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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 Jun 30 2020
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
RATIONALIZATION OF CONSUMPTION AND ITS IMPACT ON ECONOMIC DEVELOPMENT (A PRELIMINARY STUDY): RATIONALIZATION OF CONSUMPTION AND ITS IMPACT ON ECONOMIC DEVELOPMENT (A PRELIMINARY STUDY)
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The research deals with the concept of rationalization of consumption, which is legitimately legitimized, by indicating the permissibility of consumption and its limits in Islam, the legitimate aspects of spending and its controls, and the concept of development in the Islamic economy. The researcher followed the descriptive method by presenting the legal texts and jurisprudential opinions and linking them to contemporary economic problems.The research has reached several conclusions, the most important of which is that the goal of Islam in relation to consumption is to inform the Muslim of the amount of economic maturity, and the truth of alms is good in money and religion. It is necessary for achieving maturity that both means

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Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Methods of using the periodic chart in the case of the missing values of the stable AR model (2)
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In this study, we investigate the behavior of the estimated spectral density function of stationary time series in the case of missing values, which are generated by the second order Autoregressive (AR (2)) model, when the error term for the AR(2) model has many of continuous distributions. The Classical and Lomb periodograms used to study the behavior of the estimated spectral density function by using  the simulation.

 

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Publication Date
Sun Aug 17 2025
Journal Name
Al–bahith Al–a'alami
The Role of Media Coverage of the Iraqi Satellite Channels in Shaping Public Attitudes towards Terrorism (a Field Study of a Sample of an Audience of the City of Baghdad)
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Violence is one of the most serious threats facing societies because it affects their internal structure and threatens the security and stability of society. It is classified as one of the types of security crises that are emerging in Arab and Islamic societies in particular, and in most countries of the world in general.

The threat of this crisis is increasing. Terrorism is considered as one of the most serious aspects of that all the countries of the world, currently, suffer from. The terrorism has begun to penetrate deep into society in one way or another starting from the Second World War, which led to the emergence of leftist movements in Western Europe, Japan, France, Italy and other countries as a result of emerging ideas

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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Engineering
Chemical-Free Greywater Treatment Using Aeration, Sedimentation, Followed by Granular Activated Carbon Filter (GAC) -A Case Study of Baghdad city household
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Greywater is a possible water source that can be improved for meeting the quality required for irrigation. Treatment of greywater can range from uncomplicated coarse filtration to advanced biological treatment. This article presents a simple design of a small scale greywater treatment plant, which is a series of physical and natural processes including screening, aeration, sedimentation, and filtration using granular activated carbon filter and differentiates its performance with sand filter. The performance of these units with the dual filter media of (activated carbon with sand) in treatment of greywater from Iraqi house in Baghdad city during 2019 and that collected from several points including washbasins, kitchen si

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Publication Date
Fri Jul 21 2023
Journal Name
Journal Of Engineering
Development A Method For Production Of Carbon Nanotubes
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In this work chemical vapor deposition method (CVD) for the production of carbon nanotubes (CNTs) have been improved by the addition of S. Steel mesh container (SSMC) inside which the catalyst (Fe/Al2O3) was placed. Scanning electron microscopy (SEM) investigation method used to study nanotubes produced, showed that high yield of two types of (CNTs) obtained, single wall carbon nanotube (SWCNTs) with diameter and length of less than 50nm and several micrometers respectively and nanocoil tubes with a diameter and length of less than 100nm and several micrometers respectively. The chemical analysis of (CNTs) reveals that the main component is carbon (94%) and a little amount of Al (0.32%), Fe (2.22%) the reminder is oxygen. It was also fou

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Publication Date
Sun Mar 01 2020
Journal Name
Iop Conference Series: Materials Science And Engineering
Spectral fluctuations in <sup>24</sup>Mg nucleus using the framework of the nuclear shell model
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Abstract<p>Random matrix theory is used to study the chaotic properties in nuclear energy spectrum of the <sup>24</sup>Mg nucleus. The excitation energies (which are the main object of this study) are obtained via performing shell model calculations using the OXBASH computer code together with an effective interaction of Wildenthal (W) in the isospin formalism. The <sup>24</sup>Mg nucleus is assumed to have an inert <sup>16</sup>O core with 8 nucleons (4protons and 4neutrons) move in the 1d<sub>5/2</sub>, 2s<sub>1/2</sub> and 1d<sub>3/2</sub> orbitals. The spectral fluctuations are studied by two statistical measures: the nearest neighb</p> ... Show More
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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Relationship between Fiscal Policy and Human Development Analytical Studay Of Iraq Using The (ARDL)Model
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Fiscal policy is one of the important economic tools that affect economic development in general and human development in particular through its tools (public revenues, public expenditures, and the general budget).

It was hoped that the effects of fiscal policy during the study period (2004-2007) will positively reflect on human development indicators (health, education, income) by raising these indicators on the ground. After 2003, public revenues in Iraq increased due to increased revenues. However, despite this increase in public budgets, the actual impact on human development and its indicators was not equivalent to this increase in financial revenues. QR The value of the general budget allocations ha

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Publication Date
Sun Feb 17 2019
Journal Name
Iraqi Journal Of Physics
Nucleon momentum distributions and elastic electron scattering form factors for 58Ni, 60Ni, 62Ni, and 64Ni isotopes using the framework of coherent fluctuation model
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The nucleon momentum distributions (NMD) and elastic electron scattering form factors of the ground state for some 1f-2p-shell nuclei, such as 58Ni, 60Ni, 62Ni, and 64Ni
isotopes have been calculated in the framework of the coherent fluctuation model (CFM) and expressed in terms of the weight function lf(x)l. The weight function (fluctuation function) has been related to the nucleon density distribution (NDD) of the nuclei and determined from the theory and experiment. The NDD is derived from a simple method based on the use of the single particle wave functions of the harmonic oscillator potential and the occupation numbers of the states. The feature of the l

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Publication Date
Sat Aug 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
A conceptual Framework For the Relationship between Human and Social Capital
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Purpose: The research seeks to develop the implications of intellectual human capital, and social capital in business organizations, and will be accomplished on three levels, the first level (the level of description) to identify, diagnose and display content philosophical Strategic Human Resource Management at the thought of modern administrative represented by human capital and Ras social capital. The second level (level of analysis) and the analysis of the extent of the impact of alignment between human capital, and social capital in the organizational strength of the organizations. The third level (Level predict) the formulation of a plan to strengthen the organizational strength in business organizations and to develop speci

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Publication Date
Sun Apr 11 2021
Journal Name
Environment, Development And Sustainability
Developing a system for assessing the sustainability in school building projects
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