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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 01 2018
Journal Name
International Journal Of Language Academy
A LINGUISTIC INVESTIGATION OF CONTEXTUALIZATION IN RELIGIOUS DISCOURSE
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Publication Date
Sun Feb 01 2015
Journal Name
Journal Of Engineering
Vibration Analysis of a Composite Plate with Delamination
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The use of composite materials has vastly increased in recent years. Great interest is therefore developed in the damage detection of composites using non- destructive test methods. Several approaches have been applied to obtain information about the existence and location of the faults. This paper used the vibration response of a composite plate to detect and localize delamination defect based on the modal analysis. Experiments are conducted to validate the developed model. A two-dimensional finite element model for multi-layered composites with internal delamination is established. FEM program are built for plates under different boundary conditions. Natural frequencies and modal displacements of the intact and damaged

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Publication Date
Sun Sep 30 2007
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Dynamics of a single Condensing Two-Phase Bubble
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The dynamics of a single condensing two-phase bubble of two different dispersed-continuous systems were studied. The systems were, CCl4 - water and CCl4 - 100% glycerol. Cinephotography was used to determine the change in height, diameter and time. These results were used to determine the experimental rise velocity of the bubble, which was compared with a theoretical one based on some equations used. It was found that the velocity of the first system remained almost constant, while it decreased gradually for the second system.

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Publication Date
Mon Mar 01 2021
Journal Name
Global Journal Of Public Health Medicine
DEXAMETHASONE USE IN MANAGEMENT OF COVID19: A REVIEW
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The lack of active 2019 coronavirus disease (COVID-19) pandemic treatment creates a challenge for researchers and scientists to find the most appropriate treatment for this disease. Dexamethasone, according to the findings of the RECOVERY clinical trial, declared mid-June 2020 in print media was one of those therapies. Although the results from retrospective studies are not strongly supportive of corticosteroid routine use in COVID-19 despite the signals for some benefits, the dedicated RECOVERY trial found a significant reduction in death with dexamethasone only in severe cases on a ventilator or moderate cases on supplemental oxygen therapy nevertheless, no benefit observed in mild to moderate cases requiring no oxygen. More studi

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Publication Date
Wed Jan 01 2014
Journal Name
Tikrit Journal Of Social Studies And Humanities
A Cultural Window into obituaries of Iraqi Newspapers
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Publication Date
Sun Sep 01 2013
Journal Name
International Journal Of Computer Applications
Concise Architecture of a Remote Network based Controller
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The development of microcontroller is used in monitoring and data acquisition recently. This development has born various architectures for spreading and interfacing the microcontroller in network environment. Some of existing architecture suffers from redundant in resources, extra processing, high cost and delay in response. This paper presents flexible concise architecture for building distributed microcontroller networked system. The system consists of only one server, works through the internet, and a set of microcontrollers distributed in different sites. Each microcontroller is connected through the Ethernet to the internet. In this system the client requesting data from certain side is accomplished through just one server that is in

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Publication Date
Sat Oct 01 2011
Journal Name
Iraqi Journal Of Physics
Preparation of nano-microfibers with a different polymers
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In this research, nanofibers have been prepared by using an electrospinning method. Three types of polymer (PVA, VC, PMMA) have been used with different concentration. The applied voltage and the gap length were changed. It was observed that VC is the best polymer than the other types of polymers.

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Publication Date
Mon Dec 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Modeling and Simulation of a Fire Tube Boiler
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Publication Date
Sun Feb 24 2019
Journal Name
Iraqi Journal Of Physics
Design and evalution of a solar PV system
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PV connected systems are worldwide installed because it allows consumer to reduce energy consumption from the electricity grid. This paper presents the results obtained from monitoring a 1.1 kWp. The system was monitored for nine months and all the electricity generated was fed to the fifth floor for physics and renewable energy building   220 V, 50 Hz. Monthly, and daily performance parameters of the PV system are evaluated which include: average generated of system Ah per day, average system efficiency, solar irradiation around these months. The average generated kWh per day was 8 kWh/day, the average solar irradiation per day was 5.6 kWh/m2/day, the average inverter efficiency was 95%, the average modules efficien

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Publication Date
Wed Jan 01 2020
Journal Name
Medeniyet Medical Journal
SARS-CoV-2: A Piece of Bad News
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A shocking third species emerged from a family of coronaviruses (CoV) in late 2019 following viruses causing SARS (Severe Acute Respiratory Syndrome-CoV) in 2003 and MERS (Middle East Respiratory Syndrome-CoV) in 2012; it’s a novel coronavirus now called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; formerly called 2019-nCoV). First emerging in China, it has spread rapidly across the globe, giving rise to significant social and economic costs and imposing severe strain on healthcare systems. Since many attempts to control viral spread has been futile, the only old practice of containment including city lockdown and social distancing are working to some extent. Unfortunately, specific antiviral drugs and vaccines remain u

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