendly. Biofilm bacteria
existing in marketed local milk is at highly risk on population health and may be life-threatening as most
biofilm-forming bacteria are multidrug resistance. The goal of current study is to eradicate biofilm-forming
bacteria by alternative treatment green synthesis silver nanoparticles. The biofilm formation by bacterial
isolates was detected by Congo red method. The silver nanoparticles were prepared from date palm
(khestawy) fruit extract. The formed nanoparticles were characterized with UV-Vis

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Publication Date
Thu Aug 18 2016
Journal Name
Artificial Cells, Nanomedicine, And Biotechnology
Biosynthesis of silver nanoparticles from <i>Catharanthus roseus</i> leaf extract and assessing their antioxidant, antimicrobial, and wound-healing activities
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Publication Date
Tue Aug 01 2023
Journal Name
Innovative Food Science &amp; Emerging Technologies
Non-thermal pasteurization of milk by an innovative energy-saving moderate electrical field equipped with elongated electrodes and process optimization
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Publication Date
Thu Nov 07 2024
Journal Name
Journal Of Thermal Analysis And Calorimetry
Performance improvement of phase change material (PCM)-based shell-and-tube-type latent heat energy storage system utilizing curved fins
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Publication Date
Fri Feb 01 2019
Journal Name
International Journal Of Biology, Pharmacy And Allied Sciences
PREVALENCE OF HEPATITIS B AND C VIRUS INFECTION AMONG PATIENTS WITH VON- WILL BRAND DISEASE AT MEDICAL CITY / BAGHDAD 2018
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ABSTRACT Background: Viral hepatitis places a heavy burden on the health care. Large number of patient with bleeding disorders has chronic hepatitis C infection, while few are chronic carriers of hepatitis B virus. Aims of study: evaluate the prevalence of HBV, HCV infection among patient with Von Willebrand disease and to find factors that associated with the chance of getting the infection.

Publication Date
Sat Dec 17 2022
Journal Name
Iraqi Journal Of Laser
PDF Photodynamic effect of Rose Bengal activated by low-level laser light on S. aureus : Qusay K. Abbas*, Layla M. Hassan
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Abstract: Background: Staphylococcus aureus is Gram-positive bacteria that lives as a normal flora in living organisms but can be pathogenic to humans. Although a relatively unspectacular, nonmotile coccoid bacterium, S. aureus is a dangerous human pathogen in both community-acquired and nosocomial infections. Due to the increasing emergence of new strains of this antibiotic-resistant bacteria, it has become essential to approach different methods to control this pathogen. One of these methods is the antimicrobial photodynamic inactivation process using a low-level laser, in this paper, the Photodynamic effects of Rose Bengal and LLLL on the virulence factors of S.aureus were evaluated.

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Publication Date
Mon Jun 30 2014
Journal Name
Al-kindy College Medical Journal
Unstable Angina /Non ST Elevation Myocardial Infarction: Frequency of Conventional Risk Factors; TIMI Risk Score, and Their Impact On Angiographic Data
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Background: Appreciation of the crucial role of risk factors in the development of coronary artery disease (CAD) is one of the most significant advances in the understanding of this important disease. Extensive epidemiological research has established cigarette smoking, diabetes, hyperlipidemia, and hypertension as independent risk factors for CADObjective: To determine the prevalence of the 4 conventional risk factors(cigarette smoking, diabetes, hyperlipidemia, and hypertension) among patients with CAD and to determine the correlation of Thrombolysis in Myocardial Infarction (TIMI) risk score with the extent of coronary artery disease (CAD) in patients with unstable angina /non ST elevation myocardial infarction (UA/NSTEMI).Methods: We

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Publication Date
Wed Apr 19 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Synthesis and Spectral Studies of Some Metal Complexes with Bis[O,O-2,3;O,O-5,6(Chlorocarboxylic Methyliden)] L-Ascorbic Acid
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&nbsp;The reaction of L-ascorbic acid with the tirchloroacetic acid in the presence of potassium hydroxide gave new product Bis[O,O-2,3;O,O-5,6(chlorocarboxylicmethyliden)]Lascorbic acid (H2L) which was isolated and characterized by 1H,13C-NMR, elemental analysis (C,H,N), UV-Visible and Fourier Transform Infrared (FTIR). The complexes of the ligand (H2L) with metal ions, M+2= (Cu, Co, Ni, Cd and Hg) were synthesized and characterized by FTIR, UV-Visible, molar conductance, atomic absorption, magnetic susceptibility and the molar ratio. The analysis evidence showed the binding of the metal ions with (H2L) through the bicarboxylato group manner resulting in six-coordinated metal ion. The TLC for (H2L) and complexes showed one spot for eac

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Publication Date
Sun Mar 02 2014
Journal Name
Baghdad Science Journal
Inhibition activity of Saccharomyces boulardii and Lactobacillus acidophilus against pathogenic E.coli isolates from Recurrent Urinary Tract Infection in women In Vitro
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The aims of study is to detect the inhibitory effect of Saccharomyces boulardii and Lactobacillus acidophilus on Escherichia coli that has been isolated from recurrent urinary tract infection in women. The sensitivity of E.coli isolates to antibiotics had been studied and the most resistant E.coli isolate to antibiotics had been studied .The cup assay was used on nutrient agar and Muller-Hinton agar to detect the inhibitory activity for each S.boulardii yeast grown on YEGP media and L.acidophilus grown on MRS media in which the result showed a high inhibition activity for each of them .Also in this study the adhesion property of E.coli had been evaluated in the presence of S.boulardii at concentration of 1×109 and L.acidophilus at conc

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Publication Date
Mon Feb 01 2016
Journal Name
Journal Of Engineering
Impact of Different H/D Ratio on Axial Gas Holdup Measured by Four-Tips Optical Fiber Probe in Slurry Bubble Column
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In wide range of chemical, petrochemical and energy processes, it is not possible to manage without slurry bubble column reactors. In this investigation, time average local gas holdup was recorded for three different height to diameter (H/D) ratios 3, 4 and 5 in 18" diameter slurry bubble column. Air-water-glass beads system was used with superficial velocity up to 0.24 m/s. the gas holdup was measured using 4-tips optical fiber probe technique. The results show that the axial gas holdup increases almost linearly with the superficial gas velocity in 0.08 m/s and levels off with a further increase of velocity. A comparison of the present data with those reported for other slurry bubble column having diameters larger than

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