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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
Fri Sep 30 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Evaluation of direct withholding tax procedures as a tool to increase tax proceeds : applied research in the General Tax Authority / Direct Deduction Department
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The research aims to evaluate the direct deduction department’s procedures for the process of collecting income tax using the direct deduction method for state departments and the public sector in light of direct deduction tax instructions No. (1) of 2007 and Income Tax Law No. (113) of 1982 (amended) through Giving a clear idea of ​​the reality of tax collection procedures because this type of tax is one of great importance because it contributes to the provision of financial revenues to the state to finance its expenses and direct the economy towards achieving its social, economic and political goals. The researcher makes comparisons between the procedures of the General Tax Authority in collecting the tax and what was approved b

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Publication Date
Thu Sep 01 2022
Journal Name
Iaes International Journal Of Robotics And Automation
Implementation of a complex fractional order proportional-integral-derivative controller for a first order plus dead time system
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This paper presents the implementation of a complex fractional order proportional integral derivative (CPID) and a real fractional order PID (RPID) controllers. The analysis and design of both controllers were carried out in a previous work done by the author, where the design specifications were classified into easy (case 1) and hard (case 2) design specifications. The main contribution of this paper is combining CRONE approximation and linear phase CRONE approximation to implement the CPID controller. The designed controllers-RPID and CPID-are implemented to control flowing water with low pressure circuit, which is a first order plus dead time system. Simulation results demonstrate that while the implemented RPID controller fails to stabi

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Publication Date
Sun Mar 19 2023
Journal Name
Journal Of Educational And Psychological Researches
The Effect of Using the Generative Learning Model on the Achievement of First-Grade Intermediate Students of Chemical Concepts in Science
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Abstract

The current research aims to identify the effect of using a model of generative learning in the achievement of first-middle students of chemical concepts in science. The researcher adopted the null hypothesis, which is there is no statistically significant difference at the level (0.05) between the mean scores of the experimental group who study using the generative learning model and the average scores of the control group who study using the traditional method in the chemical concepts achievement test. The research consisted of (200) students of the first intermediate at Al-Farqadin Intermediate School for Boys affiliated with the Directorate of General Education in Baghdad Governorate / Al-Karkh 3 wit

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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
Comparative Analysis for the Seasonal Variations of the IF2 and T Ionospheric Indices during Solar Cycles 23 and 24
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In this work, a comparative analysis for the behavior and pattern of the variations of the IF2 and T Ionospheric indices was conducted for the minimum and maximum years of solar cycles 23 and 24. Also, the correlative relationship between the two ionospheric indices was examined for the seasonal periods spanning from August 1996 to November 2008 for solar cycle 23 and from December 2008 to November 2019 for solar cycle 24. Statistical calculations were performed to compare predicted values with observed values for the selected indices during the tested timeframes. The study's findings revealed that the behavior of the examined indices exhibited almost similar variations throughout the studied timeframe. The seasonal variations were

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Publication Date
Mon Oct 03 2022
Journal Name
International Journal Of Interactive Mobile Technologies (ijim)
A New Feature-Based Method for Similarity Measurement under the Linux Operating System
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This paper presents a new algorithm in an important research field which is the semantic word similarity estimation. A new feature-based algorithm is proposed for measuring the word semantic similarity for the Arabic language. It is a highly systematic language where its words exhibit elegant and rigorous logic. The score of sematic similarity between two Arabic words is calculated as a function of their common and total taxonomical features. An Arabic knowledge source is employed for extracting the taxonomical features as a set of all concepts that subsumed the concepts containing the compared words. The previously developed Arabic word benchmark datasets are used for optimizing and evaluating the proposed algorithm. In this paper,

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Publication Date
Sun Apr 01 2012
Journal Name
American Journal Of Applied Sciences
A New Strategy for Signaling Overhead Reduction in the Proxy Mobile IPv6 Protocol
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Publication Date
Wed Mar 01 2023
Journal Name
Journal Of Engineering
Recycled Concrete Aggregated for the use in Roller Compacted Concrete: A Literature Review
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The using of recycled aggregates from construction and demolition waste (CDW) can preserve natural aggregate resources, reduce the demand for landfill, and contribute to a sustainable built environment. Concrete demolition waste has been proven to be an excellent source of aggregates for new concrete production. At a technical, economic, and environmental level, roller compacted concrete (RCC) applications benefit various civil construction projects. Roller Compacted Concrete (RCC) is a homogenous mixture that is best described as a zero-slump concrete placed with compacting equipment, uses in storage areas, dams, and most often as a basis for rigid pavements. The mix must be sufficiently dry to support

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Publication Date
Tue Jun 01 2021
Journal Name
Journal Of Planner And Development
Urban sustainability assessment for the urban renewal project in Al Shawaka a rea
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Sustainability is a major demand and need pursued by cities in all areas of life due to the environmental, social and economic gains they provide, especially in the field of city planning and urban renewal projects that aim to integrate the past, present and future.

 

The research aims to evaluate the Haifa Street renewal project, and Al-Shawaka district, one of the Baghdad districts located next to Al-Karkh, was elected by comparing the sustainability indicators of urban renewal with the reality of the situation through a field survey and questionnaire form and focusing on the social and economic impacts and environmental for the project on the study area. To reach the most important conclusions and recommendations

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Publication Date
Fri Nov 30 2018
Journal Name
Iop Conference Series: Materials Science And Engineering
Estimating the PVT Properties for Crude Oil from a Southern Iraqi Oil Field
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Publication Date
Wed Nov 21 2018
Journal Name
International Journal Of Control, Automation And Systems
Design and Stability Analysis of a Fractional Order State Feedback Controller for Trajectory Tracking of a Differential Drive Robot
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