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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 Jul 01 2024
Journal Name
Journal Of Language Teaching And Research
Emotional Blackmail in Breaking Bad Series: A Pragma-Stylistic Study
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Although language research has focused on blackmail in general, less attention has been paid to emotional blackmail. To date, researchers could not locate any literature that examines emotional blackmail from a linguistic standpoint. The current study is intended to fill this gap by scrutinizing emotional blackmail from a pragma-stylistic point of view by examining the style of the characters in selected episodes extracted from the American Breaking Bad series. To carry out the study, an eclectic model comprising kinds of emotional blackmailers by Forward and Frazier (1997), Searles’ speech acts (1979), Grice’s maxims (1975), Brown and Levinson’s politeness (1987), Culpeper’s impoliteness (1996), and Simpson’s stylistic le

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
A Study on Cosmetic Products Marketed in Iraq: Microbiological Aspect
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Cosmetic products contain variable amounts of nutrients that support microbial growth. Most contaminants   in   cosmetic   products   include bacteria such as Staphylococcus, Pseudomonas, Klebsiella,   Achromobacter   and   Alcaligenes. Contaminated water  is  a  likely  source  of organisms found in cosmetic products. Products such as shampoo, hand and body lotion, facial cleanser,  and liquid soaps were analyzed. In this study, out of 60 cosmetic products analyzed, 26.4% were found to be contaminated.    Most of the contamination was from bacteria and no fungal contamination was detected.  The highest level o

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Publication Date
Thu Aug 25 2022
Journal Name
Ira International Journal Of Education And Multidisciplinary Studies
Gender and Olds’ Advice in Written Signs: A Pragmatic Study
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Giving advice refers to an attempt by the speaker to express what the addressee should do in a particular situation or what is good for him/her. It is also a feature of making social relations and communications move smoothly and become stronger. The current study aims to investigate the strategies of the speech act of advice by old females and males for the younger generation in written signs. Comparison is made between old females and males regarding their pragmatic use of advice and the way they are manifested in expressing gender identity differences. The sample of the study consists of (30) written signs of advice divided equally between the two gender groups. Hinkel’s (1997) classification of the strategies for perceiving th

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Publication Date
Fri Feb 14 2020
Journal Name
Progress In Industrial Ecology, An International Journal
3D image reconstruction from its 2D projection - a simulation study
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A simulation study of using 2D tomography to reconstruction a 3D object is presented. The 2D Radon transform is used to create a 2D projection for each slice of the 3D object at different heights. The 2D back-projection and the Fourier slice theorem methods are used to reconstruction each 2D projection slice of the 3D object. The results showed the ability of the Fourier slice theorem method to reconstruct the general shape of the body with its internal structure, unlike the 2D Radon method, which was able to reconstruct the general shape of the body only because of the blurring artefact, Beside that the Fourier slice theorem could not remove all blurring artefact, therefore, this research, suggested the threshold technique to eliminate the

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Engineering
Modeling and Simulation of Solar Module performance using Five Parameters Model by using Matlab in Baghdad City
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This work presents the modeling of the electrical response of monocrystalline photovoltaic module by using five parameters model based on manufacture data-sheet of a solar module that measured in stander test conditions (STC) at radiation 1000W/m² and cell temperature 25 . The model takes into account the series and parallel (shunt) resistance of the module. This paper considers the details of Matlab modeling of the solar module by a developed Simulink model using the basic equations, the first approach was to estimate the parameters: photocurrent Iph, saturation current Is, shunt resistance Rsh, series resistance Rs, ideality factor A at stander test condition (STC) by an ite

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Publication Date
Thu Aug 01 2024
Journal Name
Al-kindy College Medical Journal
Through the Eyes of Healthcare Providers, the Necessity and Challenges of Implementing Medication Reconciliation at Hospital Discharge: A Qualitative Study
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Background: Medication reconciliation can include medication reviewing and providing counseling and a list of all the medications during every transition of care. Objectives: to explore in-depth the perspectives of Iraqi physicians and pharmacists regarding the necessity of medication reconciliation at hospital discharge and identify the possible benefits and challenges that could face its implementation. Subjects and Methods: A qualitative study included semi-structured interviews with pharmacists and physicians working at a public teaching hospital in Iraq. The interviews were conducted face-to-face from February to March 2023. Thematic analysis was used to analyze the qualitative data generated from the interviews. Results: In th

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Publication Date
Wed Sep 21 2022
Journal Name
Journal Of Planner And Development
The effect of technology on achieving contemporary levels in the space of Arab Islamic architecture “Mosques is a case study”
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Arab-Islamic architecture has undergone a change at multiple levels affected by modern technology, so the research sought to address the role of contemporary technologies on a fundamental and fundamental component of architecture, which is the architectural space, what is known as the essence of architecture and its ultimate destination, with a focus on the architectural space in the architecture of the contemporary Arab Islamic mosque, because the mosque’s architecture is so important in Islamic law and the belief of the Muslim person himself, where the mosque is the functional style produced by the Islamic faith and embodied in it, whereas, knowing the levels of influence of contemporary technologies in the architectural spac

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Study the effect of fish on the optical properties of CuO membranes prepared in a way that thermal spraying chemical
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In this research study the effect of fish on the properties optical films thickness 1200-1800 and calculated energy gap Basra direct transport permitted and forbidden to membranes and urged decreasing values ??of Optical Energy Gap increase fish included accounts optical also calculate the constants visual as factories winding down and the refractive index and reflectivity membranes also by real part and imaginarythe dielectric constant

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Publication Date
Tue Nov 01 2022
Journal Name
Rimak International Journal Of Humanities And Social Sciences
THE PRESS TREATMENT OF THE VISIT OF "POPE FRANCIS" AND ITS REPERCUSSIONS ON COMMUNITY PEACE IN IRAQ... A SURVEY STUDY...
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The importance of the research from a practical point of view lies in the fact that it presents a set of statistics and data that give a clear picture of how the Iraqi newspapers (the subject of the study) deal with the visit of "Pope Francis" to Iraq ، and what are the most prominent indicators and manifestations of that visit in promoting societal peace among the Iraqi public. From a scientific point of view، the research provides another scientific addition to the media library، especially with regard to journalistic treatments and methods of framing the Arab international press for the subject of the visit، which could be a starting point for other researchers to complete qualitative research in this field. The research prob

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Publication Date
Tue Jun 30 2020
Journal Name
Kuwait International Law School Journal
The Duration of the Contract – A Study in Light of French Decree No. 131-2016 Issued on February 10, 2016
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After the Napoleonic Code of 1804 came without any legal rules specific to the duration of the contract, and was content to refer to it in scattered legal texts, Legislative Decree No. 2016-131 came to establish a comprehensive legal system for the duration of the contract, starting from the period of its formation, through the period of its implementation, and ending with its continuation after the expiration of its term, in the third section of the fourth chapter related to the effects of the contract (Articles 1210 - 1215), relying on judicial precedents on the one hand - which are many, as will be shown through the research pages - and contractual practices on the other hand. Perhaps the main motive that prompted the French legislator t

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