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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 Jun 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
The Convective Heat Transfer of Fluid Flowing Across a Vertical Plate
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Publication Date
Sat Jun 24 2023
Journal Name
Arab World English Journal
The Construction of Racism in Cartoon Films: A Critical Discourse Analysis
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Animation is an industry that is expanding more quickly than ever. Every child’s favorite activity is watching cartoons. Therefore, it is essential to be cautious of the kinds of cartoon films children and teenagers tend. Because children and teenagers are the target audience for these films. This study aims at exposing a hidden enactment, namely racism, in a well-known cartoon film, Lion King, which has been selected accurately by the researchers because it shapes a set of ideas about black people and constructs prejudiced beliefs in their minds. This study is to answer the inquiry ‘Is the ideology of racism imposed in Lion King? And how?’ The significance of the present paper lies in highlighting the educational function of

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Publication Date
Thu Apr 04 2024
Journal Name
Chemchemtech
ANALYTICAL TECHNIQUES IN PHARMACEUTICAL POLLUTION OF THE WORLD’S RIVERS; A REVIEW
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Recent reports of new pollution issues brought on by the presence of medications in the aquatic environment have sparked a great deal of interest in studies aiming at analyzing and mitigating the associated environmental risks, as well as the extent of this contamination. The main sources of pharmaceutical contaminants in natural lakes and rivers include clinic sewage, pharmaceutical production wastewater, and sewage from residences that have been contaminated by drug users' excretions. In evaluating the health of rivers, pharmaceutical pollutants have been identified as one of the emerging pollutants. The previous studies showed that the contaminants in pharmaceuticals that are widely used are non-steroidal anti-inflammatory drugs, ant

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Publication Date
Sat Jan 01 2022
Journal Name
Materials Today: Proceedings
Studying the impact of condensate blockage on gas production: A review
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When the drawdown pressure amounts to a value below the dew point pressure, a minor droplet of condensate is shaped and accumulated in the close area of wellbore. As the accumulation happens, the saturation of the liquid will grow and a reduction in gas relative permeability will happen, therefore it will affect the productivity. Generally, condensate baking problem in gas wells is being deliberated and studied and numerous techniques have been suggested to solve the problem. The studying of condensate banking dynamics is essential to evaluate the productivity and behavior of the wells of the gas fields.

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Publication Date
Tue Aug 20 2024
Journal Name
مجلة جامعة ذي قار لعلوم التربية البدنية
A historical approach to the games of futsal and blind football
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Futsal and blind football are group games of a competitive nature due to their excitement, excitement, fun, and aesthetic goals with charming artistic touches. This explains the public's passion for these two games, whether healthy people or blind people play them, to expand their vision and knowledge. About these two games, a historical approach is presented about their origins, development, and how they became globally recognized competitive sports with unified rules and world championships at various levels. Studying the origin and global spread of both futsal and blind football and identifying the most prominent developments in the rules and tools for futsal and blind football. The most important findings were that both futsal and footb

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Publication Date
Sun Jan 01 2023
Journal Name
Ath-thaqafa Al-ajnabiah
Sufi Tafsir Reconsidered: Exploring the Development of a genre, Foreign Culture
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Publication Date
Sat Sep 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
The economic viability of a bee breeding project and adrift proposal
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Bee keping projects is one of the most important agricltural investment projects because it generate profit in a short period . In addition to the multiplicity of products and other benefits . Research aimed at study the feasibility of two projects one hand in the origin of the Al – Mashrok since 2006 , kicking off with ten hives , and the scond proposal , kicking of 100 hives using the criteria of the world bank . Results showed that the bee keeping projects is economically feasible, whether small or large .. Even when the analysis of the sensitivity of the project to changes which may occur in the price of output and resources by reducing costs and increasing revenues by 10% it remains economically viable .

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Publication Date
Thu Jan 01 2015
Journal Name
Journal Of The College Of Languages (jcl)
A Critical Discourse Analysis of the 2012 American Presidential Election Debates
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This study discusses the Critical Discourse Analysis of 2012 American Presidential Election Debate’. The researcher adopts a model proposed by Van Dijk’s (2006 d). Six ideological categories have been selected within the overall strategies of the ideological square are used. The categories are of three levels of discourse structure : (the meaning, the argumentation, and the rhetoric) .They have shown effective criteria for detecting the most disguised systems of racism and manipulation.

            Based on the analysis, it can be concluded that the elite discourses of candidates contribute to the reproduction of domination, Orientalism, and Islamophobia. This can be appl

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Publication Date
Mon Dec 01 2025
Journal Name
مجلة القادسية للقانون والعلوم السياسية
The Tax Regulation of Digital Currencies: A Financial and Criminal Perspective
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Publication Date
Tue Jan 01 2019
Journal Name
Plant Archives
The role and importance of amino acids within plants: A review
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