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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
Sat Dec 01 2012
Journal Name
Journal Of Engineering
Effect Of Technology Based Learning As A Supplement To Traditional Technology On Student's Achievement
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This paper describes a practical study on the impact of learning's partners, Bluetooth Broadcasting system, interactive board, Real – time response system, notepad, free internet access, computer based examination, and interaction classroom, etc, had on undergraduate student performance, achievement and involving with lectures. The goal of this study is to test the hypothesis that the use of such learning techniques, tools, and strategies to improve student learning especially among the poorest performing students. Also, it gives some kind of practical comparison between the traditional way and interactive way of learning in terms of lectures time, number of tests, types of tests, student's scores, and student's involving with lectures

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Comparison of Shear Bond Strength of Three Different Brackets Bonded on Zirconium Surfaces (In Vitro Study)
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Background: With the increased in the demands of adult orthodontics, the challenge of direct bonding to non-enamel surface (zirconium) had been increased. The present study was carried out to compare the shear bond strength of three different brackets (stainless steel, sapphire and composite) bonded to zirconium surface and study the mode of bond failure. Materials and methods: The sample was comprised of 30 models (8mm *6mm*1.5mm) of full contour zirconium veneers. They were divided into three groups according to the brackets type; all samples were treated first by sandblast with aluminum oxide particle 50 µm then coated by z-prime plus primer. A central incisor bracket of each group was bonded to the prepared zirconium surface with lig

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Publication Date
Wed Oct 24 2018
Journal Name
Journal Of Economics And Administrative Sciences
Training Programs And Their Impact On The Quality Of municipal Services /Field Research In The Municipality Of Baghdad
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     The objective of this research is to measure the training programs and identify the nature and then measure how it reflected on the quality of municipal services provided by the municipal departments investigated by measuring the quality of services based on quality standards, the researcher chose four municipal departments in the Rusafa / Baghdad (164 people) representing the directors and their assistants, officials of the municipal departments, the people and the engineering staff in charge of the task forces as well, including the survey of the views of the concerned persons in the management of the Vocational Training Institute in the Secretariat of the Republic, The quality of the municipal services

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Publication Date
Wed Oct 01 2014
Journal Name
Al–bahith Al–a'alami
Student Survey in Public Relations Services, Registration and Counseling, A Case Study of Petra University for the academic year 2013/2014.
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The research discusses the public relations services, registration, and academic advising at Petra University for the years 2013-2014. Using a field study and surveying Petra University students to be informed about the services and to cover the tiny details that have to do with public relations role in the university as a specialized department interested in serving public and gaining their trust in terms of what is legal and possible to build and enhance the university reputation. And gain mutual trust between the university and its publics.
The public relations is consi

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Publication Date
Sun Mar 02 2008
Journal Name
Baghdad Science Journal
A study of analysis and comparison to the low nutrient density foods that more normality for children age (3 –5 years)
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Through the early childhood and after the ablactating the child learns acquired food habbits that might studying with him throughout his life. Here the parents role arises: teaching the child the sound food habits and hygienic styles and whatever beneficial to the health and with the sufficient quantities for the body. In this way the experiences the child learns at home will be of great help in his future life in choosing the suitable food after becoming more dependent in making his decisions and choices away from his parents. The results in this study showed that the averages of the children’s consumption of the high energy foods in comparison with the other highest consumption average , after that comes the con sumption of soft drills

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Publication Date
Sun Oct 01 2023
Journal Name
Baghdad Science Journal
Detecting DNA of multispecies dinoflagellate cysts in the sediment from three estuaries of Makassar strait and fishing port using CO1 primer: Is it CO1 primer suitable for detecting DNA dinoflagellate?
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Most dinoflagellate had a resting cyst in their life cycle.  This cyst was developed in unfavorable environmental condition. The conventional method for identifying dinoflagellate cyst in natural sediment requires morphological observation, isolating, germinating and cultivating the cysts.  PCR is a highly sensitive method for detecting dinoflagellate cyst in the sediment.  The aim of this study is to examine whether CO1 primer could detect DNA of multispecies dinoflagellate cysts in the sediment from our sampling sites. Dinoflagellate cyst DNA was extracted from 16 sediment samples. PCR method using COI primer was running. The sequencing of dinoflagellate cyst DNA was using BLAST. Results showed that there were two clades of dinoflag

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Publication Date
Wed Aug 19 2020
Journal Name
International Journal Of Research In Social Sciences And Humanities
HUMOUR IN THE AMERICAN AND BRITISH COMEDYEPISODES: A DISCOURSE ANALYSIS STUDY
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DBNRAAK Mohammed, International Journal of Research in Social Sciences and Humanities, 2020

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
A systematical study about the genus Lycopus L. (Labiatae) in Iraq
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The study included gross morphology and pollen of plants – which collected during field trips , and dry ones for most specimen preserved with the Iraqi herbaria – related to the genus Lycopus L. , and to identify the unidentified species and rectify the error there in , so according to that the species L. europaeus L. only were specified for the genus . Through this work the varity L. europaeus var. glabrescens Schmidely were found at the first time , and suggested to record anew for Iraq . Pollen were of medium size, and had an ellipsoid shape in the equatorial view , and hexagonal in the polar view. The ecological and soil quality where these genus plants grows were specified , and were geographically distribut

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Publication Date
Mon Sep 07 2020
Journal Name
Environmental Science And Pollution Research
The biosorption of reactive red dye onto orange peel waste: a study on the isotherm and kinetic processes and sensitivity analysis using the artificial neural network approach
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Publication Date
Thu Dec 24 2020
Journal Name
Advances In Civil Engineering
Analytical study on torsional behavior of concrete beams strengthened with fiber reinforced polymer laminates using softened truss model
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This study aimed at evaluating the torsional capacity of reinforced concrete (RC) beams externally wrapped with fiber reinforced polymer (FRP) materials. An analytical model was described and used as a new computational procedure based on the softened truss model (STM) to predict the torsional behavior of RC beams strengthened with FRP. The proposed analytical model was validated with the existing experimental data for rectangular sections strengthened with FRP materials and considering torque-twist relationship and crack pattern at failure. The confined concrete behavior, in the case of FRP wrapping, was considered in the constitutive laws of concrete in the model. Then, an efficient algorithm was developed in MATLAB environment t

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