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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
Thu Mar 31 2022
Journal Name
Journal Of The College Of Education For Women
Social Risks and Development Gaps in Iraq: A Social Study in the City of Baghdad
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Social risks posed a great challenge to the development path in Iraq, which resulted in widening the development gaps, whether these gaps were between rural and embargoed areas, or between Iraqi governorates, and the gender gap. Besides, the nature of the reciprocal relationship between the social risks and the development process requires the adoption of development trends that are sensitive to the risks that take upon themselves the prompt and correct response to these risks, away from randomness and confusion that Iraq suffered from for decades. However, currently, the situation has differed a great deal. This is because the size and types of such gaps have widened and become more complicated than before; a matter which has led to hav

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Publication Date
Wed Jan 01 2014
Journal Name
Journal Of The College Of Languages (jcl)
A Contrastive Study on the Syntactic Structure of Standard English and Standard Arabic Determiner Phrase
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The determiner phrase is a syntactic category that appears inside the noun phrase and makes it definite or indefinite or quantifies it. The present study has found wide parametric differences between the English and Arabic determiner phrases in terms of the inflectional features, the syntactic distribution of determiners and the word order of the determiner phrase itself. In English, the determiner phrase generally precedes the head noun or its premodifying adjectival phrase, with very few exceptions where some determiners may appear after the head noun. In Arabic, parts of the determiner phrase precede the head noun and parts of it must appear after the head noun or after its postmodifying adjectival phrase creating a discontinu

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Publication Date
Sat Dec 01 2018
Journal Name
Political Sciences Journal
American strategic performance towards Middle East in the era of president Trump - A future study
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Abstract The strategic performance of the United States depends on dealing with the Middle East countries and its variants on several bases and motives that enabled them to achieve American hegemony and invest its interests at the expense of the region countries. Within this performance, the administration of the United State President Donald Trump presented the Strategic Document on December 18, 2017, which focused on the principle of "America First", to determine the direction of future US strategic performance in the formulation of means of cooperation and intersections or hostility in addition to interests and threats.The future vision of the Arab region and the Middle East as a whole, this strategy is based on the fact that

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Publication Date
Sun Feb 08 2026
Journal Name
Journal Of Baghdad College Of Dentistry
The Soft Tissue Changes Following Orthodontic Treatment of Bimaxillary Protrusion (A Clinical and Photographical Study)
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Background: Bimaxillary protrusion is considered as one of the most important causes to seek the orthodontic treatment to get better esthetics. This study aimed to test the effect of orthodontic treatment in improvement the facial esthetics. Materials and Methods: Ten Iraqi Arab females having bimaxillary protrusion based on Class I malocclusions treated with fixed orthodontic appliance and extraction of the maxillary and mandibular 1st permanent premolars. Pre and post-treatment facial profile photographs were taken for each patients and the effect of treatment was tested in comparison with the pre-treatment photographs by using seven angular measurements. Results: After treatment, the upper and lower lip projections were decreased signifi

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Publication Date
Tue Dec 31 2019
Journal Name
Revue Académique De La Recherche Juridique
Consent in Reality TV Program Contracts – A Legal Study in Light of the American Experience
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The development of the television industry has led to the emergence of a new type of entertainment program in which producers have abandoned stereotypes in traditional programs, known as (Reality TV show). This type of program has spread rapidly in America, (where there are more than 40 series of these programs), as well as Europe and more than twenty countries around the world, including the Arab countries, where the number of these programs today to about 1000 programs and the number is increasing , Especially with the readiness of the production networks to produce more of these programs for the huge profits they derive from them (because of the high viewing rates and the large number of ads broadcast through them) in return for low prod

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Publication Date
Mon Sep 30 2024
Journal Name
The Scientific World Journal
Relationship Between the Level of Vitamin D3 Deficiency and Successful Osseointegration: A Prospective Clinical Study
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Purpose: This study aimed to evaluate the influence of vitamin D3 levels on bone density, primary dental implant stability, and successful osseointegration.

Materials and Methods: Clinical and radiological examination with a standardized cone‐beam computed tomography (CBCT) machine and laboratory investigation for serum levels of vitamin D3 were performed for all patients. Only patients in need of single or multiple straightforward dental implant surgery in either jaw with no history of systemic disease or condition that may interfere with bone healing were included in this study to receive the dental implant by the same oral and maxillofacial surgeon, which re‐opened

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Publication Date
Mon Sep 30 2024
Journal Name
The Scientific World Journal
Relationship Between the Level of Vitamin D3 Deficiency and Successful Osseointegration: A Prospective Clinical Study
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Purpose: This study aimed to evaluate the influence of vitamin D3 levels on bone density, primary dental implant stability, and successful osseointegration.

Materials and Methods: Clinical and radiological examination with a standardized cone‐beam computed tomography (CBCT) machine and laboratory investigation for serum levels of vitamin D3 were performed for all patients. Only patients in need of single or multiple straightforward dental implant surgery in either jaw with no history of systemic disease or condition that may interfere with bone healing were included in this study to receive the dental implant by the same oral and maxillofacial surgeon, which re‐opened

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Publication Date
Sat Dec 01 2012
Journal Name
Iraqi Journal Of Physics
A computer experiment to study the charging process of dust grains in negative ion plasma
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This work presents a computer studying to simulate the charging process of a dust grain immersed in plasma with negative ions. The study based on the discrete charging model. The model was developed to take into account the effect of negative ions on charging process of dust grain.
The model was translated to a numerical calculation by using computer programs. The program of model has been written with FORTRAN programming language to calculate the charging process for a dust particle in plasma with negative ion, the time distribution of a dust charge, number charge equilibrium and charging time for different value of ηe (ratio of number density of electron to number density of positive ion).

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Publication Date
Wed Jan 01 2020
Journal Name
International Journal Of Innovation, Creativity And Change
Sustainable development in islam: A study regarding the possibility of achieving development goals in Iraq
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Sustainable human development means meeting the basic needs of society and striving for continuous improvement in quality, as it seeks to increase economic well-being while providing adequate housing and nutrition, as well as providing electricity, water, health and education services . Ten centuries ago, Islam highlighted the importance of the development effort and the necessity of its sustainability before the West took it in the 1970s. There are a number of challenges that greatly affect the reality of achieving and ensuring Millennium Development Goals. The research recommends the importance of fighting administrative and financial corruption, as this is one of the biggest challenges facing the possibility of advancing the economy and

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Publication Date
Mon Jan 01 2024
Journal Name
Corporate And Business Strategy Review
The role of entrepreneurial leadership strategy in promoting organizational sustainability: A descriptive and analytical study
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The paper aims to build a model that supports organizational sustainability by analyzing the correlations and revealing the impact between the two main variables (entrepreneurial leadership) with its dimensions of proactive outlook, risk, and creativity (Van Zyl & Mathur-Helm, 2007), and (organizational sustainability) with its economic, environmental, and societal dimensions (Hansmann et al., 2012). As well as identifying the level of awareness and informing managers in the General Company for the Automotive and Equipment Industry, of the theoretical implications and performance, and its vital importance to society and the surrounding ecological environment, and drawing attention to that and improving performance, and indicatin

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