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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
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
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
Wed Sep 07 2016
Journal Name
Journal Of The Faculty Of Medicine
Non discogenic lumbar radiculopathy ((A study of 104 cases))
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AW Ali T, Journal of the Faculty of Medicine, 2016 - Cited by 1

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Publication Date
Fri Nov 03 2023
Journal Name
Lecture Notes In Electrical Engineering
A Survey Study and Comparison of Drones Communication Systems
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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
Thu Jun 01 2023
Journal Name
Journal Of Composite Materials
Fabrication and characterization of bioactive composite: A pilot study
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The increasing requirement and use of dental implant treatments has rendered dental implantology indispensable in dentistry. The aim of this study is to determine the optimum concentration of calcium silicate to be incorporated into a polyetherketoneketone (PEKK) matrix used as an implant material to enhance the bioactivity and mechanical properties of the composite compared with unmodified PEKK. In this study, different weight percentage (wt%) of micro-calcium silicate (m-CS) is incorporated into PEKK with ethanol as a binder. Subsequently, the mixture is dried in a forced convection oven at 120°C and poured into customized molds to fabricate a bioactive composite via compression molding (310°C, 15 MPa, and 20 min holding time

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Publication Date
Wed Jan 01 2020
Journal Name
Reviews In Medical Microbiology
Molecular study of some virulence genes of Pseudomonas aeruginosa isolated from different infections in hospitals of Baghdad
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One hundred isolates of Pseudomonas aeruginosa were obtained from patients admitted to Baghdad hospitals, Iraq during the period between May 2018 until July 2018. These isolates were distributed as 15 isolates from blood, 25 isolates from urinary tract infections, 10 isolates from sputum, 12 isolates from wounds, 15 isolates from ear infections, 15 isolates from bronchial wash of patients suffering from respiratory tract infections in addition to 8 isolates from cystic fibrosis patients. The isolates were initially identified by culturing on MacConkey agar, blood agar and P. aeruginosa agar then diagnosed by performing some morphological and biochemical tests. The second diagnosis was done by API 20E system followed by Vitek 2 compact syste

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Publication Date
Thu Oct 01 2015
Journal Name
Journal Of Educational And Psychological Researches
Early marriage for the minors: a phenomenon of family violence against children
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It is certain that marriage has the favor of the continuity of human kind since the Prophet Adam till now. But this important event is threatened by some justifications which lead to its delay or abandonment. In the West, sexual relations, illegal friendships, and disrespect of marriage sacredness lead to this delay. While the reasons behind the delay of marriage in the Arab world refer to high dowries, women go out to work, and the religious and scientific ignorance of the need and importance of marriage. The problem also differs according to the difference between the rural and urban regions. On one hand, we find that early marriage is a necessity in the rural regions; on the other hand, the delay of marriage is a clear and nat

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Publication Date
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
The role of road elements in providing a safe environment for pedestrians
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In the years recently city planning projects have been confirmed sustainable high concentration on planning streets and pedestrian paths being the most prominent component of the urban structure in the city and these me and diverse departments link the city’s sectors and serve as a space for economic, service, and social activities. On the other hand, pedestrian traffic is an essential component of the various means of transportation within the city. Suffer cities in the Middle East and Arab cities in particular are neglecting pedestrian paths in the vital urban environment. Vehicle control mechanisms on roads, and changing the uses of pedestrian paths as result of encroaching on the sidewalks designated for pedestrians. Which leads to a

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