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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
Fri Apr 01 2016
Journal Name
Al–bahith Al–a'alami
Indicators of Mental image among Students of the University of Baghdad about Iraqi Political Parties-(a research based on a master thesis)
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Media studies have focused mostly on the issue of the mental image because the image that is formed in the mind has become not only a photo of a human being and having kept for himself. This image has an outside influence which may sometimes up to the formation of the fate of others and it sometimes includes individuals and groups together.
This study comes in the context of identifying the image of Iraqi political parties among Iraqi university students and the nature of the view that students have in their minds about these parties.
Chapter one includes the problem of the research, the importance of the study, the goals and method used. Chapter two is divided into two sections: section one deals with the concept of the mental i

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Publication Date
Fri Jul 23 2021
Journal Name
International Journal Of Nonlinear Analysis And Applications
On the dynamical behavior of an eco-epidemiological model
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The aim of this article is to study the dynamical behavior of an eco-epidemiological model. A prey-predator model comprising infectious disease in prey species and stage structure in predator species is suggested and studied. Presumed that the prey species growing logistically in the absence of predator and the ferocity process happened by Lotka-Volterra functional response. The existence, uniqueness, and boundedness of the solution of the model are investigated. The stability constraints of all equilibrium points are determined. The constraints of persistence of the model are established. The local bifurcation near every equilibrium point is analyzed. The global dynamics of the model are investigated numerically and confronted with the obt

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Publication Date
Mon Jul 05 2010
Journal Name
Evolutionary Algorithms
Variants of Hybrid Genetic Algorithms for Optimizing Likelihood ARMA Model Function and Many of Problems
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Optimization is essentially the art, science and mathematics of choosing the best among a given set of finite or infinite alternatives. Though currently optimization is an interdisciplinary subject cutting through the boundaries of mathematics, economics, engineering, natural sciences, and many other fields of human Endeavour it had its root in antiquity. In modern day language the problem mathematically is as follows - Among all closed curves of a given length find the one that closes maximum area. This is called the Isoperimetric problem. This problem is now mentioned in a regular fashion in any course in the Calculus of Variations. However, most problems of antiquity came from geometry and since there were no general methods to solve suc

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Publication Date
Tue Apr 26 2011
Journal Name
Evolutionary Algorithms
Variants of Hybrid Genetic Algorithms for Optimizing Likelihood ARMA Model Function and Many of Problems
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Publication Date
Sat Dec 28 2019
Journal Name
Journal Of Mechanics Of Continua And Mathematical Sciences
NEW ROBUST ESTIMATOR OF CHANGE POINT IN SEGMENTED REGRESSION MODEL FOR BED-LOAD OF RIVERS
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Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Social responsibility and obstacles application (Comparative research departments in the Municipality of Baghdad)
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Abstract

The research aims to identify the extent of the practice of social responsibility in accordance with the social dimension and diagnosis of constraints applied.

Find the problem represented by the Social Responsibility and obstacles facing application in Baghdad Municipality through their workers trends analysis.

The adoption of the statistical method to analyze the data and information gathering, and selected municipalities of Adhamiya and Kadhimiya deliberate manner applied as a state and municipal councils of both cities as representatives of the local community to be the subject of research and comparison between them to see the reality of soci

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Publication Date
Tue Jan 01 2019
Journal Name
Advances On Computational Intelligence In Energy
A Theoretical Framework for Big Data Analytics Based on Computational Intelligent Algorithms with the Potential to Reduce Energy Consumption
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Within the framework of big data, energy issues are highly significant. Despite the significance of energy, theoretical studies focusing primarily on the issue of energy within big data analytics in relation to computational intelligent algorithms are scarce. The purpose of this study is to explore the theoretical aspects of energy issues in big data analytics in relation to computational intelligent algorithms since this is critical in exploring the emperica aspects of big data. In this chapter, we present a theoretical study of energy issues related to applications of computational intelligent algorithms in big data analytics. This work highlights that big data analytics using computational intelligent algorithms generates a very high amo

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Publication Date
Thu Oct 01 2020
Journal Name
Plant Archives
Taxonomical study for the species volkameria inermis l. (lamiaceae)
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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
The impact of the strategic foresight capabilities in green creativity An exploratory study for the State Company for Food Products
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The current research variables have received increasing attention in the recent period because they are one of the important issues affecting the future of organizations, as a result of the speed of environmental variables that have greatly affected organizations and for the purpose of explaining the relationships and links between research variables, as this research presents a test "the type and direction of the relationship between strategic foresight capabilities As an independent variable and green creativity "as a respondent variable. A set of questions has arisen about the basic research problem, including what is the nature and level of interest in the research variables (strategic foresight capabilities an

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Publication Date
Tue Nov 25 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Stem cells a novel approach to periodontal regeneration (A review of literature)
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In this review of literature, the light will be concentrated on the role of stem cells as an approach in periodontal regeneration.

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