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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 Nov 01 2022
Journal Name
Japanese Dental Science Review
Pathogenesis of periodontitis – A potential role for epithelial-mesenchymal transition
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Publication Date
Tue Nov 01 2022
Journal Name
Japanese Dental Science Review
Pathogenesis of periodontitis – A potential role for epithelial-mesenchymal transition
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Epithelial mesenchymal transition (EMT) is a process comprising cellular and molecular events which result in cells shifting from an epithelial to a mesenchymal phenotype. Periodontitis is a destructive chronic disease of the periodontium initiated in response to a dysbiotic microbiome, and dominated by Gram-negative bacteria in the subgingival niches accompanied by an aberrant immune response in susceptible subjects. Both EMT and periodontitis share common risk factors and drivers, including Gram-negative bacteria, excess inflammatory cytokine production, smoking, oxidative stress and diabetes mellitus. In addition, periodontitis is characterized by down-regulation of key epithelial markers such as E-cadherin together with up-regulation of

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of The College Of Education For Women
Social indications (Marriage websites) - A field study in internet cafes
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Marriage is considered one of the strongest ties that links between two human beings , but after the evolutions that happened in our Arab communities and specifically in the Iraqi community , marriage through the internet websites appeared . this kind of marriage is considered one of the new phenomena that appeared in the present time in many societies. That was through internet websites like yahoo , Facebook and other websites that have chat features.
The Islamic sharia looks negatively at marriage through the internet announcing that this way is harmful for both the man and the woman

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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
Wed Oct 02 2024
Journal Name
Translation&linguistics
Verbal forms in French and Iraqi Arabic: a contrastive study
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Publication Date
Fri Dec 30 2016
Journal Name
Al-kindy College Medical Journal
Congenital Thrombasthenia In Children Welfare Teaching Hospital: A Descriptive Study
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Background: Thrombasthenia is an inherited genetic disorder affecting platelets, which is characterized by spontaneous muco-cutaneous bleeding and abnormally prolonged bleeding in response to injury or trauma. Objectives: The aim of this study was to assess the diagnosis and treatment of thrombasthenia in Children Welfare Teaching Hospital. Type of the study: A cross-sectional study. Methods: This descriptive study was performed on 66 patients with thrombasthenia from the first of October 2013 till the first of July 2015.The diagnosis of the disease was done by a wide spectrum of characteristics including family history, clinical manifestations, laboratory tests.. Results: The common manifestations of the disease at time of diagnosis wer

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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
Sun Jan 01 2023
Journal Name
Rawal Medical Journal
Procalcitonin Level In COVID-19 Patients: A single center study
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Objective: The study the association of procalcitonin (PCT) and c-reactive protein (CRP) levels in COVID-19 patients and it's role as a guide in progress and management of those patients. Methodology: This cross-sectional study analyzed 200 CIOVID-19 patients in a single privet center in Baghdad, Iraq from January 1, 2021 to January 1, 2022. Demographic data like age, sex, and clinical symptoms were recorded. High sensitivity CRP and PCT in the serum were measured via dry fluorescence immunoassay (Lansionbio-China). Results: Out of 200 patients, 50 had moderate Covid and 150 had severe disease. Mean serum PCT levels was 0.039±0.05 ng/mL in the moderate group (range 0.011-0.067) and 0.43±0.21 ng/mL in the severe group (range 0.21

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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
Tue Jul 18 2023
Journal Name
Journal Of Current Researches On Social Sciences
A Study on Sociocultural Features among Turkish and Iraqi Women
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SM ADAI, BN RASHID, Journal of Current Researches on Social Sciences, 2023

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