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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
Wed Feb 20 2019
Journal Name
Political Sciences Journal
US policy toward the political movement in the Arab countries Egypt a model
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The whole world and the Arab world, especially an important part of this international system, is undergoing a radical transformation at all levels. This mosaic of political, economic, social and military relations and alliances, whether based on the special interests of the major Powers or on the basis of mutual interests, The major transformations to social, economic, political and military conflict and these transformations still bear more surprises, at all levels, nothing remains constant, all changed, relations changed and alliances changed and loyalties fell and the principles of the M changed and the spectacular imperial economies collapsed and the will of the masses was no longer fixed.

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Publication Date
Sat Jan 05 2019
Journal Name
Iraqi Journal Of Physics
Characterization of (SnO2)1-x(TiO2:CuO)x films as NH3 gas sensor
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Tin dioxide (SnO2) were mixed with (TiO2 and CuO) with concentration ratio (50, 60, 70, 80 and 90) wt% films deposited on single crystal Si and glass substrates at (523 K) by spray pyrolysis technique from aqueous solutions containing tin (II) dichloride Dihydrate (SnCl2, 2H2O), dehydrate copper chloride (CuCl2.2H2O) and Titanium(III) chloride (TiCl3) with molarities (0.2 M). The results of electrical properties and analysis of gas sensing properties of films are presented in this report. Hall measurement showed that films were n-type converted to p- type as titanium and copper oxide added at (50) % ratio. The D.C conductivity measurements referred that there are two mechanisms responsible about the conductivity, hence it possess two act

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Publication Date
Thu Sep 01 2022
Journal Name
Brazilian Journal Of Chemical Engineering
A computational study on the potential application of Ca12O12 cluster for sensing of fungicide molecule
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Density functional theory calculations are employed to investigate the impact of edifenphos molecule on the reactivity and electronic sensitivity of pure calcium oxide (CaO) nanocluster. The strong adsorption of edifenphos molecule on CaO nanocluster occurs by the sulfur head of the adsorbate, and the amount of the energy of this adsorption is around − 84.40 kcal/mol. The adsorption of edifenphos molecules results in a decrease in the values of Eg of CaO from 4.67 to 3.56 eV, as well as an increase in the electrical conductance. Moreover, the work function of CaO nanocluster is significantly affected, which changes the current of the field emission electron. Eventually, the recovery time is calculated around 99 ms at ambient temperature f

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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
A New Model Design for Combating COVID -19 Pandemic Based on SVM and CNN Approaches
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       In the current worldwide health crisis produced by coronavirus disease (COVID-19), researchers and medical specialists began looking for new ways to tackle the epidemic. According to recent studies, Machine Learning (ML) has been effectively deployed in the health sector. Medical imaging sources (radiography and computed tomography) have aided in the development of artificial intelligence(AI) strategies to tackle the coronavirus outbreak. As a result, a classical machine learning approach for coronavirus detection from      Computerized Tomography (CT) images was developed. In this study, the convolutional neural network (CNN) model for feature extraction and support vector machine (SVM) for the classification of axial

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Publication Date
Thu Dec 01 2011
Journal Name
International Review Of Physics (e-journal) (irephy)
Red shift band enhancement of the nanostructure ZnO100-xAlx thin films as a function of Al concentration for optoelectronic applications
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Publication Date
Mon Jul 04 2016
Journal Name
University Of Plymouth
‘History Engraved on his Shoulder’: A Comparative Study of the Influence of British First World War Poetry on Post 1980 Iraqi War Poetry "embargoed indefinitely"
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Abstract This study aims to compare British war poetry of the First World War with Iraqi poetry from the mid-20th century with special reference to Iraqi war poetry of the 1980’s Iraq-Iran War and the period that followed it. It will also investigate the influence of the designated British war poetry on the chosen body of Iraqi poetry. Through the comparison of sample poems the study presents, firstly, the direct influence of the British poetry of the Great War and its translation which formed the seeds of a more radical movement in Iraqi poetry during the 1980’s Iran/Iraq War and the period that followed it. The study also presents a comparison of the works of British and Iraqi civilian poets during and after the war time and their con

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Publication Date
Sun Dec 02 2012
Journal Name
Baghdad Science Journal
Study of Spectroscopy and Thermodynamic Properties for Phoshours dioxide PO2 Molecular and Influence Study of Bond ( P-O ) on Spectroscopy Properties
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In This research a Spectroscopic complement and Thermodynamic properties for molecule PO2 were studied . That included a calculation of potential energy . From the curve of total energy for molecule at equilibrium distance , for bond (P-O), the degenerated of bond energy was (4.332eV) instate of the vibration modes of ( PO2 ) molecule and frequency that was found active in IR spectra because variable inpolarization and dipole moment for molecule. Also we calculate some thermodynamic parameters of ( PO2 ) such as heat of formation , enthalpy , heat Of capacity , entropy and gibb's free energy Were ( -54.16 kcal/mol , 2366.45 kcal/mol , 10.06 kcal /k/mol , 59.52 k

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Publication Date
Thu Jan 23 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Loss Reduction and prevention programs
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The risks are considered as a large challenge facing the human communities. This challenge creates an economic and social burden which obstruct the community progress and influences on its evaluation in a negative way. In the last years, these risks began to increase and now it is necessary to face these risks in a regular and instructive methods in order to control over these risks and to limit its effects and reducing the losses, if it happened. The loss reduction and prevention programs produced by risks management are considered as a successful solution which enable to control these risks. These programs would not finish the danger in the community in a final way but it produces a practical solution reduces the negative effects and c

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Publication Date
Sun Sep 28 2025
Journal Name
Journal Of Physical Education
A survey Study to Measure the level of Motivation a Squash lesson for junior students in the College of Physical Education and Sports Sciences
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            Human behavior is one of the topics that has captured the attention of researchers throughout the ages, and motivation is one of the manifestations of this behavior, which indicates the extent of interest in a particular topic and their unwillingness to rush towards a particular topic. The topic of motivation is one of the important topics of interest to the teacher and coach in the field of sports. The aim of this research was identifying the level of motivation for junior students, and the differences in the dimensions of motivation for junior students in squash lessons. We used the descriptive survey method, and the research sample was chosen randomly. Only male of the junior students in the College of Phys

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of the Current Financial Crisis : Causes and Solutions (Iraqi crisis a model , based on the public budget for the fiscal year 2016)
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The research aims to analysis of the current financial crisis in Iraq through knowing its causes and then propose some solutions that help in remedy the crisis and that on the level of expenditures and revenues, and has been relying on the Federal general budget law of the Republic of Iraq for the fiscal year 2016 to obtain the necessary data in respect of the current expenditures and revenues which necessary to achieve the objective of the research , and through the research results has been reached to a set of conclusions which the most important of them that causes of the current financial crisis in Iraq , mainly belonging to increased expenditures and especially the current ones and the lack of revenues , especially non-oil o

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