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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
Sun Dec 16 2018
Journal Name
Al-academy
Alienation in Contemporary Sculpture between the Works of Anthony Caro and Tony Cragg (A Comparative Study)
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  • The subject of this research is the study of the formal alienation of contemporary English sculpture, by comparing the most important sculptors of the new contemporary generation. This research problem is to look for the important factors in the formation of the contemporary sculptural structure of the exotic, and what is the mechanism of formation and output of these forms. The research seeks to explore (Alienation in contemporary sculpture between the works of Anthony Caro and Tony Cragg) in a comparative study. The importance of the research is to identify the concept of alien forms in contemporary British sculpture, especially in the cases of Anthony Caro and Tony Cragg that this research is considered a know

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Publication Date
Fri Oct 28 2022
Journal Name
Political Sciences Journal
The Difficulties of Teaching Political Science Research Methods: A Comparative Study between Western and Arab Universities
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This research aims to identify the reality of teaching political science research methods curriculum, to observe practices, and differences in teaching and learning between the Arab and Western universities. Moreover, it focuses on the difficulties that face students' acquisition of the course skills. The research uses the course model of some Western and Arab universities as case study.

This research shows that the curriculum do not reach yet the final form as other political science curriculums, and its upcoming changes will reflect the needs of stakeholders. The best method to teach this curriculum is to use applied learning in groups, learning by doing, and finally problem-based learning approach. Using optimal assessment deep

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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
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Apical Extrusion of Debris and Irrigants After using Different Irrigation Needles and Systems With Different Depth of Penetration (A Comparative Study)
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Publication Date
Sun Mar 06 2022
Journal Name
Al–bahith Al–a'alami
THE ETHICAL RESPONSIBILITY OF THE COMMUNICATOR IN PRESS INSTITUTIONS TO CONSOLIDATE THE VALUES OF TOLERANCE: A Study of the Communicator in the Newspapers (Al-Zaman, Al-Sabah, Al-Mada) For the period: 1/5/2020 to 1/10/2020
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This research deals with the role that the media can play in spreading awareness, culture and sound behavior among members of society, due to its ability to reach the largest number of individuals; its wide spread within society; and the moral responsibility of the media in consolidating the components of civil peace. The media works on forming intellectual convictions and behavioral attitudes by publishing opinions and ideas, introducing them to people's awareness and enhancing them in the practice of their daily lives, he was its media medium. Sociologists and psychologists confirm that the media. The significance of the research comes due to the broadening of violence and sectarian fighting; the absence of a culture of civil social pe

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Publication Date
Thu Nov 13 2025
Journal Name
Journal Of Baghdad College Of Dentistry
A comparative study to evaluate the shear bond strength of different resin sealers to dentin (An in vitro study)
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Background: One of the major problems in endodontics is micro-leakage of root canal fillings which might contribute to the failure of endodontic treatment. To avoid this problem, a variety of sealers have been tested. The objective of this, in vitro, study was to evaluate the shear bond strength of four resin based sealers (AH plus, silver free AH26, RealSeal SE and Perma Evolution permanent root canal filling material) to dentin. Materials and Methods: Forty non-carious extracted lower premolars were used. The 2mm of the occlusal surfaces of teeth were sectioned, to expose the dentin surface. The exposed dentin surfaces of teeth were washed with 5ml of 2.5% NaOCl solution followed by 5ml of 17 % EDTA then rinsed by deionized water to remov

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Publication Date
Tue Apr 18 2023
Journal Name
Al–bahith Al–a'alami
Media policy and its impact on the level of objectivity in the Iraqi media : A study from the communicators’ point of view in the Iraqi medi outlets for the period from (1/5/2021 to 1/9/2021)
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The research aims to reveal the impact of media policy in Iraqi media outlets on the level of objectivity in these outlets. A study from the communicators’ point of view where the researcher used a survey method on the communicators in media outlets to reveal the extent of media policies knowledge as well as the pressures exerted by this policy on communicators in media outlets. It also reveals the extent of their commitment to objectivity, neutrality in dealing with information and the way used to transfer it.
The research sample included (179) respondents from communicators in a range of Media outlets such as (Press, Radio, and Television), The researcher was careful with the diversity of the sample, and

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Publication Date
Wed Dec 15 2021
Journal Name
Al-academy
The aesthetic work of theatrical rehearsal and its directing applications "Taqasim on Al-Hayat Play as a model"
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This research reviews the aesthetic variables that were founded according to (theatrical rehearsal) as one of the most important pillars on which the theatrical process is based, because of its necessity in developing theatrical art on several levels that helped the theatrical director in organizing his work, and this became clear through the research chapters represented in the first chapter (methodological framework) and the second chapter, which consisted of the first topic (the duality of watching / rehearsal) and the second topic (the applications of theatrical rehearsal in theatrical experiences), all the way to the third chapter (research procedures), which included the analysis of theatrical rehearsals (sharing on life), and the

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Publication Date
Tue Aug 15 2023
Journal Name
Al-academy
Trends in Contemporary Ceramic Art and the Overlapping of Stylistic Concepts (Installation Art and Assemblage as a Model)
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Contemporary arts have achieved, in accordance with the transition of concepts, a new logic in presentation and expression in general, and specifically in the field of ceramic art. The shift towards the logic of rejection and subversion of prevailing methods, which have been almost a constant foundation for a long period, has directly influenced the direction of visual arts in the contemporary world.
The growth and cultural transformations that the world has witnessed after the two World Wars have produced cognitive shifts based on strategies that diverge from the dominant culture. These approaches vary according to existential needs, as the language of art has become conceptual and a medium for contemporary culture with its rapid an

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Publication Date
Thu Nov 13 2025
Journal Name
Al–bahith Al–a'alami
The Role of Public Relations in Observing Media Publishing During International Conferences: (Arab Summit 2012 as a Model)
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This study aims to identify the issue of observing media publishing and its importance for public relations in the management of special events; and its role in building the positive image of the target audience through communication messages that illustrate the political, economic and diplomatic importance of the Arab Summit. As such Summit is one of the conferences that Iraq sought to secure the requirements of its convening to re-activate its political and diplomatic role in the Arab Ocean, especially after the circumstances and crises that Iraq went through.

The convening of the Arab Summit under the auspices of Iraq was a qualitative transition, during which Iraq sought to achieve some gains b

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