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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 Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of the competitiveness for commercial banks in Iraq for a period of 2004 – 2012
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This study was conducted on a sample of commercial banks in Iraq, chosen according number of considerations for twenty banks, contained two public banks and eighteen private banks.                                                                                             &

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Publication Date
Sat Apr 01 2017
Journal Name
Al–bahith Al–a'alami
Digital Communication: The Future of Identity in Arab TV Drama: A Field Study on a Sample of Arab Society in the UAE in 2017
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The digital communication of a product of communication and information revolution. It is characterized by accurate and comprehensive in its services and its effects, which brought changes in the structure of many communities and their organizational structures. They have significant impacts on the social systems and social relations, especially in the Arab societies, which are the focus of the globalized Western media, for many reasons: economical, political , cultural and social.
According to this perception, the Arab identity has become in an encounter with big challenges by the globalized media of trade and the media, which aims to achieve greater profits because of identity and its importance to the communities. This occurs par

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Publication Date
Sun Feb 10 2019
Journal Name
Iraqi Journal Of Physics
Experimental study for the properties of Fe3O4 dusty plasma using the air in vacuum chamber system
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In this work, we carried out an experimental study of thedusty
plasma by taking the dust material Fe3O4 with radius of the any grain
0.1μm - 0.5μm. In experiment we use air in the vacuum chamber
system under different low pressure (0.1-1) Torr. The results
illustrated that the present of dust particles in the air plasma did not
effect on Paschen minimum which is 0.5 without dust and with Fe3O4
dusty grains.
The effect of Fe3O4 dust particles on plasma parameters can be
notice in direct current system in glow discharge region. The plasma
parameters which were studied in this work represent plasma
potential, floating potential,electron saturation current, temperatu

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Publication Date
Wed Feb 22 2023
Journal Name
Iraqi Journal Of Science
Extraction Drainage Network for Lesser Zab River Basin from DEM using Model Builder in GIS
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ArcHydro is a model developed for building hydrologic information systems to synthesize geospatial and temporal water resources data that support hydrologic modeling and analysis. Raster-based digital elevation models (DEMs) play an important role in distributed hydrologic modeling supported by geographic information systems (GIS). Digital Elevation Model (DEM) data have been used to derive hydrological features, which serve as inputs to various models. Currently, elevation data are available from several major sources and at different spatial resolutions. Detailed delineation of drainage networks is the first step for many natural resource management studies. Compared with interpretation from aerial photographs or topographic maps, auto

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Publication Date
Thu Feb 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison Some Robust Estimators for Estimate parameters logistic regression model to Binary Response – using simulation)).
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 The logistic regression model of the most important regression models a non-linear which aim getting estimators have a high of efficiency, taking character more advanced in the process of statistical analysis for being a models appropriate form of Binary Data.                                                          

Among the problems that appear as a result of the use of some statistical methods I

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Publication Date
Tue Jan 01 2019
Journal Name
International Journal Of Information Systems And Change Management
Designing a knowledge management measurement for educational institutions: a qualitative research
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Publication Date
Sun Aug 10 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of canal dryness and flaring on the accuracy of two electronic apex locators
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Background: This in vitro study evaluated the effect of canal dryness and flaring on the accuracy of two electronic apex locators for working length (WL) determination. Materials and methods: Sixty extracted teeth were used, after access opening was done, the occlusal surface was flattened to create stable reference point. The teeth were randomly divided into two equal main groups of flared and unflared group each one of 30 teeth. The flaring was done with Gates Glidden drills. The two main groups were further subdivided into two subgroups: dry canal and wet canal using 5.25% sodium hypochlorite groups, Electronic WL of each sample was determined using both Root ZX and i-Root apex locator. Consequently, histologic WL was determined by shav

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Publication Date
Wed Aug 26 2020
Journal Name
Iraqi Journal Of Agricultural Sciences
COMPARISON THE ACCURACY OF COMPUTING POINT COORDINATS BETWEEN DIFFERENT INSTRUMENTS AND APPLICATIONS OF GPS
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The study was aimed to determine the coordinates of  the points were measured by different ways and different instruments, the most precise way using the differential global positioning system (DGPS) that will be the reference measurements in comparison, less precise way using navigator GPS. Google earth (pro.), and the other applications of GPS mobile ( Samsung and I-phone). In this research (8 points) were chosen that are occasional in location. The comparison of the different observations can give us an idea of ​​the extent to which the accuracy of the observations differs from the different devices used in the observing, as well as through the knowledge of the best device and the best way to measure coordinates accurately t

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Publication Date
Wed Jan 31 2024
Journal Name
Journal Of The Faculty Of Medicine Baghdad (jfacmed Baghdad)
The Role of Activin A levels, Body Mass Index and Beta-Human Chorionic Gonadotropin in Ectopic Pregnancies and Missed Abortions – A Study on a Group of Iraqi Women
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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
The Homomorphism of a cubic set of a semigroup in a KU-algebra
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Abstract<p>The study of homomorphisms in cubic sets is considered one of the important concepts that transfer algebraic properties between different structures, so we study a homomorphism of a cubic set of a semigroup in a KU-algebra and defined the product of two cubic sets in this structure. Firstly, we define the image and the inverse image of a cubic set in a KU-semigroup and achieve some results in this notion. Secondly, the Cartesian product of cubic subsets in a KU-semigroup is discussed and some important characteristics are proved.</p>
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