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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 Jan 14 2020
Journal Name
College Of Islamic Sciences
(Social Reform in the Light of Modern Islamic Thought (Malik bin Nabi model
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Social reform is the main pillar of the organization of societies. Therefore, all religions and theories were directed to focus on this aspect as the most important element for the development of economic and cultural development. In addition to the analysis and application of the Islamic Sharia, he did not present a theory, but offered real solutions and remedies to the crises in our Arab and Islamic societies alike, despite the criticism directed at him. Z his opinions.<

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Publication Date
Thu Nov 01 2012
Journal Name
Iraqi Journal Of Science
THE EVOLUTION OF PLANETARY NEBULAE(PN) AND FADING TIME ACCORDING TO SYNTHETIC MODEL
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Abstract Planetary nebulae (PN) represents the short phase in the life of stars with masses (0.89-7) M☉. Several physical processes taking place during the red giant phase of low and intermediates-mass stars. These processes include :1) The regular (early ) wind and the envelope ejection, 2) The thermal pulses during Asymptotic Giant Branch (AGB ) phase. In this paper it is briefly discussed how such processes affect the mass range of Planetary Nebulae(PN) nuclei(core) and their evolution, and the PN life time, and fading time for the masses which adopted. The Synthetic model is adopted. The envelope mass of star (MeN ) and transition time (ttr) calculated respectively for the parameter (MeR =1.5,2, 3×10-3 M☉). Another time scale is o

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Publication Date
Mon Mar 30 2020
Journal Name
College Of Islamic Sciences
Social Reform in the Light of Modern Islamic Thought (Malik bin Nabi model)
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      Social reform is the main pillar of the organization of societies. Therefore, all religions and theories were directed to focus on this aspect as the most important element for the development of economic and cultural development. In addition to the analysis and application of the Islamic Sharia, he did not present a theory, but offered real solutions and remedies to the crises in our Arab and Islamic societies alike, despite the criticism directed at him. Z his opinions.

 

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Publication Date
Sat Oct 01 2022
Journal Name
Baghdad Science Journal
The Effect of Combination Ovariectomy and D-galactose Administration on Alzheimer's Animal Model
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Background and purpose: Animal model helps researchers to evaluate new treatment plan for human and understand pathological mechanism involved in a development of disease. The use of rats as an animal model for Alzheimer's research has become a favorite among researchers. Rats are capable in mimicking Alzheimer disease due to their intelligence and quick adaptation to nature. At present there are several methods that can be used to induce Alzheimer's animals, but each method has advantages and disadvantages. We need to learn other methods that can provide many advantages and few disadvantages. The Amyloid-beta 42 (Aβ-42) and Reactive Oxygen Species (ROS) are thought to play an important role in the pathology of Alzheimer’s disease. Th

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Publication Date
Fri May 01 2015
Journal Name
Journal Of Engineering
Using Spatial Videos, Google Earthtm and Geographic Information System to Dynamically Monitor Built Environment Changes In a Challenging Environment: Baghdad, Iraq.
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Urban expansion and its environmental and safety effects are one of the critical information needed for future development planning, safety considerations and environmental management. This work used two methods to monitor urban expansion and it's environmental and safety effects, the first is based on Google Maps for the years 2002 and 2010, and the second was the usage of spatial videos for the year 2013. Although the usage of satellite images is critical to know and investigate the general situation and the total effects of the expansion on a large piece of area, but the Spatial videos do a very detailed fine scale investigation, site conditions regarding both environmental and safety cannot be easily distinguished fr

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Publication Date
Sat Mar 31 2018
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparison between the Product-Refill and the Equalization Oxygen Pressure Swing Adsorption Processes
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This work presents a design for a pressure swing adsorption process (PSA) to separate oxygen from air with approximately 95% purity, suitable for different numbers of columns and arrangements. The product refill PSA process was found to perform 33% better (weight of zeolite required or productivity) than the pressure equalization process. The design is based on the adsorption equilibrium of a binary mixture of O2 and N2 for two of the most commonly used adsorbents, 5A & 13X, and extension from a single column approach. Zeolite 13X was found to perform 6% better than zeolite 5A. The most effective variables were determined to be the adsorption step time and the operational pressure. Increasing the adsorption step

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Publication Date
Sun Sep 01 2019
Journal Name
Journal Of Physics: Conference Series
The informatics adequacy on the spraying technology in Iraqi agricultural researches: A literature review
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Abstract<p>Many of the Iraqi agricultural researches are used spraying technique to add chemical products including pesticides and growth regulators. Various studies were performed to study the effect of these substances at different concentrations to improve plant production. In order to adopt specific criteria of spraying researches and to replicate them easily, it is a necessary to mention all information related to the spraying processes and regulations for improving sprayer’s performance by increasing the amount of pesticide deposited on the target. The current study aims to survey Iraqi researches in details and analyse them randomly. Also, to highlight on the importance of information applied in sprayi</p> ... Show More
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Publication Date
Fri May 10 2019
Journal Name
Research Journal Of Chemistry And Environment
Solid Phase Extraction of Theophylline in Aqueous Solutions by Modified Magnetic Iron Oxide Nanoparticles as an Extractor Material and Spectrophotometry Technique for the Determination
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new, simple and fast solid-phase extraction method for separation and preconcentration of trace theophylline in aqueous solutions was developed using magnetite nanoparticles (MIONPs) coated with aluminium oxide (AMIONPs) and modified with palmitate (P) as an extractor (P@AMIONPs). It has shown that the developed method has a fast absorbent rate of the theophylline at room temperature. The parameters that affect the absorbent of theophylline in the aqueous solutions have been investigated such as the amount of magnetite nanoparticle, pH, standing time and the volume, concentration of desorption solution. The linear range, limit of quantification (LOQ) and limit of detection (LOD) for the determination of theophylline were 0.05-2.450 μg mL-

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Publication Date
Tue May 19 2026
Journal Name
Al–bahith Al–a'alami
ADDRESSING THE GOALS OF SUSTAINABLE DEVELOPMENT IN THE ARAB PRESS:: (An analytical study in the newspapers (Al-Sabah Iraqi newspaper, Algerian ech-chaab Newspaper, and UAE Al-Ittihad Newspaper) (A Research Drawn from Master Thesis)
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The problem of this research is:

What are the sustainable development goals that received the priority in the press addressing of the newspapers under study?

What are the journalistic arts adopted by these newspapers in addressing the sustainable development goals?

What are the journalistic sources that Arab newspapers depended on when addressing the sustainable development goals?

What are the geographic range the Arab newspapers adopted in addressing the sustainable development goals? The research is categorized into descriptive research, adopting the survey method, and using the content analysis method.

The sample of research was determined by the preparation of the Arabic newspapers (Al-

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Publication Date
Tue Apr 04 2023
Journal Name
Journal Of Techniques
Comparison Between the Kernel Functions Used in Estimating the Fuzzy Regression Discontinuous Model
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Some experiments need to know the extent of their usefulness to continue providing them or not. This is done through the fuzzy regression discontinuous model, where the Epanechnikov Kernel and Triangular Kernel were used to estimate the model by generating data from the Monte Carlo experiment and comparing the results obtained. It was found that the. Epanechnikov Kernel has a least mean squared error.

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