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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
Mon Jan 18 2016
Journal Name
Open Journal Of Biophysics
Structural and Characteristics of Manganese Doped Zinc Sulfide Nanoparticles and Its Antibacterial Effect against Gram-Positive and Gram-Negative Bacteria
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The Manganese doped zinc sulfide nanoparticles of the cubic zinc blende structure with the average crystallite size of about 3.56 nm were synthesized using a coprecipitation method using Thioglycolic Acid as an external capping agent for surface modification. The ZnS:Mn2+ nanoparticles of diameter 3.56 nm were manufactured through using inexpensive precursors in an efficient and eco-friendly way. X-Ray Diffraction (XRD), Scanning Electron Microscopy (SEM) and Fourier Transform Infrared (FTIR) spectroscopy are used to examine the structure, morphology and chemical composition of the nanoparticles. The antimicrobial activity of (ZnS:Mn2+) nanocrystals was investigated by measuring the diameter of inhibition zone using well diffusion mechanism

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Publication Date
Wed Aug 10 2016
Journal Name
Fourth International Conference On Genetics And Scientific Environment. Cairo / Arab Republic Of Egypt For The Period From July 23 To 30
Efficacy of Arbuscular mycorrhiza (AM) in inducing non-enzymatic antioxidants in tomato leaves infected with Fusarium oxysporum f. sp. Lycopersici.
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Publication Date
Tue Jan 01 2013
Journal Name
The Iraqi Journal Of Veterinary Medicine
Detection of methicillin or multidrug resistant Staphylococcus aureus (MRSA) in locally produced raw milk and soft cheese in Baghdad markets.
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In order to investigate the presence of methicillin or multidrug resistant Staphylococcus aureus in food-chain especially Cows raw milk and white raw soft cheese and its whey, a total of 30 samples were collected randomly from different markets in Baghdad Province during December 2012 till February 2013, in which samples were analyzed by a standard isolation protocols of food microbiology with some modification processing by new, modern and rapid technology tools such as chromogenic medium Baird-Parker agar, Electronic RapIDTM Staph Plus Code Compendium Panel System (ERIC®) Dryspot Staphytect Plus and Penicillin Binding Protein (PBP2') Plus assays; as well as, studying the susceptibility of isolates to different selected antibiotics. The r

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
Images of Woman, She-Camel and Horse and Their Manifestations in Tarafah-ibnulAbd's Poetry between Symbolic Reference and Poetic Function
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This paper tries to understand the poetic reference in the images of woman, she-camel, horse and their manifestations in Tarafah-ibnulAbd's poetry. There has got my attention the fact that these three images have their own distinct taste which is characterised by a clear rhythm, let alone the  lively nature that is filled with liveliness and activity to be in harmony with the poet's youth. For these three images represented the best manifestations of his psychological and artistic poetics. The paper adopts an artistic analysis to arrive at the psychological aspects of these experiences-the woman, the she-camel, and the horse- and to understand the functions of their images and symbolic reference.

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Publication Date
Wed Aug 07 2019
Journal Name
Iraqi National Journal Of Nursing Specialties
Evaluation of Nursing Performance Concerning Nasogastric Tube in Neonatal Intensive Care Unit at al-Batool Teaching Hospital in Baqubah City
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Objectives: The study aim to evaluate nursing performance during nasogastric tube feeding in neonatal intensive care unit. Methodology: A descriptive study was carried out in Neonatal Intensive Care Unit at al–Batool Teaching Hospital, for the purpose of evaluate of quality of nursing performance for premature baby during nasogastric tube feeding in neonatal intensive care unit. The study consumed the period from 4th of December 2017 to the 24nd of April 2018, Non-probability purposive sample of (25) nurses working in the neonatal intensive care unit. The data were collected through the use of Observational instrument which consist of socio-demographic characteristics, quality of nursing care. Results: The study shows that the majority

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Publication Date
Sun Jun 27 2021
Journal Name
Iraqi National Journal Of Nursing Specialties
Practices of Early Childhood’s Mothers Regarding Toilet Training at Primary Health Care Centers in Al-Rusafa District in Baghdad City
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Objective(s): To assess the practices of early childhood’s mothers regarding toilet training and to find out the relationship between mothers’ practices and their socio-demographic characteristics and their children’s demographic characteristics.
Methodology: A descriptive study is conducted at primary health care centers in Al-Rusafa District in Baghdad City for the period of September 19th 2020 to March 16th 2021. Non probability “convenient” sample of (225) early childhood’s mothers is selected. A questionnaire format is designed and composed of two parts: the first part includes mothers’ socio-demographic characteristics and their children and the second part includes structured close-ended questions to assess the p

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Publication Date
Mon Dec 25 2017
Journal Name
Oriental Journal Of Chemistry
Adsorption of 4-Chlorophenol from Aqueous Solution Onto Iraqi Bauxite and Surfactant–Modified Iraqi Bauxite: Equilibrium, Kinetic, and Thermodynamic Studies
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Publication Date
Tue Feb 10 2015
Journal Name
Al-qadisiyah Journal For Science
*Synthesis, spectral studies and antimicrobial evaluation of 6,6--(1,2-benzenediazo) bis (3-amino benzoic acid) complexes with some metal ions
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The Ligand 6,6--(1,2-benzenediazo) bis (3-aminobenzoicacid) derived from o-phenylenediamine and 3-aminobenzoicacid was synthesized. The prepared ligand was identified by Microelemental Analysis, 1HNMR, FT-IR and UV-Vis spectroscopic techniques. Treatment of the ligand with the following metal ions (CoII, NiII, CuII and ZnII ) in aqueous ethanol with a 1:1 M:L ratio and at optimum pH. Characterization of these compounds has been done on the basis of elemental analysis, electronic data, FT-IR and UV-Vis, as well as magnetic susceptibility and conductivity measurements. The nature of the complexes formed were studied following the mole ratio and continuous variation methods, Beer's law obeyed over a concentration range (1×10-4 - 3×10-4 M). H

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Publication Date
Fri Jan 13 2023
Journal Name
Journal Of Research In Medical And Dental Science
Phytochemical Screening and Antibacterial Effect of Stevia Rebaudiana (Bertoni) Alcoholic Leaves Extract on Streptococcus Oralis (Dental Plaque’s Primary Colonizer)
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Phytochemical Screening and Antibacterial Effect of Stevia Rebaudiana (Bertoni) Alcoholic Leaves Extract on Streptococcus Oralis (Dental Plaque’s Primary Colonizer), Manar Ibrahim

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Publication Date
Sat Jan 31 2015
Journal Name
Journal Of Al-qadisiyah For Pure Science
synthesis ,spectral studies and antimicrobial evalution of 6,6-(1,2-benzenediazo)bis(3-amino benzoic acid) complexes with some metal ions
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