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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 Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Strategic Risk's Variation as a function of Competitive Intelligence Investment - An applied research on some Iraqi's manufacturing Companies –
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ABSTRUCT

          The main aim of this research has been associated with the study of relationship between competitive intelligence and strategic risk, and to deduct their specific trends, which are interpreted as predicted by research hypotheses according to a review of literature including prior studies. The basic theme  of these hypotheses is related to the probability that declining levels of strategic risk and competitive positions of industrial companies is dependent upon the growing capacity to stay ahead of competitors in the market.

    A purposive non-random

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Publication Date
Wed Sep 15 2021
Journal Name
Journal Of Baghdad College Of Dentistry
Salivary Cortisol as a Stress Biomarker and Total Viable Count of Salivary Bacterial Microbiome among COVID-19 Patients
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Background: The COVID-19 virus outbreak had a massive effect on many parts of people's lives, as they were advised to quarantine and lockdown to prevent the virus from spreading, which had a big impact on people's mental health, anxiety, and stress. Many internal and external factors lead to stress. This negatively influences the body's homeostasis. As a result, stress may affect the body's capacity to use energy to defend against pathogens. Many recent investigations have found substantial links between human mental stress and the production of hormones, prohormones, and/or immunological chemicals. some of these researches have verified the link between stress and salivary cortisol levels. The aim of this study is to measure salivary corti

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Publication Date
Thu Jan 01 2009
Journal Name
مجلة العلوم الاحصائية
Robust Estimator for Semiparametric Generalized Additive Model
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Generalized Additive Model has been considered as a multivariate smoother that appeared recently in Nonparametric Regression Analysis. Thus, this research is devoted to study the mixed situation, i.e. for the phenomena that changes its behaviour from linear (with known functional form) represented in parametric part, to nonlinear (with unknown functional form: here, smoothing spline) represented in nonparametric part of the model. Furthermore, we propose robust semiparametric GAM estimator, which compared with two other existed techniques.

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Publication Date
Wed Nov 05 2025
Journal Name
Journal Of Oral Biology And Craniofacial Research
The effect of thermocycling on fracture resistance of zirconia crowns cemented with polylysine modified resin cements (Comparative in vitro study)
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ABSTRACT Background: resin cement type and intraoral temperature fluctuations may affect the fracture performance of successful zirconia restorations. To fill this gap, the purpose of this study is to evaluate and compare the influence of thermocycling on fracture resistance and mode of failure of monolithic zirconia crowns luted with Rely X™ U200 and BreezeTMself-adhesive resin cements as well as imply the effect of adding 2 % of polylysine (PLS) to these cements. Materials: 64 maxillary premolars were milled out of zirconia blocks using CAD/CAM milling system. They were divided into four groups (n = 16) according to the cement type. Four different resin cements were used (RelyXTMU200, Breeze™, RelyX™ U200 with 2 % PLS

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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
Study of the Spectral Energy Distribution Model of the Protoplanetary Disk Geometric around the Brown Dwarf CFHT-BD-Tau 4
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The accretion circumstellar disk of young stars and the Brown dwarf plays an essential role in the formation and evaluation of the planet. Our main work in this paper is to investigate the geometrical shape model for the protoplanetary disk around one of the Brown Dwarfs. The photometric measurements for the brown dwarf CFHT-BD-Tau 4 were extracted from the Vizier archive. We used a numerical simulation to build a model of the spectral energy distribution of our target CFHT-BD-Tau 4. The spectral energy distribution model was fitted with observational data for the brown dwarf CFHT-BD-Tau 4. A transitional disk has been assumed around CFHT-BD-Tau 4. We obtained physical properties of the two disks and the size of the gap between them

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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Comparing the Impact Strength and Transverse Flexure Strength of Three Different Dentures Base Materials
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Publication Date
Sun May 01 2016
Journal Name
Journal Of Engineering
Three-Dimensional Finite Element Simulation of the Buried Pipe Problem in Geogrid Reinforced Soil
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Buried pipeline systems are commonly used to transport water, sewage, natural oil/gas and other materials. The beneficial of using geogrid reinforcement is to increase the bearing capacity of the soil and decrease the load transfer to the underground structures.

This paper deals with simulation of the buried pipe problem numerically by finite elements method using the newest version of PLAXIS-3D software. Rajkumar and Ilamaruthi's study, 2008 has been selected to be reanalyzed as 3D problem because it is containing all the properties needed by the program such as the modulus of elasticity, Poisson's ratio, angle of internal friction. It was found that the results

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Publication Date
Sun Feb 22 2026
Journal Name
Al–bahith Al–a'alami
Information Pollution in Iraqi Journalism…Study in Causes and Sources - A research drawn from a Master Degree thesis
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Information pollution is regarded as a big problem facing journalists working in the editing section, whereby journalistic materials face such pollution through their way across the editing pyramid. This research is an attempt to define the concept of journalistic information pollution, and what are the causes and sources of this pollution. The research applied the descriptive research method to achieve its objectives. A questionnaire was used to collect data. The findings indicate that journalists are aware of the existence of information pollution in journalism, and this pollution has its causes and resources.

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Publication Date
Thu Sep 01 2022
Journal Name
Iaes International Journal Of Robotics And Automation
Implementation of a complex fractional order proportional-integral-derivative controller for a first order plus dead time system
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This paper presents the implementation of a complex fractional order proportional integral derivative (CPID) and a real fractional order PID (RPID) controllers. The analysis and design of both controllers were carried out in a previous work done by the author, where the design specifications were classified into easy (case 1) and hard (case 2) design specifications. The main contribution of this paper is combining CRONE approximation and linear phase CRONE approximation to implement the CPID controller. The designed controllers-RPID and CPID-are implemented to control flowing water with low pressure circuit, which is a first order plus dead time system. Simulation results demonstrate that while the implemented RPID controller fails to stabi

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Publication Date
Mon Sep 30 2024
Journal Name
Al-mustansiriyah Journal Of Science
A Transfer Learning Approach for Arabic Image Captions
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