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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
Fri Oct 01 2021
Journal Name
Journal Of Engineering
Experimental Study of Natural Convection in a Closed Cavity (Static Type Domestic Fridge)
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This work provides an analysis of the thermal flow and behavior of the (load-free) refrigerator compartment. The main goal was to compare the thermal behavior inside the refrigerator cavity to the freezer door (home refrigerator) effect and install a fan on the freezer door while neglecting the heat transmitted by thermal radiation. Moreover, the velocity distribution, temperature, and velocity path lines are theoretically studied. This was observed without affecting the shelves inside the cabinet and the egg and butter places on the refrigerator door as they were removed and the aluminum door replaced with a glass door. This study aims to expand our knowledge about the temperature and flow fields of this refrigerator mo

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Publication Date
Thu Jan 30 2014
Journal Name
Al-kindy College Medical Journal
Orbital Hydatid Disease: A case study of young patients with primary orbital lesion
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Background:This is a prospective study of three children presented to us in the Orbital clinic in AL ShahidGazi Al Hariri Hospital with painless proptosiswith suspension of Hydatid disease.Objectives: : Orbital hydatid disease is a rare lesion accounting for less than 1% of the total lesions of the body (1, 2). Orbital cysts presented as a primary lesion in our study which is rare to have such lesion without involvement of other organs (3). Humans represent the intermediate host where the commonly affected organ are liver and the lung (10-15%) (4). Methods:This is a prospective study of three Children presented to us in the Orbital clinic in Al Shahid Ghazi Alhariri Hospital with painless proptosis with suspension of Hydatid disease, dep

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Publication Date
Thu Jan 30 2014
Journal Name
Al-kindy College Medical Journal
Quality of Life among People Survived from Terroristic Explosions: A Retrospective Cohort Study
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Background: Increasing interest in quality of life (QoL) is the new approach for understanding and improvement of health care. Although there are many studies about quality of life, there is deficiency of data about quality of life of peoples survived from terroristic explosions.Objectives: To study the QoL for peoples survived from terroristic explosions and compare it with that of a controlled people. Methods: This study was conducted between, 1st of July till 31st of December 2013. The sample of this study was collected from peoples attending the outpatient clinics in four primary health care centers, Baghdad city (2 from Rusafa and 2 from Karkh). 183 individuals proved to be exposed to terroristic explosion and 199 individual not exp

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Publication Date
Sun Feb 24 2019
Journal Name
Iraqi Journal Of Physics
Construction and performance study of a solar - powered hybrid cooling system in Iraq
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The systems cooling hybrid solar uses solar collector to convert solar energy into the source of heat for roasting Refrigerant outside of the compressor and this process helps in the transformation of Refrigerant from the gas to a liquid state in two-thirds the top of the condenser instead of two-thirds the bottom of the condenser as in Conventional cooling systems and this in turn reduces the energy necessary to lead the process of cooling. The system cooling hybrid use with a capacity of 1 ton and Refrigerant type R22 and the value of current drawn by the system limits (3.9-4.2A), the same value of electric current calculated by the system are  Conventional  within this atmosphere of Iraq, and after taking different readings

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Publication Date
Sun Jan 01 2023
Journal Name
Second International Conference On Innovations In Software Architecture And Computational Systems (isacs 2022)
Permeability estimation of Yamama formation in a Southern Iraqi oil field, case study
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Permeability is one of the essential petrophysical properties of rocks, reflecting the rock's ability to pass fluids. It is considered the basis for building any model to predict well deliverability. Yamama formation carbonate rocks are distinguished by sedimentary cycles that separate formation into reservoir units and insulating layers, a very complex porous system caused by secondary porosity due to substitute and dissolution processes. Those factors create permeability variables and vary significantly. Three ways used for permeability calculation, the firstly was the classical method, which only related the permeability to the porosity, resulting in a weak relationship. Secondly, the flow zone indicator (FZI) was divided reservoir into

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Publication Date
Sat Nov 15 2025
Journal Name
Baghdad Science Journal
A Study of Dipeptidyl Peptidase-4 in Iraqi Patients with Coronary Artery Disease
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Publication Date
Thu Oct 10 2019
Journal Name
Plant Archives
A study of qualitative, classification soil algae in some areas from Baghdad, Iraq
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A study of taxonomic quality of soil algae was conducted with some environmental variables in three sites of local gardens (Kadhimiya, Adhamiya and Dora) within the governorate of Baghdad for the period from October 2016 to March 2017. The study identified 28 species belonging to 16 species in which the predominance of blue green algae (18 species) Followed by Bacillarophyta algae (7 species) and three types of Chlorophyta. The study showed an increase in species of Oscillatoria. The results showed no significant differences between sites in temperature, pH and relative humidity, while there were clear differences between sites for salinity and nutrient The study showed a difference of irrigation water quality and use of different fertilize

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Publication Date
Thu Oct 03 2024
Journal Name
Heat Transfer
Field study of a cubical integrated solar collector storage tank under Baghdad province
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Abstract<p>A new, easy‐to‐manufacture, and low‐cost integrated cubical solar collector tank for domestic usage is concerned in this work. Three models are prepared, side by side, and tested to point out their seasonal performance. Tank Model I has three vertical sides, black painted and glazed to act as an absorber; the other sides are insulated. Tank Model II has two black painted and glazed sides, with four insulated surfaces. The models are south‐oriented at different positions and tested versus the conventional tank (Model III) to validate and assess their performance in summer and winter. In summer, the temperatures in Models I and II are lower than those for Model III since they have insulated sid</p> ... Show More
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Publication Date
Tue Sep 27 2022
Journal Name
Al–bahith Al–a'alami
POLITICAL DEBATES AND THEIR ARTISTIC CONSTRUCTION IN IRAQI SATELLITE CHANNELS ( AN ANALYTICAL STUDY ) : (A research drawn from a Master Thesis)
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The problem of research on the study of political debate programs in the Iraqi satellite channels, in the "People decide" program by Afaq channel and " electoral competition " by Fallujah channel), and its importance for the community and researchers in the scientific field, as new programs to enter the Iraqi media after we have been the world media a lot in this area at the academic and practical levels (The field), and seeks to find out what the technical construction of the programs of political debates in Iraqi satellite channels and methods of construction and methods of employment used by the technical elements in the presentation of the programs and The study adopted the surve

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Publication Date
Wed Mar 01 2023
Journal Name
Iraqi Journal Of Physics
Theoretical Computation of Electron Density in Laser-Induced Carbon Plasma using Anisimov Model
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In this work, electron number density calculated using Matlab program code with the writing algorithm of the program. Electron density was calculated using Anisimov model in a vacuum environment. The effect of spatial coordinates on the electron density was investigated in this study. It was found that the Z axis distance direction affects the electron number density (ne). There are many processes such as excitation; ionization and recombination within the plasma that possible affect the density of electrons. The results show that as Z axis distance increases electron number density decreases because of the recombination of electrons and ions at large distances from the target and the loss of thermal energy of the electrons in

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