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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 Aug 18 2025
Journal Name
Journal Of Genetic And Environment Conservation
Ultrasound application as a new green technology for preservation of table eggs: A review
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In recent years, there has been a significant increase in research demonstrating the new and diverse uses of non-thermal food processing technologies, including more efficient mixing and blending processes, faster energy and mass transfer, lower temperature and selective extraction, reduced thermal and concentration gradients, reduced equipment size, faster response to extraction control, faster start-up, increased production, and a reduction in the number of steps in preparation and processing. Applications of ultrasound technology have indicated that this technology has a promising and significant future in the food industry and preservation, and there is a wide scope for its use due to the higher purity of final products and the

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Publication Date
Sun May 02 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Value at risk simulation in a fixed return stock portfolio using the Monte Carlo simulation model The concept of a bond portfolio
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This research aims to predict the value of the maximum daily loss that the fixed-return securities portfolio may suffer in Qatar National Bank - Syria, and for this purpose data were collected for risk factors that affect the value of the portfolio represented by the time structure of interest rates in the United States of America over the extended period Between 2017 and 2018, in addition to data related to the composition of the bonds portfolio of Qatar National Bank of Syria in 2017, And then employing Monte Carlo simulation models to predict the maximum loss that may be exposed to this portfolio in the future. The results of the Monte Carlo simulation showed the possibility of decreasing the value at risk in the future due to the dec

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Publication Date
Mon Jan 01 2018
Journal Name
Al–bahith Al–a'alami
The Role of TV Programs in Spreading the Culture of Community for Peace: Studying the Attitudes of the Publics towards a Program entitled Mosamih Kareem on YouTube
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The fundamental problem in determining the role of television programs in broadcasting the culture of community for peace through studying almosamig kareem program by studying the topics addressed in this program. It is a descriptive study and it follows the approach survey method.  In this study, the spatial framework is limited to the program of almosamih kareem on YouTube, while the temporal framework is concerned with the episodes that are raised on YouTube from the second half of 2014 to 2015 of almosamih kareem program. The fundamental problem in determining the role of television programs in broadcasting the culture of community for peace through studying almosamig kareem program by studying the topics addressed in this

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Publication Date
Mon Feb 19 2018
Journal Name
Al-academy
The Mechanisms of build up the dramatic construction in the films of the world of nature - National Geographic's films as a model-
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The subject of  research entitled "The Mechanisms of build up the dramatic construction in the films of the world of nature - National Geographic's films as a model" emerges from the importance of the subject of the dramatic construction and its departure from its classic style due to the evolution of the visual  presentation and its instruments and the specificity and emergence of a form of television production represented by the films of the world of nature which began to occupy an important space in the map of television and television channels specialized in this subject, which drove the researcher to study the mechanisms of producing the dramatic construction in this kind of film s. This research came in three  chapt

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Publication Date
Tue Nov 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Performance evaluation of policies and programs accordance with guide prepared by a dutch court of audit and the board of supreme audit (case study in wasit state company for textile industries)
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Abstract\

preparation process of performance evaluation in organizations is of extreme importance, and under development in organizations and the opening of markets and technological developments in the industry and heightened competition among industrial organizations imposed systems are built for performance give a clear picture about performance and competition,  And centered research problem in answering the following questions: Is performance evaluation system is available in Wasit State Company for Textile Industries(Research sample ), This research aims to assess the performance of policies and programs in the company, according to guide performance evaluation of programs and policies prepared by the Dutch Cou

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Publication Date
Sun Jun 07 2015
Journal Name
Baghdad Science Journal
A comparative study to determine the nature of the eye lens protein in the two types of birds Iraqi
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The study showed significant differences between the average weight lens and the average amount protein in the lens between that Kestrel Falco tinnunculus L. and the Collared Dove Streptopelia decaocto F. , also the study electrical migration of lens proteins having one bundle of crystalline –? in Kestrel compared with three bundles in Collared Dove, two bundles of crystalline – ? in both , and crystalline – ? appeared as one bundle in both birds.

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Publication Date
Wed Jul 01 2020
Journal Name
Plant Archive
A comparative taxonomic study of seeds of some plants of rosaceae family in Iraq
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Publication Date
Wed Oct 01 2025
Journal Name
Al–bahith Al–a'alami
Selective Exposure Patterns to the Iraqi Daily Newspapers and Its Motives for Iraqi University Students (College of Mass Communication - University of Baghdad as a Model)
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This study examines patterns of exposure of Iraqi university students to selective daily Iraqi newspapers and the motives of this exposure, as well as its associated factors that affect the average exposure. It tries to answer several questions, including those related to the levels of exposure of Iraqi university students to daily Iraqi newspapers and classification of patterns of selective exposure to daily Iraqi newspapers and the most prominent Iraqi daily newspapers that are selectively exposed by Iraqi university students. It also examines the motives of this selective exposure and factors that increase the degree of exposure to the daily Iraqi newspapers, and the most prominent stages in which Iraqi university students find their

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Publication Date
Tue Jul 01 2014
Journal Name
International Journal Of Artificial Intelligence And Mechatronics
Building a Three-Axis CNC Milling Machine Control System
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CNC machines are widely used in production fields since they produce similar parts in a minimum time, at higher speed and with possibly minimum error. A control system is designed, implemented and tested to control the operation of a laboratory CNC milling machine having three axes that are moved by using a stepper motor attached to each axis. The control system includes two parts, hardware part and software part, the hardware part used a PC (works as controller) connected to the CNC machine through its parallel port by using designed interface circuit. The software part includes the algorithms needed to control the CNC. The sample needs to be machined is drawn by using one of the drawing software like AUTOCAD or 3D MAX and is saved in a we

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Publication Date
Tue Apr 01 2025
Journal Name
Iop Conference Series: Earth And Environmental Science
A Comparative Study of Organic and Mineral Acids in the Release of Potassium from Potassium Feldspar Minerals
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Abstract<p>A study conducted a laboratory experiment to measure the release of potassium and the dissolution of feldspar minerals in soils from different locations in Karbala Province (Ain Al-tamur, Qasr Al-Akhyar, Fadak Farm). The study involved the addition of organic acids (fulvic and humic) and mineral acids (sulfuric and phosphoric) at concentrations of 5% and 10% to sand-separated soil samples obtained through wet sieving. Feldspar minerals were identified using a polarized light microscope, and the percentage of each type of feldspar mineral was calculated. The results demonstrated that organic acids outperformed mineral acids in releasing potassium at both concentrations. Among the organ</p> ... Show More
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