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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
Fri Nov 09 2018
Journal Name
International Journal Of English Linguistics
A Discourse Analysis Study of Comic Words in the American and British Sitcoms
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DBN Rashid, International Journal of English Linguistics, 2019 - Cited by 2

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Publication Date
Sun Feb 10 2019
Journal Name
Journal Of The College Of Education For Women
A Study of Person Deixis in J. M. Singe's Riders to the Sea
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This study deals with an important area in the field of linguistics, namely person deixis.
The study aims at: (1) Describing the notion of deixis, its importance, and its place in the field
of linguistics, (2) Presenting a detailed illustration of person deixis, and (3) Conducting an
analysis of person deixis in one of Synge‟s plays Riders to The Sea according to Levinson‟s
model. The most important aim of these three is the third one (the analysis). To achieve this
aim, the researcher depends on Levinson‟s (1983) descriptive approach. According to the
descriptive approach of deixis, the category of person deixis can be defined as the encoding of
the participant roles in the speech situation. This encoding is r

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Publication Date
Fri Jun 06 2025
Journal Name
Discover Education
A qualitative study on the beliefs and perceptions of inaugural PharmD program graduates
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Background There is an increasing need for pharmacists to incorporate more patient care targeting. Consequently, the productivity of pharmacy programs can be enhanced by evaluating the advantages and disadvantages of pharmacy curriculum. Objectives To assess the beliefs, perceptions, and challenges of the College of Pharmacy –The University of Baghdad PharmD graduates regarding the PharmD program. Method Qualitative research methodology was implemented. Graduate PharmD candidates were interviewed either inperson or via telephone. The interviews were conducted in a semi-structured format, utilizing a predetermined interview guide that included open-ended questions. Thematic analysis was implemented to analyze the data. Results A total of 2

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Publication Date
Mon Jan 01 2024
Journal Name
Corporate And Business Strategy Review
The role of strategic agility in promoting organizational excellence: A descriptive analytical study
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The study aims to build a model that revolves around the main question of the role of strategic agility (SA) in enhancing organizational excellence (OE). For the purpose of achieving OE and to determine the extent of interest and knowledge of managers at the Midwest Refineries Company (MRC) on the theoretical and practical implications, and on the performance foundations of these two vital variables with the aim of continuous improvement. A questionnaire was used and distributed to a random sample of 54 managers in this important energy production company. The study followed the descriptive analytical approach to answer the questions raised. The study model and dimensions were built according to reference models, most notably the mo

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Publication Date
Fri Apr 26 2024
Journal Name
Corporate And Business Strategy Review
THE ROLE OF STRATEGIC AGILITY IN PROMOTING ORGANIZATIONAL EXCELLENCE: A DESCRIPTIVE ANALYTICAL STUDY
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he study aims to build a model that revolves around the main question of the role of strategic agility (SA) in enhancing organizational excellence (OE). For the purpose of achieving OE and to determine the extent of interest and knowledge of managers at the Midwest Refineries Company (MRC) on the theoretical and practical implications, and on the performance foundations of these two vital variables with the aim of continuous improvement. A questionnaire was used and distributed to a random sample of 54 managers in this important energy production company. The study followed the descriptive analytical approach to answer the questions raised. The study model and dimensions were built according to reference models, most notably the models (Al-

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Publication Date
Thu Jan 20 2022
Journal Name
Webology
The Effect of Strategic Information System in Global Marketing Channel: A Case Study
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The research dealt with the issue of strategic information systems and its impact on the global marketing channel. As the research aims to know the strategic information systems used in the cement company. Which support the senior management in supporting decisions taken in the process of global orientation and moving to foreign markets by choosing the marketing channel that will suit the company. Product and competition with it. With other companies' products. The problem of the study focused on how to move to global markets, and any marketing channel that can be followed to move the cement product globally, what are the strategic information systems used in the company and how will it contribute to supporting senior management dec

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Publication Date
Sun Dec 02 2018
Journal Name
Journal Of The College Of Education For Women
The Famous Muslims' Graveyards in the Persian Country in the Islamic Ages: A Historical Study in the Maraqid Al-Maaraf Book for Harz Aldeen
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There are many studies that discussed the famous museum's graveyards in the Islamic worlds, to study the lives of these figures, there are many difficulties for their studies because the first we need the regularity and history information, and many sciences support, such as in language, geography information.

I am studying the research from Maraqid Al-Maaraf book by Harz Aldeen, the book has large members about the persons have graved in Persian Country in the middle ages, there are more than (30) figures in my study, I have studied every figure in this research depending on the sources and references books.

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Publication Date
Sat Dec 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
Business incubators the entrance of organizations to shift towards pioneering performance a study by a number of employees of the technical education organizations in mosul
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     The importance of this research is due to its importance goals, Which are about the attempt of researchers to investigate the probability of depending on businesses, environments to transform organizations, performance in away that enhance the leading  role of organizations  in their environments , and through views of a number of the staff working in the foundation of technical institutes in Mosul.  .

     After deciding the methodology of the study that ,in one hand ,performs the goals of the study , and achieving a suitable theoretical framework to present the concepts of businesses, environments and the leadin

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Publication Date
Wed Jan 01 2020
Journal Name
Karbala Journal Of Physical Education Sciences
The effect of using a designed device to develop the technical performance of the descending landing skill facing with half a cycle on the parallel device of the technical men's
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The research included five sections containing the first section on the introduction of the research and its importance and was addressed to the importance of the game of gymnastic and skilled parallel effectiveness and the importance of learning, but the problem of research that there is a difference in learning this skill and difficulty in learning may be one of the most important reasons are fear and fear of falling and injury, And a lack of sense of the movement of the movement is one of the obstacles in the completion of the skill and the goal of research to design a device that helps in learning the skill of descending Almtor facing with half a cycle according to the typical locomotor track on the parallel device of the technical men'

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
Comparative study of the antioxidant effects of lavender and flax oils in recurrent aphthous ulceration treatment
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Background: Recurrent aphthous ulceration (RAU) is an inflammatory condition of unknown etiology characterized by painful recurrent (single or multiple) ulcerations of the oral mucosa. It is one of the most common and poorly understood mucosal disorders. It occurs more frequently in times of stress. Local and systemic conditions, genetic, immunologic, microbial factors, and oxidative stress may play a role in the pathogenesis of RAU. The objective of this study was to evaluate the free radical metabolism and antioxidant activity of RAU patients treated by lavender or flax oil paint.

Materials and Methods: Sixty-six RAU patients were enroll

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