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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 Oct 01 2009
Journal Name
Journal Of The College Of Languages (jcl)
A RAISIN IN THE SUN: the dream of RECOGNITION
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Lorraine Hansberry’s A Raisin in the Sun (1959) appeared at the beginning of renewed political activity on the part of the blacks; it is a pamphlet about the dream of recognition of black people and the confusion of purposes and means to reach such recognition. It embodies ideas that have been uncommon on the Broadway stage in any period. Situations such as a black family moving into an all-white neighborhood were not familiar before this time; they were just beginning to emerge. In depicting this so realistically, Hansberry depends more on her personal experience as an African American embittered by social prejudices and discrimination. 

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Publication Date
Fri Dec 15 2017
Journal Name
Journal Of The College Of Education For Women
Identity in Sonia Sanchez's Poem "right on: white america" :A Stylistic Study
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Language is an important means through which one can construct one's social world. Accordingly, the way we view ourselves and the world is basically formed by language use whereby identities, relations, and values are constructed and maintained. Most discourse analysts consider narrative not only the locus of construction and enactment of identity, but also a distinguished genre for its analysis.The present study is concerned with how identity can poetically be informed, hence exploring the way black poets use language when reflecting their identity and culture. The poem, right on: white america by the black American poetess Sonia Sanchez, is chosen to be analyzed based on Simpson's stylistic model (2004). In this model, the ana

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Publication Date
Sat Feb 15 2025
Journal Name
Iraqi Journal Of Pharmaceutical Sciences
Physician and Medical Representative Interaction in Iraqi Private Sector: A Qualitative Study
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Pharmaceutical companies assign a budget for activities and promotions that aim to change the prescription habits of the physicians to choose the most suitable medications for their patients, which will eventually grow their sales. The study's objectives were to explore physicians' and medical representatives' perspectives on the criteria of impactful professional PP and the factors influencing the interaction between physicians and medical representatives. Qualitative in-depth interviews with flexible probing techniques were carried out in 2023. A semi-structured, open-ended interview questionnaire was used to interview physicians and medical representatives (MRs) from different private clinics in several governorates in Iraq. Ten physicia

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Publication Date
Wed Mar 01 2023
Journal Name
Baghdad Science Journal
A Study on Nψβ and Nβψ - Closed sets in Neutrosophic Topological spaces
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The aim of this paper is to introduce the concept of N  and Nβ -closed sets in terms of neutrosophic topological spaces. Some of its properties are also discussed.

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Publication Date
Wed Dec 30 2020
Journal Name
Al-kindy College Medical Journal
A Population-Based Study on Agreement between Actual and Perceived Body Image
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Background: Obesity tends to appear in modern societies and constitutes a significant public health problem with an increased risk of cardiovascular diseases.

Objective: This study aims to determine the agreement between actual and perceived body image in the general population.

Methods: A descriptive cross-sectional study design was conducted with a sample size of 300. The data were collected from eight major populated areas of Northern district of Karachi Sindh with a period of six months (10th January 2020 to 21st June 2020). The Figure rating questionnaire scale (FRS) was applied to collect the demographic data and perception about body weight. Body mass index (BMI) used for ass

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Publication Date
Fri Mar 04 2022
Journal Name
Journal Of Water Resources And Geosciences
A Review Study on Gypseous Soils Stabilized with Different Additives in Iraq
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Publication Date
Thu May 30 2024
Journal Name
Iraqi Journal Of Science
A Review Study on Forgery and Tamper Detection Techniques in Digital Images
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Digital tampering identification, which detects picture modification, is a significant area of image analysis studies. This area has grown with time with exceptional precision employing machine learning and deep learning-based strategies during the last five years. Synthesis and reinforcement-based learning techniques must now evolve to keep with the research. However, before doing any experimentation, a scientist must first comprehend the current state of the art in that domain. Diverse paths, associated outcomes, and analysis lay the groundwork for successful experimentation and superior results. Before starting with experiments, universal image forensics approaches must be thoroughly researched. As a result, this review of variou

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Speech Acts Through Ages - A Comprative Study between Traditional and Modren Approches
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This study has been developed axes of the search, including: Search (deliberative) language and idiomatically, and Description Language (b social phenomenon), and the definition of the theory of (acts of speech), and discussed the problem of the conflict between tradition and innovation, as defined objectively have a target aimed at reviving the deliberative thought when Arab scholars , and the balance between the actual done Arab and Western rhetoric, but Meet in intellectual necessity, a sober reading that preserve the Arab language prestige, and its position in the light of the growing tongue Sciences, as long as we have inherited minds unique, and heritage huge able to consolidate the Arab theory lingual in linguistics.

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Publication Date
Sat Sep 30 2023
Journal Name
Journal Of The College Of Education For Women
Topic Management in Selected Dementia Patients' Speeches: A Clinical Discourse Analysis Study
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Topic management is the awareness of how speakers deal with initiating, developing, changing, and ending a topic and how they fix the relationship when a misunderstanding occurs. It is such an important unit of conversation as it includes the transition from one strategy to the other to be accomplished in a systematic and orderly manner. These strategies are impaired in dementia patients thus lead to communication breakdown. This study aims at detecting the dementia patients' topic management strategies in selected speeches and answering the questions of which of these strategies are fully or partially detected in these speeches. The researchers use a qualitative method to examine the speeches of those patients and they adopt an eclectic

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Publication Date
Tue Dec 19 2023
Journal Name
Journal Of Ethnic And Cultural Studies
Request Constructions in Classical Arabic versus Modern Arabic: A Corpus-based Study
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The present study aims to investigate the various request constructions used in Classical Arabic and Modern Arabic language by identifying the differences in their usage in these two different genres. Also, the study attempts to trace the cases of felicitous and infelicitous requests in the Arabic language. Methodologically, the current study employs a web-based corpus tool (Sketch Engine) to analyze different corpora: the first one is Classical Arabic, represented by King Saud University Corpus of Classical Arabic, while the second is The Arabic Web Corpus “arTenTen” representing Modern Arabic. To do so, the study relies on felicity conditions to qualitatively interpret the quantitative data, i.e., following a mixed mode method

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