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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
Thu Oct 31 2019
Journal Name
Al-kindy College Medical Journal
Contraception as a Risk Factor of Trichomonas vaginalis Infection Among Women Attending Outpatient of Al-Batool Teaching Hospital for Maternity and Children-Baqubah-Iraq
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Background:The effects of contraception on Trichomonas vaginalis have important implications for women who suffer from infections associated with disruptions in the vaginal ecology, such as bacterial vaginitis and urinary tract infections.

Objective: To find the association of the common types of contraceptions with the Trichomonasvaginalis infection in women admitted to the Al-BatoolTeaching Hospital for Maternity and Children in Baqubah city.

Type of study: Cross-sectional study

Methods: This study consist of 75 women with contraception use and71 apparently healthy non contraception user women  admitted to outpatient in Al

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Publication Date
Sun Sep 01 2013
Journal Name
Baghdad Science Journal
Comparison study of Interleukin-1 alpha between Unstable Angina and Acute Myocardial Infarction patients
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Multiple studies support a role for inflammation in the pathogenesis of coronary atherosclerosis and unstable cardiac syndromes. However, of the known pro-inflammatory cytokines, only elevated plasma levels of interleukin-6(IL-6) have been linked to Unstable Angina. We sought to examine the plasma levels of other major proinflammatory cytokines in similar clinical settings patients with unstable angina and acute myocardial infarction and the relationship extent between them. This study aimed to investigate and compare the level of IL-1 in Unstable Angina and Acute Myocardial Infarction patients. Thirty patients with unstable angina and thirty patients with Acute Myocardial Infarction, also thirty healthy individual as control were included

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Publication Date
Sun Jun 07 2009
Journal Name
Baghdad Science Journal
Investigation of the Optical Properties of the Achromatic Quadrupole Lens by Using the Rectangular Potential Distribution Model
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An optimization calculation is made to find the optimum properties of combined quadrupole lens which consists of electrostatic and magnetic lens. Both chromatic and spherical aberration coefficients are reduced to minimum values and the achromatic aberration is found for many cases. These calculations are achieved with the aid of transfer matrices method and using rectangular model of field distribution, where the path of charged-particles beam traversing the field has been determined by solving the trajectory equation of motion and then the optical properties for lens have been computed with the aid of the beam trajectory along the lens axis. The computations have been concentrated on determining the chromatic and spher

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Publication Date
Tue Nov 01 2016
Journal Name
Journal Of The College Of Basic Education
A study effect Histological changes in Kidney
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Publication Date
Wed Oct 02 2024
Journal Name
Journal Of Craniofacial Surgery
Maxillofacial Trauma in Females: A Retrospective Study
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Maxillofacial trauma in females is not widely reported. This study aimed to analyze the clinical characteristics and the patterns of maxillofacial injuries in females and to determine the differences in these patterns among different causes. This retrospective study analyzed several variables, including demographic, social, injury-related, and treatment-related variables, and compared these variables in relation to the main etiologies of maxillofacial trauma. The main etiologies of maxillofacial injuries involving females were assault, followed by road traffic accidents, and falls. There were significant differences in relation to the 3 etiologies in age groups (P= 0.002) and marital status (<

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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
A Word Cloud Model based on Hate Speech in an Online Social Media Environment
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Social media is known as detectors platform that are used to measure the activities of the users in the real world. However, the huge and unfiltered feed of messages posted on social media trigger social warnings, particularly when these messages contain hate speech towards specific individual or community. The negative effect of these messages on individuals or the society at large is of great concern to governments and non-governmental organizations. Word clouds provide a simple and efficient means of visually transferring the most common words from text documents. This research aims to develop a word cloud model based on hateful words on online social media environment such as Google News. Several steps are involved including data acq

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Publication Date
Tue Feb 18 2025
Journal Name
Iranian Journal Of Science
Exploring Neimark-Sacker Bifurcation and Chaos Control in a Tri-species Discrete-Time Model
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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Building a Sustainable GARCH Model to Forecast Rubber Price: Modified Huber Weighting Function Approach
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The unstable and uncertain nature of natural rubber prices makes them highly volatile and prone to outliers, which can have a significant impact on both modeling and forecasting. To tackle this issue, the author recommends a hybrid model that combines the autoregressive (AR) and Generalized Autoregressive Conditional Heteroscedasticity (GARCH) models. The model utilizes the Huber weighting function to ensure the forecast value of rubber prices remains sustainable even in the presence of outliers. The study aims to develop a sustainable model and forecast daily prices for a 12-day period by analyzing 2683 daily price data from Standard Malaysian Rubber Grade 20 (SMR 20) in Malaysia. The analysis incorporates two dispersion measurements (I

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Publication Date
Tue Oct 23 2018
Journal Name
Journal Of Economics And Administrative Sciences
Compare some wavelet estimators for parameters in the linear regression model with errors follows ARFIMA model.
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The aim of this research is to estimate the parameters of the linear regression model with errors following ARFIMA model by using wavelet method depending on maximum likelihood and approaching general least square as well as ordinary least square. We use the estimators in practical application on real data, which were the monthly data of Inflation and Dollar exchange rate obtained from the (CSO) Central Statistical organization for the period from 1/2005 to 12/2015. The results proved that (WML) was the most reliable and efficient from the other estimators, also the results provide that the changing of fractional difference parameter (d) doesn’t effect on the results.

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Publication Date
Mon Jun 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Simulation of material requirements planning system According to FOQ, EOQ, L4L A study in the General Company for woolen industries / blankets factory
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This paper is submitted as anew approach to simulate manufacturing control & planning system to define the problem of designing control system on the needs for materials.

Production planning & control is a total and complex operation, resides in the essence of manufacturing companies operations. The successful process of production planning and control systems is critical for the staying of manufacturing organizations in markets leading to the increasing consumer competition and which dominate most of manufacturing sectors because of the market oriented economy , thus , what has happened previously , that the companies possessed a great inventory of crude material, components, and groupings and they use in flexible techni

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