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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 Apr 02 2019
Journal Name
Journal Of Environmental Health Science And Engineering
Adsorptive performance of a mixture of three nonliving algae classes for nickel remediation in synthesized wastewater
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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
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
A comparative study of the effects of argon laser and continuous Nd: YAG laser on blood vessel
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Several types of laser are used in experimental works in order to study the effects of laser on blood vessel. They differ from each other by a lot of properties mainly in wavelength, energy of the laser and pulse duration. In this study argon laser (488 nm- 514 nm) and continuous Nd: YAG laSer (1064 nm), have been applied to 50 samples of sheep blgod tesselS. Histologically, tha results of the study were different According to the txpe of L`sar used; apgon larer had distrabtave effects on $he blood vessal while continuous Nd: YAG laser Appeaped to be the safesd one on the blmod vessel architecture. This study concluded that argoj laser has da-aging ef&ect on

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Publication Date
Thu May 30 2024
Journal Name
Proximus Journal Of Sports Science And Physical Education
A COMPARATIVE STUDY OF THE MOST IMPORTANT PERSONALITY TRAITS BETWEEN PRACTITIONERS AND NON-PRACTITIONERS OF SPORTS ACTIVITY
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The researchers reached many conclusions, the most important of which was the distinction of practitioners of sports activity with high degrees in the trait (social). At the same time, it was low in the trait (aggression –restraint-desisting) and non-practitioners were distinguished by sports activity with high degrees in the trait (aggression –restraint-desisting). In contrast, the degree was low in the trait (social), and there were significant differences in favor of practitioners of the activity of the athlete, Through the conclusions, the researchers recommend the need for university students to practice sports activities because of their positive impact on their health in general and on the deve

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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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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
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
Fri Aug 11 2023
Journal Name
Communications In Mathematical Biology And Neuroscience
Three-species food chain model with cannibalism in the second level
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This article suggests and explores a three-species food chain model that includes fear effects, refuges depending on predators, and cannibalism at the second level. The Holling type II functional response determines food consumption between stages of the food chain. This study examined the long-term behavior and impacts of the suggested model's essential elements. The model's solution properties were studied. The existence and stability of every probable equilibrium point were examined. The persistence needs of the system have been determined. It was discovered what conditions could lead to local bifurcation at equilibrium points. Appropriate Lyapunov functions are utilized to investigate the overall dynamics of the system. To support the a

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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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