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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 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
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
Thu Jan 25 2024
Journal Name
Iraqi Journal Of Agricultural Sciences
SPRAYING NANO CHITOSAN LOADED WITH NPK, NETTEL AND GREEN TEA EXTRACTS AS A TOOL FOR IMPROVEMENT POTATO PRODUCTIVITY
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This study was aimed to evaluate the effect of spraying nano chitosan loaded with NPK fertilizer and nettle leaf and green tea extracts on the growth and productivity of potato for the spring and fall seasons of 2021.It was conducted at private farm in Wasit Governorate, Iraq, as a factorial experiment (5 × 5) within randomized complete block design using three replicates. The first factor included spraying with four concentrations of chitosan nanoparticles loaded with NPK fertilizer 0, 10. 15 and 20% in addition to chemical fertilization treatment, the second factor was spraying nettle leaf extract 25 and 35 gL-1 and green tea extract with 2 and 4 g.L-1, in addition to the control treatment, spraying with distilled water only. The

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Publication Date
Sat Apr 30 2022
Journal Name
Al-kindy College Medical Journal
Safety profile of immediate post-partum intrauterine device insertion during caesarean delivery – a clinical trial with three years of follow up
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Background Many countries recommend the use of long-acting reversible contraceptive intrauterine device immediately after cesarean delivery. The cesarean delivery rate in Iraqi public hospitals is 32.2% and may reach 85.8% in private hospitals. Immediate post-partum intrauterine device insertion at cesarean is rarely done in Iraq. Objectives To assess the safety and practicality of immediate post-partum intrauterine device insertion during cesarean delivery for family planning and pregnancy spacing in Iraqi women. Subjects and Methods A single arm clinical trial included 150 eligible women who attended Al-‎Elwiyah Maternity Teaching Hospital or Al Hayat Rahibat Hospital for term delivery. A copper intrauterine device was placed in the ute

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Publication Date
Wed Jan 29 2020
Journal Name
Advances In Rheumatology
Neutrophil/lymphocyte and platelet/lymphocyte ratios as potential markers of disease activity in patients with Ankylosing spondylitis: a case-control study
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Abstract<sec> <title>Background

The neutrophil/ lymphocyte ratio (NLR) and platelet/lymphocyte ratio (PLR) have the potential to be inflammatory markers that reflect the activity of many inflammatory diseases. The aim of this study was to evaluate the NLR and PLR as potential markers of disease activity in patients with ankylosing spondylitis.

Methods

The study involved 132 patients with ankylosing spondylitis and 81 healthy controls matched in terms of age and gender. Their sociodemographic data, disease activity scores using the Bath Ankylosing

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Publication Date
Sat Mar 30 2013
Journal Name
College Of Islamic Sciences
The comparative approach (stabilizer) and the need for Arabic to it
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Linguistic research according to modern curricula:
   It is one of the important matters that occupy the ideas of those concerned with linguistic studies, whether Arabic or otherwise. Recent years have witnessed the advancement of this methodological approach, and books and studies in Arabic have been written on important, multifaceted issues, of grammatical and linguistic origins, and their balance with new developments and ideas attracted mostly from Western studies.
    The comparative approach - as they call it - is one of the modern approaches that is based on balancing a language with other sisters belonging to its family, to reach similarities and differences between them, and to know the c

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Publication Date
Wed Nov 15 2023
Journal Name
Dirasat: Human And Social Sciences
Media Usage for Pope Francesco's Visit to Iraq March 5, 2021 (A Semiotic Study of the Photograph Welcoming Of the Pope)
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Objectives: The research aims to highlight the semiotic approach and apply it to a photograph of the Pope's reception at Baghdad International Airport, published on the page of the Media Office of Iraqi Prime Minister Mustafa Al-Kazemi in the Twitter application, in order to study its components, analyze its contents and clarify its implications, as well as approach the image as a political and media act. Methods: The stages of research were accomplished by "investigation, observation, and analysis", and the dismantling of the composition of the photograph, thus revealing the hidden and hidden aspects, relying on the semiotic approach to analysis. Results: The study showed that the ideas and meanings included in the image in form

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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
A book in the science of rhyme for the father of conquest Othman bin Jinni ‹v 392 e›: Investigation and study
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This book in our hands is a 'book in the science of rhymes' written by the linguistic and grammatical world 'Othman bin Jenni' 'T 392 AH', and included in it: the concept of rhyme, its characters, movements, and disadvantages, with mention of its ramifications, defining them by definition, clarification and martyrdom poetry, It is concise in size, but it is a book containing a full science in its content.
The study was divided into two parts, the first: the study, and included a study of the author and the author, I talked first about his life, such as his name and origin, and scientific status, and the words of scientists in it, and so on, and secondly: the name of the book, and his percentage, and the time of its composition, etc. I

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Publication Date
Sun Feb 03 2019
Journal Name
Iraqi Journal Of Physics
A study of the characterization of CdS/PMMA nanocomposite thin film
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Nanocomposites of polymer material based on CdS as filler
material and poly methyl methacrylate (PMMA) as host matrix have
been fabricated by chemical spray pyrolysis method on glass
substrate. CdS particles synthesized by co-precipitation route using
cadimium chloride and thioacetamide as starting materials and
ammonium hydroxide as precipitating agent. The structure is
examined by X-ray diffraction (XRD), the resultant film has
amorphous structure. The optical energy gap is found to be (4.5,
4.06) eV before and after CdS addition, respectively. Electrical
activation energy for CdS/PMMA has two regions with values of
0.079 and 0.433 eV.

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