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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 Sep 30 2012
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Polyvinyl Alcohol – Sodium Nitrite Water Soluble Composite as a Corrosion Inhibitor for Mild Steel in Simulated Cooling Water
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The inhibitive action of polyvinyl alcohol –sodium nitrite (PVASN) composite on the corrosion of mild steel in simulated cooling water (SCW) has been investigated by weight loss and potentiodynamic polarization. The effect of composite concentration (PVA/SN) , pH, and exposure time on corrosion rate of mild steel were verified using 2 levels factorial design and surface response analysis through weight loss approach, while the electrochemical measurements were used to study the behavior of mild steel in (SCW) with pH between 6 and 8 and in absence and presence of (PVA) in solution containing different concentration of NaNO2. It was verified that all three main variables studied were statistically significant while their interaction is

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Publication Date
Tue May 30 2023
Journal Name
Rawal Medical Journal
Elevated lactate dehydrogenase (LDH) and C- reactive protein (CRP) level as a risk factor for critical COVID-19
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Abstract Objective: To identify correlation of elevated LDH & CRP levels with the outcomes of COVID-19. Methodology: The cross-sectional retrospective study consisted of 200 COVID-19 patients who presented at a private clinical in Baghdad, Iraq. It was carried out from February 2021 to February 2022. Data included age, gender and clinical presentation. Blood samples were taken for high sensitivity CRP and LDH in the serum. Results: Out of 200 patients, 50 were critical and 150 severe according to clinical features. LDH and CRP showed a significant increase (p=0.000) in critical patients. This group involved admission to the respiratory intensive care unit requiring mechanical ventilation than in patients with severe COVID-19 (760.5±6.3 vs.

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Publication Date
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
Semantic features in the phenomena in the pottery of Dr. Ahmed Sulaiman Al-Ahmed / Trees behind fence as a sample: Semantic features in the phenomena in the pottery of Dr. Ahmed Sulaiman Al-Ahmed / Trees behind fence as a sample
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Abstract
This research deals with studying and analysis of a poetic group under the
title (Trees behind fence) of the great poet Dr. Ahmed Sulaiman AlAhmed
who is the some of the Shek , Sulaiman Al-Ahmed who is the linguist - poet
and famous jurist member in the Arabic scientific assemble in Damascus and
brother of the great poet Badawi Al-Jabal. This poetic group include two big
poetic legends : the first one is (Trees behind fence , ) which include one
hundred and eighty four line and the second one ( AZ-Mebadia ) which is
consists of one hundred and seventy eight line, both of them from the (Al-
Camil ) meter which is free rhyme which bears a many meaning and pictures
and just the great poet composite the

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Publication Date
Tue Dec 15 2020
Journal Name
Journal Of Pharmaceutical And Biological Sciences
Fascinating approach for using metabolites products of living microorganisms as reducing agents for preparing silver nanoparticles
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A crucial area of research in nanotechnology is the formation of environmentally benign nanoparticles. Both unicellular and multicellular play an important role in synthesis nanoparticles through the production of inorganic materials either intracellularly or extracellularly. The agents (pigments, siderophores, cell extracted metabolites and reducing compounds) were used to prepare silver nanparticles with different sizes and shapes. The color variations (dark yellow, slightly dark yellow and golden yellow) arising from changes in the composition, size, and shape of nanoparticles, surrounding medium can be monitored using UV-visible spectrophotometer. These effects are due to the phenomena called surface plasmon resonance. The silver nanopa

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Publication Date
Fri Oct 02 2020
Journal Name
International Journal Of Pharmaceutical Research
A turbidimetric method for the quantitative determination of cyproheptadine hydrochloride in tablets using an optoelectronic detector based on the LEDs array
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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Biological activity and protease inhibitor from watery extract of lentil (Lens culinaris) against some bacterial species
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Biological activity substances was investigated in watery extract of lentil which found to contain phenols, tannin, saponins and resins while, flavons, terpens and steroids were not exist in the extract details explained that 5%, 10% of lentil extract largly inhibited the growth of Psedumonas aeruginosa then Escherichia coli and Bacillus subtilis. The growth of both Staphylococcus aureus and Salmonella typhimurium were slightly affected by all extract concentration. Extracellular protease were screened in all bacterial species under study. Complete inhibition was achieved for extracellular protease while different percentage of protease inhibition were seen for intracellular proteases.

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Publication Date
Mon Jun 21 2021
Journal Name
International Medical Journal
Immediate and Delay Antimicrobial Activity of Three Disinfection Solutions on Gutta-Percha Cones as Routine Chair-Side Procedure
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Objective: The antimicrobial efficacy of three disinfection solutions: 5.25% sodium hypochlorite (NaOCl), 2% chlorhexidine (CHX) and Listerine mouthwash were investigated as routine chair-side gutta-percha (GP) disinfection reagents. Design: four groups of gutta percha points were contaminated with E. faecalis bacteria then disinfected by immersion in different solutions (5.25% sodium hypochlorite, 2% chlorhexidine gluconate, Listerine mouth wash and distilled water as control) after 1 and 7 days culturing periods. The antibacterial efficacy of these disinfection solutions was evaluated by using colonies per units (CPU) Methods: Forty GP cones (F3 Dentsply) were sterilized with ethylene oxide gas before immersed contamination within broth m

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Publication Date
Tue Nov 09 2021
Journal Name
Abu Dhabi International Petroleum Exhibition & Conference
Numerical Simulation of Gas Lift Optimization Using Artificial Intelligence for a Middle Eastern Oil Field
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Abstract<p>Artificial lift techniques are a highly effective solution to aid the deterioration of the production especially for mature oil fields, gas lift is one of the oldest and most applied artificial lift methods especially for large oil fields, the gas that is required for injection is quite scarce and expensive resource, optimally allocating the injection rate in each well is a high importance task and not easily applicable. Conventional methods faced some major problems in solving this problem in a network with large number of wells, multi-constrains, multi-objectives, and limited amount of gas. This paper focuses on utilizing the Genetic Algorithm (GA) as a gas lift optimization algorit</p> ... Show More
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Publication Date
Fri Jun 30 2017
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Comparative Study for Removal of Zn+2 Ions from Aqueous Solutions by Adsorption and Forward Osmosis
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The aim of this paper was to investigate the removal efficiencies of Zn+2 ions from wastewater by adsorption (using tobacco leaves) and forward osmosis (using cellulose triacetate (CTA) membrane). Various experimental parameters were investigated in adsorption experiment such as: effect of pH (3 - 7), contact time (0  - 220) min, solute concentration (10 - 100) mg/l, and adsorbent dose (0.2 - 5)g. Whereas for forward osmosis the operating parameters studied were: draw solution concentration (10 - 150) g/l, pH of feed solution (4 - 7), feed solution concentration (10 - 100) mg/l. The result showed that the removal efficiency by using adsorption was 70% and the removal efficiency by using forward osmosis was 96.2 %. 

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Publication Date
Tue Jun 20 2023
Journal Name
Baghdad Science Journal
Assessment of image quality of cervical spine complications using Three Magnetic Resonance Imaging Sequences
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Examining and comparing the image quality of degenerative cervical spine diseases through the application of three MRI sequences; the Two-Dimension T2 Weighed Turbo Spin Echo (2D T2W TSE), the Three-Dimension T2 Weighted Turbo Spin Echo (3D T2W TSE), and the T2 Turbo Field Echo (T2_TFE). Thirty-three patients who were diagnosed as having degenerative cervical spine diseases were involved in this study. Their age range was 40-60 years old. The images were produced via a 1.5 Tesla MRI device using (2D T2W TSE, 3D T2W TSE, and T2_TFE) sequences in the sagittal plane. The image quality was examined by objective and subjective assessments. The MRI image characteristics of the cervical spines (C4-C5, C5-C6, C6-C7) showed significant difference

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