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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
Sun Jul 30 2023
Journal Name
Iraqi Journal Of Science
Estimation of the Standard Atmospheric Earth Model Parameters at 86 km Altitude
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     Utilizing the Turbo C programming language, the atmospheric earth model is created from sea level to 86 km. This model has been used to determine atmospheric Earth parameters in this study. Analytical derivations of these parameters are made using the balancing forces theory and the hydrostatic equation. The effects of altitude on density, pressure, temperature, gravitational acceleration, sound speed, scale height, and molecular weight are examined. The mass of the atmosphere is equal to about 50% between sea level and 5.5 km. g is equal to 9.65 m/s2 at 50 km altitude, which is 9% lower than 9.8 m/s2 at sea level. However, at 86 km altitude, g is close to 9.51 m/s2, which is close to 15% smaller than 9.8 m/s2.  These resu

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Publication Date
Fri Mar 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Improving the Effectiveness of Internal Control System In Accordance with COSO Model
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        The research aims to improve the effectiveness of internal control system according to a model COSO, by identifying the availability of system components according to the model and then improve the effectiveness of each component by focusing on areas for improvement in each component, as it was addressed to a model COSO and then Maamth with the environment, the current Iraqi by introducing some improvements on the form of some mechanisms of corporate governance of the Council of Directors, and senior management, the Audit Committee, Committee appointments, especially that supplies application available in the laws and legislation, the current Iraqi, taking into consideration to make some

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Publication Date
Fri Jun 23 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
The dynamic of an eco-epidemiological model involving fear and hunting cooperation
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In the present paper, an eco-epidemiological model consisting of diseased prey consumed by a predator with fear cost, and hunting cooperation property is formulated and studied. It is assumed that the predator doesn’t distinguish between the healthy prey and sick prey and hence it consumed both. The solution’s properties such as existence, uniqueness, positivity, and bounded are discussed. The existence and stability conditions of all possible equilibrium points are studied. The persistence requirements of the proposed system are established. The bifurcation analysis near the non-hyperbolic equilibrium points is investigated. Numerically, some simulations are carried out to validate the main findings and obtain the critical values of th

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Publication Date
Sat Sep 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
The Role of Knowledge Economy in Financial Reporting System Development proposed model ""
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This  world is moving towards knowledge economy which basically depends on knowledge and information. So, the economic units need to develop its financial reporting system which helps to provide useful information in timeliness for investors in accordance with the requirements of  the knowledge economy and meets the needs of those investors. This  research aims to revealing the reflects of knowledge economy on the approaches of financial reporting and suggesting a financial reporting model in the environment of knowledge economy,  depending on combining the value approach with the events approach using database and communication technology and providing useful accounting information for all users regardless of

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Publication Date
Thu Jul 24 2014
Journal Name
Desalination And Water Treatment
Performance of granular dead anaerobic sludge as permeable reactive barrier for containment of lead from contaminated groundwater
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Publication Date
Sun Mar 01 2015
Journal Name
Baghdad Science Journal
Determination of Serum CA125 and evaluate its efficiency as screening tool For Early Detection of Ovarian Tumors
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Epithelial ovarian cancer is the leading cause of cancer deaths in women. To date, an effective screening tool for ovarian cancer has not been identified Several clinical and biological factors including serum cancer antigen 125 (CA- 125) have been assessed for prognostic and predictive relevance CA-125 is an epithelial marker derived from coelomic epithelium. It is elevated in 90% of advanced ovarian cancers and in 50% of early ovarian cancers while 20% of ovarian cancers have low or no expression of CA- 125 CA-125 concentrations were measured by Mini Vidas test (VIDAS CA125 II / BIOMERIEUX / France). The median CA-125 levels were significantly higher in the sera of ovarian cancer patients than in those with benign tumors an

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Publication Date
Fri Dec 23 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Preparation and in-vitro Evaluation of Secnidazole as Periodontal In-situ Gel for Treatment of Periodontal Disease
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This study aims to develop a thermosensitive mucoadhesive periodontal in situ gel of secnidazole for local release of drug for treatment of periodontitis, in order to increase the drug residence time and to increase patient compliance while lowering the side effects of the drug.

Cold method was used to prepare 30 formulas of secnidazole periodontal in situ gel, using different concentrations of thermosensitive polymers (poloxamer407 alone or in combination with poloxamer 188) and methyl cellulose (MC ) or hydroxypropyl methylcellulose (HPMC K4M )in different concentrations used as mucoadhesive polymer and the resultant formulations were subjected to several tests such as   gelation temperature GT, appearance and pH value. The fo

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Publication Date
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
The attitude of Arabic - Islamic caliphate toward the A raab in the prophet and rightly guided caliphate
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Publication Date
Fri Jun 30 2023
Journal Name
Journal Of The College Of Education For Women
The Construction of the Iraqi Child in the UNICEF Reports during Covid19 Pandemic: A Critical Discourse Analysis
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The present paper aims at investigating the linguistic image portrayed by UNICEF reports on the Iraqi child from a critical discourse analysis perspective during Covid19 pandemic (2020). The paper attempts to fill a gap in research literature concerning the linguistic construction of the Iraqi child by the UNICEF reports during the critical health crisis of Covid19. Van  Leeuwen’s (2008) approach of social actor representation has been adopted for this purpose. From Van  Leeuwen’s approach, the category of determination (single determination and overdetermination) has been selected to be the main analytical tool for its high compatibility with the set of objectives put forward to figure out how such a globally effective and

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Publication Date
Wed Feb 01 2023
Journal Name
International Journal Of Rheumatic Diseases
A 5 item version of the Workplace Activity Limitation Scale successfully identifies impaired work productivity in rheumatoid arthritis patients: A split‐sample factor analysis approach
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Abstract<sec><title>Background

There is a growing interest in studying the effects of arthritis on a person's work productivity using a growing variety of outcome indicators.

Objectives

To develop a valid and reliable shortened version of the Workplace Activity Limitation Scale 12 (WALS‐12) for assessing work productivity limitations in rheumatoid arthritis (RA) patients.

Methods

A cross‐sectional study involving 277 RA patients was conducted. An exploratory factor analysis on WALS‐12 was used for item reduction on the first sample. Then confirmatory factor ana

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