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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
Thu Dec 24 2020
Journal Name
Psychology And Education
The Use of Ergative Verbs to Background the Role of the Agent in two Selected Short Stories: A Syntactico-Semantic Study
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The study explores the use of ergative verbs in constructing clauses and their impact on the backgrounding of the agent's role in two selected short stories. Contrary to hypothesis No. 1, the research indicates that changes in sentence patterns don't affect the meaning of the process. Additionally, hypothesis No. 2 is refuted as the middle structure is found to highlight the agent's role in the science fiction short story, Terra Infirmum, rather than concealing it as hypothesized for "The Invisible Man." The analysis uncovers that writers utilize ergative processes to narrate stories in various ways, including transitive/active voice, intransitive/active voice, and transitive/passive voice. Furthermore, the findings suggest that writers emp

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Publication Date
Sun Feb 22 2026
Journal Name
Al–bahith Al–a'alami
THE SEMIOTICS OF PROPAGANDA SPEECH IN SOCIAL MEDIA SITES (A Semiotic Study of the News Reports on the Israeli "Makan" Channel)
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Technological and digital development has allowed the emergence of many methods of producing semantics on social media sites within semiotic and propagandistic frameworks. This is what made the image appear in different molds and shapes, especially as it is the first material for visual perception.
This made the Israeli propaganda discourse use it as an important tool to manage the content of suggestive messages with semiological connotations. By doing so, such tool uses social networking sites as an appropriate environment to achieve those goals, which are related to cases of manipulating emotions and minds. It, moreover, changes convictions, attitudes, trends and behaviors according to what the propaganda planner wants.
Many Isra

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
The Role of the Auditor in Confirming the Integrated Reports - An Exploratory Study on a Sample of External Auditors in Iraq-
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  The aim of the research is to identify the extent of the ability to ensure the integrated reports by the auditor in verifying the credibility of these reports, and their implications for the benefit of all parties dealing with the economic unit, as well as measuring the impact of the assurance procedures followed by the auditors and their role in confirming these reports.

  The research methodology was designed after studying the previous literature related to the research variables, and then the relationship between these variables was tested, through the use of a questionnaire list. A questionnaire targeting the community of auditors in the local environment, and the results of the study wer

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
The Role of the School Garden, and its Importance in the school Building - A field study in the social school service
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This research concerns the fact of the school garden and how can we tackle this issue. The research starts with a question forwarded to those who are interested in the ministry of education matters; the question is that how is the extent of interest in the school garden project? And how it is activated in the Iraqi Educational Institution program? In addition, the analysis reveals the importance of the school garden since we, as teachers and students, suffer from seeing the view of the trashes, the wastes of school furniture, the stinking water and the weeds and how it is accumulated in the back yard of the school. To add fuel to the fire, the increase in number of the students; year after year. This increase leads to adding more classes

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Publication Date
Tue Nov 03 2020
Journal Name
Modern Sport
Exercises based on the phosphogenic energy system to develop the ability to perform with precision and accuracy
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Each sport has its own energy requirements that differ from the energy requirements of other sports, and a different method is used in each of them, so the trainer must first rely on the principle of privacy in training first, that is, privacy according to the working energy system, that is, he defines the controlling energy system In that event, and how the muscles use the available energy to perform according to the energy production systems. As we find the serving skill is the first volleyball skill with which the team starts the match in order to be able to gain points directly, through knowledge it turns out that there is a weakness in the skill performance, especially the skill of serving and being The key to victory for volle

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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
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
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
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
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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