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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
Mon Apr 17 2017
Journal Name
Wireless Personal Communications
ITPMAP: An Improved Three-Pass Mutual Authentication Protocol for Secure RFID Systems
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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of King Saud University - Science
Three iterative methods for solving second order nonlinear ODEs arising in physics
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Publication Date
Sun Sep 27 2020
Journal Name
Journal Of The College Of Education For Women
Feminization and Masculinization of the Word Sun in the Holy Quran: A Semantic Study
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It is no secret for those concerned with language concerns that the issue of figurative feminization is one of the issues that does not follow a grammatical rule governed by the fact that the subject of knowledge of this is due to hearing as indicated by linguistic references and lexicons.This research opts to find out the origin of the feminization of the word sun in the Arabic language and in light of what some language specialists have argued that the origin of figurative feminization was due to non-linguistic motives related to religious and metaphysical beliefs, and that it was memory preserved in light of the linguistic heritage.The research concluded that the feminization of the sun goes back to what settled in their minds, which

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Publication Date
Mon Jan 28 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Managerial Skills and It`s Role in Strengthening the Competitive Edge of Companies: A Case Study in the General Company for Construction Industries
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This research tries to reveal how to manage and control the competitive edge for business by building managerial skills in various organizational levels. Our research aims at finding out the nature of various technical, human and in tellectual skills of a new president whose superiority is his competitive ness in the application field at general company for construe tioual  industriesand testing the surveyed minor and major changes through a questionnaire to collect information from officials. The sample was composed of (45) director. The data was analyzed  using some methods and statistical programs. The most prominent of these is (SPSS) that was used to extract the arithmetic mean, standard deviation, correlation coefficient

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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Zankoy Sulaimani - Part A
A Comparison Study on the Formation of Administrative and Leadership Policies for the Team and Individual Olympic Games in the Iraqi National Olympic Committee
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The planning for the formation of administrative policies and guidance through leadership are important things for managing administrative processes and sporting activities. As both contribute in the stability of the administrative conditions, and their development in the sport federations, whether they both were attentive about team and individual Olympic Games. The two researchers observe that, there is a variation in the correct way of application. Particularly in the formulation of administrative policies and leadership describing it as, modern management standards for both team and individual Olympic Games in the Iraqi National Olympic Committee. That led to cause a misconception and lack of clarity for some administrators of those uni

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Publication Date
Wed Dec 25 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Non-interest income and its impact on the profits of the Iraqi banking sector: (Comparative study)
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     In this study,  has been discussed the issue of non-interest income and its impact on the Iraqi banking sector profit for the period between (2008-2017) as it was the main objective of the study is to find the relationship between the non-interest income and the profits of the banking sector in order to know  the size of the sector's dependence on non-interest income As well as an analysis of its profitability compared to selected countries, And to test hypotheses, the financial ratios and some statistical tests to determine the stability of the time series such as the test (Correlegram , Dickey -Fuller (depending on the statistical program (E-Views V8) and a simple linear regression method by (Minitab

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Publication Date
Wed May 17 2023
Journal Name
Journal Of Engineering
A Simulation of Core Displacement Experiments for the Determination of the Relative Permeability
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Computations of the relative permeability curves were made through their representation by two functions for wetting and nonwetting phases. Each function contains one parameter that controls the shape of the relative permeability curves. The values of these parameters are chosen to minimize an objective function, that is represented as a weighted sum of the squared differences between experimentally measured data and the corresponding data calculated by a mathematical model simulating the experiment. These data comprise the pressure drop across core samples and the recovery response of the displacing phase. Two mathematical models are constructed in this study to simulate incompressible, one-dimensional, two-phase flow. The first model d

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Publication Date
Sat Sep 30 2023
Journal Name
Al–bahith Al–a'alami
The Role of Website Users in the Consumption of Notifications: A Field Study of Websites
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This research seeks to explore the impact of notifications on enhancing user engagement with websites, primarily through user subscriptions and their interaction with notifications on these websites. The significance of this study lies in its implications for crafting compelling headlines that capture users' attention, streamline their access to journalistic content, and align with the objectives and editorial policies of news websites. It sheds light on the factors influencing users' preferences for specific notifications and their engagement with content based on their individual interests, motivations, and the satisfaction derived from such interactions.
The researcher has reached several key findings, inc

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Publication Date
Fri Jan 11 2019
Journal Name
Iraqi Journal Of Physics
A study of the effect of nano materials on the physical properties of epoxy composites
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This research studies the effect of addition of some nanoparticles
(MgO, CuO) and grain size (30,40nm) on some physical properties
(impact strength, hardness and thermal conductivity) for a matrix
blend of epoxy resin with SBR rubber. Hand –Lay up method was
used to prepare the samples. All samples were immersed in water for
9 weeks.
The Results showed decreased in the values of impact strength and
hardness but increased the coefficient of thermal conductivity.

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Publication Date
Thu Jan 31 2019
Journal Name
Journal Of The College Of Education For Women
A study of some morphological characteristics of the Tigris River in the city of Baghdad
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Change the morphological characteristics with the change of the factors affecting it has been shown that the Tigris River has the characteristics of the morphology of the low values in terms of depth, width and perimeter wet and gradient which in turn affected the morphological and other characteristics in terms of the direction and pattern of runoff came through the study of 48 cross-section is taken of the Tigris River Year 2008 by section for each 1 km, it has been shown that the average width of the Tigris River does not exceed 221.1 meters and the average depth of 3.9 meters either wet ocean amounted to 268.9 meters and changed the cross-section area of the last section at a rate of 4594.3 square meters, and through the study turned

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