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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
Mon Dec 14 2020
Journal Name
The Fourth International Conference Of Linguistic Studies
A pragmatic study of refusals among Iraqi EFL learners
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The speech act of refusals has been studied widely either alone or in relation to such areas as apology, requests, promotion, and invitation. The present study aims to investigate the strategies employed by Iraqi females in refusing marriage proposals. It attempts to explore their preferences to respond directly or indirectly in relation to their ages and educational background of the parents. The sample of the study consists of 25 participants; they are learners of English as a foreign language (EFL) at the College of Education for Women/ University of Baghdad. The data are collected by using a discourse completion task (DCT) followed by a follow up interview. The researchers used a Google form shared via emails to get responses from the p

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Publication Date
Tue Feb 01 2022
Journal Name
Baghdad Science Journal
Application of Groebner Bases to Study a Communication System
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This paper introduces a relationship between the independence of polynomials associated with the links of the network, and the Jacobian determinant of these polynomials. Also, it presents a way to simplify a given communication network through an algorithm that splits the network into subnets and reintegrates them into a network that is a general representation or model of the studied network. This model is also represented through a combination of polynomial equations and uses Groebner bases to reach a new simplified network equivalent to the given network, which may make studying the ability to solve the problem of network coding less expensive and much easier.

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Publication Date
Fri Feb 02 2024
Journal Name
Kurdish Studies
A Linguistic Study of Metaphorical Expressions in Political Interviews
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In recent years, the linguo-philosophical studies of metaphor have tended to define metaphor as an interaction of the object, that is the referent of conceptualization and some features that are associated with sensual manner realities, whose name is used when resolving the conceptual problem-nominative situation, namely the situation of the formation of a new concept and its verbalization. The objective of this term paper lies in the phenomenon of metaphors used in modern political discourse. In our understanding a metaphor is not only of a linguistic nature, but also political. This paper approaches the subject of conceptual metaphor and political argumentation through the prism of synergies of the political topic, affirmative or negative

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Publication Date
Wed Nov 01 2023
Journal Name
Journal Of Sustainable Studies
A Socio-Pragmatic Study of Insulting in English News
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Media has become a common platform for communication as a tool of offense. English language has many insult words which are commonly used in the world of media. This study investigates the socio-pragmatic aspect of insulting in English news. It aims at identifying and analysing insult words and expressions used by news presenters. To specify the problem of the study, language has a harmful power that hurts the addressees and seriously harm their psychological well-being. The insulting words that are an element of all human languages are the source of this abusive power. The study questions sought to find out are if news presenters use insult words, which insult words, and in what social contexts. In this study, the descriptive method is use

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Publication Date
Sun May 01 2022
Journal Name
Journal Of Engineering
Parametric Study of a Two-Phase Closed Thermosyphon Loop
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A theoretical and experimental investigation was carried out to study the behavior of a two-phase closed thermosyphon loop (TPCTL) during steady-state operation using different working fluids. Three working fluids were investigated, i.e., distilled water, methanol, and ethanol. The TPCTL was constructed from an evaporator, condenser, and two pipelines (riser and downcomer). The driving force is the difference in pressure between the evaporator and condenser sections and the fluid returns to the heating section by gravity. In this study, the significant parameters used in the experiments were filling ratios (FR%) of 50%, 75%, and 100% and heat-input range at the evaporator section of 215-860.2 W. When the loop reached to

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Publication Date
Sun Oct 31 2021
Journal Name
Iraqi Geological Journal
Optimizing Water Injection Performance by Using Sector Modeling of the Mishrif Formation in West Qurna-1 Oil Field, Southern Iraq
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The regular job of a reservoir engineer is to put a development plan to increase hydrocarbon production as possible and within economic and technical considerations. The development strategy for the giant reservoir is a complex and challenging task through the decision-making analysis process. Due to the limited surface water treatment facility, the reservoir management team focuses on minimizing water cut as low as possible by check the flow of formation and injected water movement through the Mishrif reservoir. In this research, a representative sector was used to make the review of water injection configuration, which is considered an efficient tool to make study in a particular area of the entire field when compared with the ful

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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
Discretionary Punishment (Al-Ta'zir) for the Interest and its Effect in Keeping the Public Regulation A Fundamental Applied Study in the Saudi Arabian Courts
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Discretionary Punishment, Public Regulation, Interest

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Publication Date
Sun Jan 10 2021
Journal Name
Open Access Macedonian Journal Of Medical Sciences
Comparative Study between Neopterin and Alvarado Score in the Diagnosis of Acute Appendicitis and Its Severity
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BACKGROUND: Acute appendicitis (AA) remains a complex case even for experienced surgeons. Rate of negative appendectomy is 5–40% and delayed intervention result in perforated appendicitis in 5–30% of cases. AIM: The aim of the study was to evaluate NPT as a marker for the diagnosis of AA concerning its severity. And compare the diagnostic value of it with the ALV scoring system. METHODS: One hundred twenty patients presented with signs and symptoms of AA and underwent appendectomy, only 84 patients proved to be AA by histopathological examination, were included in the study. Blood samples for neopterin (NPT) estimation and Alvarado (ALV) score was calculated. Control group consists of 45 healthy individual. RESULTS: NPT levels were s

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Publication Date
Tue Jun 30 2015
Journal Name
Al-kindy College Medical Journal
Serum anti-Mullerian hormone level as a marker of polycystic ovarian syndrome in Iraqi women
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Background: Polycystic ovarian syndrome is one of the common gynaecological diseases encountered nowadays in the gynaecological clinic. Many criteria and diagnostic test had been evolved to be used with different classifications methods.Objectives: The present study aimed to measure the anti-mullerian hormone levels in serum of the women with Polycystic Ovary Syndrome and to test the possibility that if it can be used as a marker for diagnosis of polycystic ovary syndrome patients.Methods: A cross sectional study that had been conductedat Kamal AL-Samaraee Hospital, AL-Suwayrah Hospital andAl-Elwiya Maternity Teaching Hospital during the periodfrom July, 1st, 2013 – Jan. 1st, 2014. Where forty women withPolycystic ovarian syndrome (wit

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Publication Date
Sat Mar 31 2018
Journal Name
Journal Of Engineering
Potential of Microalgae Cultivation in Dairy Wastewater as a Step in Low-Cost Biofuel Production
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The present study addresses adopting the organic and nutritious materials in dairy wastewater as media for cultivation of microalgae, which represent an important source of renewable energy. This study was carried out through cultivation of three types of microalgae; Chlorella sp., Synechococcus, and Anabaena. The results shows the success the cultivation of the Synechococcus and  Chlorella Sp, while the Anabaena microalgae were in low-growth level. The highest growth was in the Synechococcus farm, followed by Chlorella and Anabaena. However, the growth of Synechococcus required 10 days to achieve this increase that re

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