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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 Mar 26 2019
Journal Name
International Journal Of Mathematics And Mathematical Sciences
Stability and Bifurcation of a Prey-Predator-Scavenger Model in the Existence of Toxicant and Harvesting
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In this paper a prey-predator-scavenger food web model is proposed and studied. It is assumed that the model considered the effect of harvesting and all the species are infected by some toxicants released by some other species. The stability analysis of all possible equilibrium points is discussed. The persistence conditions of the system are established. The occurrence of local bifurcation around the equilibrium points is investigated. Numerical simulation is used and the obtained solution curves are drawn to illustrate the results of the model. Finally, the nonexistence of periodic dynamics is discussed analytically as well as numerically.

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Publication Date
Fri Jan 01 2021
Journal Name
Research Journal Of Pharmacy And Technology
Bacteriological and molecular study on S. Aureus bacteria Atala, M.L.
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Publication Date
Wed Dec 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
Comparison Between Nelson-Olson Method and Two-Stage Limited Dependent Variables (2SLDV ) Method for the Estimation of a Simultaneous Equations System (Tobit Model)
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This study relates to  the estimation of  a simultaneous equations system for the Tobit model where the dependent variables  ( )  are limited, and this will affect the method to choose the good estimator. So, we will use new estimations methods  different from the classical methods, which if used in such a case, will produce biased and inconsistent estimators which is (Nelson-Olson) method  and  Two- Stage limited dependent variables(2SLDV) method  to get of estimators that hold characteristics the good estimator .

That is , parameters will be estim

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Publication Date
Mon Feb 04 2019
Journal Name
Journal Of The College Of Education For Women
Semantic (Badi'iyah)Readings in The Prophetic Praise Poetry (Mada'h Nabawiya) (Abdel Rahim Bin Ahmad Bin Ali Al Borai as a case study)
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The importance of this topic may not be overlooked by many of the specialists, because it is one the sciences of the Arabic language, but it is an important method in the field of influencing the recipient and his aesthetic ability to create influential images as well.
The talking about Semantic (Badi'iyah)is as old as the Arabic age, so it may be talking about it not the new thing because the people who specialized have preceded us and exhausted all the talk .

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Publication Date
Tue Oct 01 2019
Journal Name
Environmental Earth Sciences
Urban geochemistry assessment using pollution indices: a case study of urban soil in Kirkuk, Iraq
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Publication Date
Fri Aug 02 2019
Journal Name
The Fifth Conference On Smart Monitoring, Assessment And Rehabilitation Of Civil Structures Smar 2019
Rehabilitation of Mohammed Al-Qassim Bridge after Fire Attack Using CFRP Sheets: A Case Study
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Publication Date
Tue Dec 31 2019
Journal Name
Journal Of Engineering
A High Resolution 3D Geomodel for Giant Carbonate Reservoir- A Field Case Study from an Iraqi Oil Field
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Constructing a fine 3D geomodel for complex giant reservoir is a crucial task for hydrocarbon volume assessment and guiding for optimal development. The case under study is Mishrif reservoir of Halfaya oil field, which is an Iraqi giant carbonate reservoir. Mishrif mainly consists of limestone rocks which belong to Late Cenomanian age. The average gross thickness of formation is about 400m. In this paper, a high-resolution 3D geological model has been built using Petrel software that can be utilized as input for dynamic simulation. The model is constructed based on geological, geophysical, pertophysical and engineering data from about 60 available wells to characterize the structural, stratigraphic, and properties distribution along

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Publication Date
Tue Dec 31 2019
Journal Name
Journal Of Engineering
A High Resolution 3D Geomodel for Giant Carbonate Reservoir- A Field Case Study from an Iraqi Oil Field
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Constructing a fine 3D geomodel for complex giant reservoir is a crucial task for hydrocarbon volume assessment and guiding for optimal development. The case under study is Mishrif reservoir of Halfaya oil field, which is an Iraqi giant carbonate reservoir. Mishrif mainly consists of limestone rocks which belong to Late Cenomanian age. The average gross thickness of formation is about 400m. In this paper, a high-resolution 3D geological model has been built using Petrel software that can be utilized as input for dynamic simulation. The model is constructed based on geological, geophysical, pertophysical and engineering data from about 60 available wells to characterize the structural, stratigraphic, and properties distri

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Publication Date
Tue Dec 01 2020
Journal Name
Iraqi Journal Of Physics
Modifications to Accelerate the Iterative Algorithm for the Single Diode Model of PV Model
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This paper discussed the solution of an equivalent circuit of solar cell, where a single diode model is presented. The nonlinear equation of this model has suggested and analyzed an iterative algorithm, which work well for this equation with a suitable initial value for the iterative. The convergence of the proposed method is discussed. It is established that the algorithm has convergence of order six. The proposed algorithm is achieved with a various values of load resistance. Equation by means of equivalent circuit of a solar cell so all the determinations is achieved using Matlab in ambient temperature. The obtained results of this new method are given and the absolute errors is demonstrated.

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Publication Date
Thu Dec 15 2022
Journal Name
Aaps Pharmscitech
Formulation and Characterization of Oleogel as a Topical Carrier of Azithromycin
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This study aims to formulate azithromycin oleogel to locally treat skin infections such as acne vulgaris and skin wound infection. Providing a form of azithromycin that can be administered topically is highly desired to prevent unwanted systemic complications including diarrhea, nausea, and abdominal pain. Additionally, it will avoid first pass metabolism, improves patient acceptance, provides an alternative in nauseated patients, decreases the dose by direct contact with the pathological site, and provides a noninvasive and convenient mode of administration. Furthermore, for treating wound infections, the gel will act as a scaffold biomaterial for wound closure besides its antibacterial effect. Herein, we propose the use of grapeseed oil-b

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