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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 Mar 01 2010
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
A Proposed Algorithm for Steganography
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Publication Date
Sat Jan 01 2022
Journal Name
Ieee Access
Wrapper and Hybrid Feature Selection Methods Using Metaheuristic Algorithms for English Text Classification: A Systematic Review
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Feature selection (FS) constitutes a series of processes used to decide which relevant features/attributes to include and which irrelevant features to exclude for predictive modeling. It is a crucial task that aids machine learning classifiers in reducing error rates, computation time, overfitting, and improving classification accuracy. It has demonstrated its efficacy in myriads of domains, ranging from its use for text classification (TC), text mining, and image recognition. While there are many traditional FS methods, recent research efforts have been devoted to applying metaheuristic algorithms as FS techniques for the TC task. However, there are few literature reviews concerning TC. Therefore, a comprehensive overview was systematicall

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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
Wed Nov 03 2021
Journal Name
Al-ghary Journal Of Economic And Administrative Sciences
The Role of Marketing Vigilance in Analyzing the Strategic Position of Tourism Organization: A Survey Study of the Opinions of a Sample of Travel and Tourism Companies
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The study aims at studying and analyzing the subject of marketing vigilance as it is one of the modern approaches in the marketing field that can be used to face changes in the competitive and strategic environment and that represents quick reactions on the part of the institution to ensure its survival and distinctiveness other aims are: Consolidating the strength of the marketing organization and its success continuously, represented by changes in the market share, awareness of the institution's position in the market and its relations with competing tourism companies, diversification of tourism services, as well as an analysis of the competitive strategic position of tourism institutions for the purpose of conducting a r

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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
Sun Dec 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The impact of wages and benefits systems on the performance of employees A field study in the General Company for Food Industries in the city of Baghdad
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The research aims to find out the impact of wages and benefits systems on the performance of employees, which included the research community on a sample of employees in the company, and the sample consisted of (50) employees and an employee, A questionnaire composed as prepared (23) paragraph, use the promised statistically methods in data collected by the questionnaire analysis. The research reached a number of results, the most prominent of which were: There is a correlation between wage systems, benefits and performance of employees, and the presence of the impact of the systems of wages and benefits to the performance of employees. The research was presented a set of recommendations including: increasing the effectiveness of

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Engineering
Design of a PID-Lead Compensator for a Twin Rotor Aerodynamic System (TRAS)
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This paper deals with a Twin Rotor Aerodynamic System (TRAS). It is a Multi-Input Multi-Output (MIMO) system with high crosscoupling between its two channels. It proposes a hybrid design procedure that combines frequency response and root locus approaches. The proposed controller is designated as PID-Lead Compensator (PIDLC); the PID controller was designed in previous work using frequency response design specifications, while the lead compensator is proposed in this paper and is designed using the root locus method. A general explicit formula for angle computations in any of the four quadrants is also given. The lead compensator is designed by shifting the dominant closed-loop poles slightly to the left in the

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Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Engineering
Design of a PID-Lead Compensator for a Twin Rotor Aerodynamic System (TRAS)
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This paper deals with a Twin Rotor Aerodynamic System (TRAS). It is a Multi-Input Multi-Output (MIMO) system with high crosscoupling between its two channels. It proposes a hybrid design procedure that combines frequency response and root locus approaches. The proposed controller is designated as PID-Lead Compensator (PIDLC); the PID controller was designed in previous work using frequency response design specifications, while the lead compensator is proposed in this paper and is designed using the root locus method. A general explicit formula for angle computations in any of the four quadrants is also given. The lead compensator is designed by shifting the dominant closed-loop poles slightly to the left in the s-plane. This has the effect

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Publication Date
Sat Oct 01 2022
Journal Name
Baghdad Science Journal
Design of a Simple Dust Removal System for a Solar Street Light System
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      Dust and bird residue are problems impeding the operation of solar street lighting systems, especially in semi-desert areas, such as Iraq. The system in this paper was designed and developed locally using simple and inexpensive materials. The system runs automatically. It Connects to solar panels used in solar street lighting, and gets the required electricity from the same solar system. Solar panels are washed with dripping water in less than half a minute by this system. The cleaning period can also be controlled. It can also control, sensing the amount of dust the system operates. The impact of different types of falling dust on panels has also been studied. This was collected from different winds and studied their impact o

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