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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
Sat Dec 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Developing strategic leadership practices in the light of transparency and organizational citizenship behavior - A field study of a sample of the staff of the Office of the Inspector General at the Iraqi Ministry of Culture
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Diversity the terms and practice the organizational filed with different concepts and environment, which Iraqi environment part from them. Some organizational in Iraqi environment leave its basic oriented to agreement with the leader desire, their fore this research focus tow basic variable (organizational citizenship behavior & transparence), we supposition which is dependent to explanation the response variable (strategic leadership). The results justification in part and not justification in another part. For example the organizational citizenship behavior effect on some parte of the strategic leadership. The transparence have faraway to fly from the relation with organizational citizenship behavior and strategic leadershi

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Publication Date
Sat Jan 01 2022
Journal Name
Communications In Mathematical Biology And Neuroscience
A careful study of the effect of the infectious diseases and refuge on the dynamical behavior of prey-scavenger modeling
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In this paper, the dynamics of scavenger species predation of both susceptible and infected prey at different rates with prey refuge is mathematically proposed and studied. It is supposed that the disease was spread by direct contact between susceptible prey with infected prey described by Holling type-II infection function. The existence, uniqueness, and boundedness of the solution are investigated. The stability constraints of all equilibrium points are determined. In addition to establishing some sufficient conditions for global stability of them by using suitable Lyapunov functions. Finally, these theoretical results are shown and verified with numerical simulations.

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
A study of the physical and chemical characteristics of the waters of the central marshes in southern Iraq after restoration
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some ecological (physical and chemical varible) of water samples were studies monthly from December 2008 to May 2009 at two stations( St.1) Al - Chibayesh marsh and (St.2) Abu – Zirik marsh which are located in the south of Iraq . These variables included : Temperature, pH, EC, Dissolved oxygen , Total alkalinity, Nitrate, Sulphate, and phosphate, Si-SiO2 and Ca ,Mg, Cl, The marsh Considered as fresh water and alkaline. Abu-Zirik less than Al-Chibayesh.

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Publication Date
Mon Dec 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The effect of promotion means in the developing the activity of financial markets: A case study of Iraqi stock Exchange
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The promotion by its means lead a vital and important role at the level of all organizations, whether (industrial or service) in general, and financial markets in particular. The promotion is earns delved to be as one of the main operations which  market uses it through various means of financial markets and companies which its shares listed in the aim of (finance or investment), with a view to the implementation and financing of public and private projects the one hand, or with a view to achieving profits through investment of speculative or... For other purposes, on the other hand.Accordingly, we find that the set of public and private goals joint between the financial markets and listed companies respectively, will serve the stra

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Publication Date
Fri Sep 30 2022
Journal Name
College Of Islamic Sciences
The Effectiveness of Combining the Meanings of Grammatical Tools in Understanding the Arabic Sentence A study of Some Linguistic Evidences
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abstract

The grammatical tools (the letters of meanings) are of great importance in understanding the meanings of the Arabic sentences,

This research is a simple attempt to show how our venerable scholars employed the meanings of these tools when they interpreted the linguistic evidence, that is, the grammatical structure largely depends on the tool in forming the meaning within the sentences and employing the meanings of these grammatical tools in explaining the linguistic evidence by clarifying their significance in the contexts of their use and effectiveness. Synthesis of the meanings of grammatical tools is an important tool in understanding the linguistic structure in order to reveal its meaning.

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Publication Date
Tue Sep 15 2020
Journal Name
Al-academy
Forbidden Montage and the transition Technique in one-snapshot Movies 1917 Film- A model: محمد عبد الجبار كاظم-عذراء محمد حسن
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  Starting from the term (forbidden montage) initiated by the French critic (Andre Bazin) as a method of processing the movies that depend on (mise en scene) achieved by the action of the camera and its ability to photograph and employ the depth of the field, in addition to the possibility of free movement without interruption in the filming environment in order to avoid montage as much as possible (the montage that distorts focus and distracts attention and moves away from realism, which is the most important theoretical pillar of Bazin in photography). The pursuit was behind a cinema that depicts its topics in one integrated snapshot with all its details thus approximating reality without any interference of montage. Our study sta

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Publication Date
Tue Sep 30 2014
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Analytical Model for Detection the Tilt in Originally Oil Water Contacts
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Many carbonate reservoirs in the world show a tilted in originally oil-water contact (OOWC) which requires a special consideration in the selection of the capillary pressure curves and an understanding of reservoir fluids distribution while initializing the reservoir simulation models.
An analytical model for predicting the capillary pressure across the interface that separates two immiscible fluids was derived from reservoir pressure transient analysis. The model reflected the entire interaction between the reservoir-aquifer fluids and rock properties measured under downhole reservoir conditions.
This model retained the natural coupling of oil reservoirs with the aquifer zone and treated them as an explicit-region composite system

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Publication Date
Thu Mar 30 2023
Journal Name
Al-mustansiriyah Journal Of Science
CA72-4 as a Promising Prognostic and Diagnostic Biomarker in Iraqi Patients with Colorectal Cancer
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Colorectal cancer (CRC), the second most fatal cancer and the 3rd most common cancer is expected to cause 0.9 million deaths globally in 2025. Carcinoembryonic antigen (CEA) is currently used in the follow-up of patients with colorectal cancer, and in this study, we are trying to find a better marker than CEA in following up on patients' health and knowing the effectiveness of the treatment used and as a diagnostic marker for colorectal cancer. To determine the significance of Cancer antigen 72-4 (CA72-4) as a prognosis predictor in patients with colorectal cancer, compare its prognostic validity to the CEA biomarker. this case-control study includes (150) participants, 100 patients (59 males and 41 females), and 50 healthy controls

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Publication Date
Fri Jan 01 2021
Journal Name
Aip Conference Proceedings
Highly-charged EDTA-2Na salt as a novel draw solution in pressure-retarded Osmosis process
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Publication Date
Sat Oct 01 2011
Journal Name
Journal Of Engineering
SOLAR WATER HEATER WITH SHELL AND HELICAL COILED TUBE HEAT EXCHANGER AS A STORAGE TANK
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In this work an experimental study is performed to evaluate the thermal performance
of locally made closed loop solar hot water system using a shell and helical coiled tube
heat exchanger as a storage tank. Several measurements are taken include inlet and outlet
temperatures of both collectors and supply water and temperature distribution within the
storage tank. This is beside the water flow rate in both collectors and load cycle. The
main parameters of the system are obtained.

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