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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 Jul 31 2025
Journal Name
مجلة واسط للعلوم الانسانية
Artificial Intelligence in English Language Education in Iraq: A Review study of Interventions and Perceptions
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AI in teaching English is reshaping language learning. While interest in AI-supported education is growing worldwide, research in this area is still emerging in Iraq. This review synthesizes empirical AI-based intervention studies to enhance English language learning in Iraqi higher education, and the perceptions of stakeholders regarding AI tools in language instruction. The reviewed intervention studies, comprising studies employed different AI platforms to support grammar instruction, speaking fluency, writing feedback, and pragmatic competence. These interventions yielded improvements in learners’ performance, motivation, and communicative confidence. In parallel, perception-focused studies revealed positive attitudes toward A

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Publication Date
Sat Oct 01 2022
Journal Name
The Egyptian Journal Of Hospital Medicine
Study on Viral Infection and Related Parameters in A Sample of Diabetes Mellitus Type 2
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Publication Date
Sat Oct 01 2022
Journal Name
The Egyptian Journal Of Hospital Medicine
Impact of Vitamin D Status on Pregnant Women and Their Neonates: A Cross-Sectional Study
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Publication Date
Sat Jun 18 2022
Journal Name
Sciencescholar Publication
Logical reasoning skills according to Piaget's model for chemistry students in the college of education for pure sciences Ibn al-Haytham in
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Abstract---The aim of the current research is to identify the level of logical reasoning skills in chemistry students at the Faculty of Education for Pure Sciences/ Ibn Al-Haytham for the academic year (2021-2022). The differences in their level of skills according to the gender variable (males and females) and the academic stages (first- second - third - fourth). The descriptive approach was adopted because it corresponds to the nature of the research objectives. The research sample consisted of (400 )students selected in a relatively random stratified way. The researcher constructed a logical reasoning test, which includes (6) sub-skills , which is (proportional - probabilistic- synthetic- deductive- logic- variable adjustment). The psych

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Publication Date
Fri Mar 01 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Impact of Accounting Thought Direction of Fair value on the Relevance: An Applied Study of a Sample of the Listed Banks Listed in the Iraqi Stock Exchange
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In accounting studies, more than one method is used to measure income and balance sheets elements. One of these methods is called the fair value, which use to determine the assets and liabilities ad it includes the benefits or self-satisfaction ability. This paper aims to focus on the importance of fair value as a basis of accounting measurement and its effects to achieve the relevant characteristics by using the equation is used by (Kythreotis) in his research, And Also , Editing this equation depending on the financial data and information of Iraqi Banks as a case.

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
(Determine the Impact of Public Relations Ethics in Strategic Decisions) Descriptive Analytical Study of a Sample of Administrative Leadership in the Ministry of Higher Education
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Role of public relations (PR) and from one community to another, depending on the different cultures of these societies in General, and different ethical values established by their practitioners in these communities organizations  , public relations in developed societies, and in  some developing countries have taken great strides to contribute to the strategic planning and decision-making, in the framework of their commitment to the values and ethical standards for practitioners, In contrast, we find that applied in Iraq still skips phase coordinate with different communication means with the aim of advertising and publicity for the organization. As a result of the limited recognition of the strategic and vital 

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Publication Date
Tue Jun 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The role of Techno strategy of Information management in achieving administrative innovation : A case study in the college of Management and Economics / University of Kirkuk
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The present research aims to identify and define the basic dimensions of the information management strategy and the administrative creativity in the Faculty of Management and Economics / the University of Kirkuk, as well as the role played by the dimensions of the information technology management strategy in achieving the administrative innovation in the college and the research problem was formulated in several questions. The research problem was formulated in several questions centered on the correlation between the research variables, and the research was based on a major hypothesis and five sub-hypotheses emerged from which it was subjected to several tests to ensure its validity. The researcher used the descriptive-analyti

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Evaluate the performance of horizontal flow wetlands as an option for tertiary treatment of secondary sedimentation basins
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Abstract<p>Constructed wetlands (CWs) are simple low-cost wastewater treatment units that use natural process to improve the effluent water quality and make it possible for its reuse.in this study used the horizontal flow system for the tertiary treatment of wastewater effluent from secondary basins at Al-Rustamiya wastewater treatment plant / old project / Baghdad / Iraq. the Phragmites Australis plant was used for wastewater treatment and the horizontal subsurface flow system was applied. the experimental study was carried out in February 2020 to October 2020. the parameters were monitored for a period of five weeks, Concentration-based average removal efficiencies for HSSF-CW were COD,53% [NO</p> ... Show More
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Publication Date
Sun Mar 01 2020
Journal Name
Al-mustansiriyah Journal Of Science
Evaluation the activity of Petroselinum crispum aqueous extract as promoter rooting for stem cuttings of some plants
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This study was conducted in the botanical garden, Department of biology, College of Science/ Mustansiriyah University in from (15 February to 15 March, 2019) under the natural environmental conditions in the greenhouse in order to evaluate the effectiveness of parsley aqueous extract as a promoter for rooting. The study included the use of aqueous extract of a plant Parsley (Petroselinum crispum) extract was used in concentrations (1.25, 2.5 g / l), compare with IBA in concentration (100 mg / L) with dipping time 24 hour for all treatments. The cutting stems were included Rosmarinus officinalis, Nerium oleander, Olea europaea, Plumeria alba, Hibiscus rosa, Pelargonium graveolens, and Myrtus communis. The following measurements were

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Publication Date
Thu Aug 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
Factors that Effect on the Level of Accounting Conservatism A sample study Of insurance companies which listed on the Amman Stock Exchange (2005-2016)
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This study aimed to measure  the accounting conservatism  and the lemited factors which  affected on it in the annual financial reports of insurance companies which listed on the Amman Stock Exchange during the period from 2005 to 2016, these factors were represented by firm age, firm debt and firm size.

Using the market value model (MV) To book value  ( BV) Beaver and Ryan (2000) The level of the accounting conservatism was measured. The study found that the insurance companies which are listed on the ASE exercise the accounting conservatism when they were  preparing financial reports. And when conducting a process  of the test of the affected of the factors (The age of the

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