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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 Sep 20 2021
Journal Name
College Of Islamic Sciences
Positive images in the Holy Quran The story of Solomon - peace be upon him - in Surat An-Naml is a model An objective study
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God Almighty put in his great book secrets that do not end, and wonders that do not expire, for he is the one from which the scholars are not satisfied, and he does not create due to the multitude of response, and it is the comprehensive and inhibitory book that God conceals to the worlds, and he challenged the two heavyweights to come up with something like it.

At all times, issues arise in the Noble Qur’an that fit the needs of the people of that time and their culture, for it is an eternal book, characterized by the ability to give, extend and respond to addressing the problems of the age and its variables, when the Arabs had little luck at the time of the message’s descent from the scientific culture, and their proficienc

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Publication Date
Sun Aug 28 2016
Journal Name
World Journal Of Pharmacy And Pharmaceutical Sciences
AN INSIGHT ON THE IDENTIFICATION OF CANCER STEM CELLS USING NOVEL IMMUNOLOGICAL AND MOLECULAR STRATEGIES
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Cancer stem cells (CSCs) are defined as a population of cells present in tumours, which can undergo self-renewal and differentiation. Identification and isolation of these CSCs using putative surface markers have been a priority of research in cancer. With this background we selected pancreatic normal and tumor cells for this study and passaged them into animal tissue culture medium. Further staining was done using alkaline phosphatase and heamatoxilin staining. Blue to purple colored zones in undifferentiated pluripotent stem cells and clear coloration in the chromatin material indicated pancreatic cells. Further studies on the cell surface marker CD 44 were done using ELISA. For this, the protein was extracted from cultivated normal and t

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Publication Date
Thu Sep 06 2018
Journal Name
Al-khwarizmi Engineering Journal
Bone Defect Animal Model for Hybrid Polymer Matrix Nano Composite as Bone Substitute Biomaterials
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Addition of bioactive materials such as Titanium oxide (TiO2), and incorporation of bio inert ceramic such as alumina (Al2O3), into polyetheretherketone (PEEK) has been adopted as an effective approach to improve bone-implant interfaces. In this paper, hot pressing technique has been adopted as a production method. This technique gave a homogenous distribution of the additive materials in the proposed composite biomaterial. Different compositions and compounding temperatures have been applied to all samples. Mechanical properties and animal model have been studied in all different production conditions. The results of these new TiO2/Al2O3/PEEK biocomposites with different

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Publication Date
Sat Dec 01 2018
Journal Name
Indian Journal Of Natural Sciences
Determination of the Electron Density Variation for Ionosphere Layer Over Iraqi Zone Using IRI Model
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KA Hadi, AH Asma’a, IJONS, 2018 - Cited by 1

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Publication Date
Wed May 10 2023
Journal Name
Journal Of Engineering
DOUBLE DIFFUSIVE FREE CONVECTION IN A PACKED BED SQUARE ENCLOSURE BY USING LOCAL THERMAL NON-EQUILIBRIUM (LTNE) MODEL
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In the present study, free convection heat and mass transfer of fluid in a square packed bed enclosure is numerically investigated. For the considered geometrical shape, the left vertical wall of enclosure was assumed to be kept at high temperature and concentration while the opposite wall was kept at low temperature and concentration with insulating both the top and bottom walls of enclosure. The Brinkman– Forchheimer extended Darcy model was used to solve the momentum equations, while the energy equations for fluid and solid phases were solved by using the local thermal non-equilibrium (LTNE) model.Computations are performed for a range of the Darcy number from 10-5 to 10-1, the porosity from 0.5 to 0.9, and buoyancy ratio from -15 t

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Publication Date
Tue Jun 01 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
Bayes estimators of a multivariate generalized hyperbolic partial regression model
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Publication Date
Wed Jan 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Numerical Investigation of Drag Reduction Techniques in a Car Model
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Abstract<p>Reducing the drag force has become one of the most important concerns in the automotive industry. This study concentrated on reducing drag through use of some external modifications of passive flow control, such as vortex generators, rear under body diffuser slices and a rear wing spoiler. The study was performed at inlet velocity (V=10,20,30,40 m/s) which correspond to an incompressible car model length Reynolds numbers (Re=2.62×10<sup>5</sup>, 5.23×10<sup>5</sup>, 7.85×10<sup>5</sup> and 10.46×10<sup>5</sup>), respectively and we studied their effect on the drag force. We also present a theoretical study finite volume method (FVM) of solvi</p> ... Show More
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Publication Date
Mon Apr 10 2017
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Histological Study of the Digestive Tract of Liza abu (Heckel) 1-Esophagus
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  The study includes histological structure of  digestive tract of  Liza abu , Anatomical results found that the digestive tract occupied the largest part of  abdominal cavity ,  the mean gut length was (45.5) cm and relative gut length was (2.9) .  esophagus was a muscular tube length (1.5) cm , esophagus wall containing longitudinal  straight unbranched folds numbering (9) . Histological study  results found that the esophagus composed of four tunica : mucosa , submucosa , muscularis and serosa . The results found that the mucosa consists of three layers : epithelium , lamina propria and muscularis mucosa . The epithelial layer was stratified squamous epithelium thickness (139.1) µ containing

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Publication Date
Wed Jun 28 2023
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
PREPARATION OF A COMBINATION OF NANO- MEDICINAL PLANTS AS ANTIOXIDANTS AND MICROORGANISMS: PREPARATION OF A COMBINATION OF NANO- MEDICINAL PLANTS AS ANTIOXIDANTS AND MICROORGANISMS
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ABSTRACT

            The controversy is currently revolving around industrial additives, including antioxidants, their negative effects on consumer health and the emergence of various and various diseases, which led scientists and researchers to intensify most studies on natural antioxidants and their synthesis from medicinal plants mentioned in ancient medicine and in divine books as potential antioxidants of increasing importance. Therefore, this study was designed to synthesize silver nitrate particles from plant leaf extracts (Figs, Olives, and Moringa) and study their effect on bacterial inhibition of each of the undesirable Coliform bacteria (E-Coli,

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Publication Date
Mon Aug 17 2020
Journal Name
Biochemical And Cellular Archives
SERUM FERRITIN AS A BIOMARKER FOR THYROID GLAND (HYPO AND HYPER) THYRODISM WITH METABOLIC SYNDROME
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