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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
Wed Jul 31 2019
Journal Name
Journal Of Engineering
Evaluation of the Accuracy of Digital Elevation Model Produced from Different Open Source Data
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This study aims to estimate the accuracy of digital elevation models (DEM) which are created with exploitation of open source Google Earth data and comparing with the widely available DEM datasets, Shuttle Radar Topography Mission (SRTM), version 3, and Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Digital Elevation Model (ASTER GDEM), version 2. The GPS technique is used in this study to produce digital elevation raster with a high level of accuracy, as reference raster, compared to the DEM datasets. Baghdad University, Al Jadriya campus, is selected as a study area. Besides, 151 reference points were created within the study area to evaluate the results based on the values of RMS.Furthermore, th

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Publication Date
Sat Jun 06 2020
Journal Name
Journal Of The College Of Education For Women
A Critical Pragmatic Study of Racism as Conceptualized in the Glorious Quran
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Racism changes its meaning, shape, purpose or function according to various factors such as time, place, motives, and backgrounds; among others. It seems, however, to have deep roots back in the history of mankind. Such a concept stems from a perceived difference with the other. It is fed by the feeling of being hierarchically superior in opposition to another party that is depicted as inferior. Since ancient times, racism is disguised in different forms and manifests itself on various levels. It is a truism that this ideology can be best presented via language.

Due to its negative implication, racism lends itself to a critical kind of research.  As such, this paper is a critical pragmatic investigation for this phenomenon a

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Publication Date
Sat Jan 01 2022
Journal Name
Acta Facultatis Medicae Naissensis
Asthma as a risk factor for The progression of COVID-19
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Background: Asthma is one of the most common chronic respiratory diseases in the world, standing for the most frequent cause for hospitalization and emergency cases. Respiratory viruses are the most triggering cause. Aim: To assess the role of viral infections, especially COVID-19, in the pathogenesis of asthma initiation and exacerbations. Method: Electronic search was done for the manuscripts focusing on asthma as a risk factor for complications after COVID-19 infection. The outcomes were titles, materials, methods and classified studies related or not related to the review study. Three hundred publications were identified and only ten studies were selected for analysis. Seven studies were review, one retrospective, one longitudin

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Publication Date
Wed Mar 01 2023
Journal Name
Human Gene
The deubiquitylase-ubiquitin-specific protease 4 absence in HeLa cells leads to a reduction in Semliki Forest virus replication
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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Evaluating Training Programs According to model Kirkpatrick / field research in the Health Maysan Directorate .
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This present paper aim at knowing  the process of evaluating the training program that could be applied  in Maysan Health office  for it significance and importance in field of management and vocational staff  preparations  of high  scientific experience in different fields of  Health.  The society of research includes staffs  working in Maysan Health Office  , of specialists ,  dentists, pharmacists, laboratories, nursing  and administrators. Their number is 100 employees, the researcher has designed questionnaire by depending on "Kirkpatrick"  for assessing  the training . The researcher has used   thorough survey and has entailed 90 questionnaire,

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
Physical Identity in the Marshes Chabaish District as a Case Study
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The marshes form large areas in southern Iraq, which are large water bodies, covered by reeds and papyrus plants. The marshes are characterized by distinctive physical elements, which have given them a unique and unique identity that can be clearly distinguished by the physical pattern. The physical environment derives its identity through a group Of inputs that interact with each other and represent both cultural and social inputs of the most important inputs that affect the formation of identity, and in the physical environment of the Marshlands many of the symbols that are associated with the collective memory of individuals, these symbols have value in the community Thus, the preservation of these symbols and inherited from one gener

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Publication Date
Sun Jun 23 2019
Journal Name
American Rock Mechanics Association
Using an Analytical Model to Predict Collapse Volume During Drilling: A Case Study from Southern Iraq
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Zubair Formation is one of the richest petroleum systems in Southern Iraq. This formation is composed mainly of sandstones interbedded with shale sequences, with minor streaks of limestone and siltstone. Borehole collapse is one of the most critical challenges that continuously appear in drilling and production operations. Problems associated with borehole collapse, such as tight hole while tripping, stuck pipe and logging tools, hole enlargement, poor log quality, and poor primary cement jobs, are the cause of the majority of the nonproductive time (NPT) in the Zubair reservoir developments. Several studies released models predicting the onset of borehole collapse and the amount of enlargement of the wellbore cross-section. However, assump

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Publication Date
Tue Jan 01 2019
Journal Name
The 53rd U.s. Rock Mechanics/geomechanics Symposium
Using an analytical model to predict collapse volume during drilling: A case study from southern Iraq
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Publication Date
Mon Aug 01 2022
Journal Name
Baghdad Science Journal
The Patterns of Poisoning Exposure in Different Ages in Duhok Governate: A three Years Study (2016, 2017, 2018)
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Poisoning with toxic substances accidently or deliberately can be life threatening and especially in some countries that lack the essential tests and facilities to identify the types and causes of these toxic substances. In Iraq, as many other countries, poisoning is one of the chronic public health problems. However, very little literature about the pattern of poisoning cases, types and age is available in Duhok Governorate. Therefore, this study was conducted to determine the most common patterns of poisoning and the related age and gender in Duhok Governorate from 2016-2018, which would possibly contribute to the early diagnosis and treatment of poisoning. The present study was conducted for three years, started from 1st of

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Publication Date
Sun Jun 02 2019
Journal Name
Baghdad Science Journal
Estimating the Reliability Function of (2+1) Cascade Model
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This paper discusses reliability R of the (2+1) Cascade model of inverse Weibull distribution. Reliability is to be found when strength-stress distributed is inverse Weibull random variables with unknown scale parameter and known shape parameter. Six estimation methods (Maximum likelihood, Moment, Least Square, Weighted Least Square, Regression and Percentile) are used to estimate reliability. There is a comparison between six different estimation methods by the simulation study by MATLAB 2016, using two statistical criteria Mean square error and Mean Absolute Percentage Error, where it is found that best estimator between the six estimators is Maximum likelihood estimation method.

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