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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
Sat Sep 24 2022
Journal Name
Arab World English Journal
A Critical Stylistic Study of the Notion of Women Empowerment in the Mona Lisa Smile (2003)
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This study unveils the ideologies of women empowerment encoded in the Mona Lisa Smile movie (2003). It reveals how the stereotypical image of women born only to be wives and do the duties of upbringing and housework is challenged. Katherine Ann Watson (Julia Roberts), the main character in the movie, wants to make a difference in the next generation of women. She rejects the imposed traditional ideologies. Linguistically, she opposes conventional thinking and seeks to persuade her students that life is about more than getting married. The primary focus of this study is to examine and clarify how the characters’ linguistic choices convey their ideologies concerning the notion of women empowerment. To do this, the researchers apply

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Publication Date
Tue Oct 30 2018
Journal Name
Journal Of Engineering
Accuracy Assessment of Stonex X-300 Laser Scanner Cameras
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Assessment the actual accuracy of laboratory devices prior to first use is very important to know the capabilities of such devices and employ them in multiple domains. As the manual of the device provides information and values in laboratory conditions for the accuracy of these devices, thus the actual evaluation process is necessary.

In this paper, the accuracy of laser scanner (stonex X-300) cameras were evaluated, so that those cameras attached to the device and lead supporting role in it. This is particularly because the device manual did not contain sufficient information about those cameras.

To know the accuracy when using these cameras in close range photogrammetry, laser scanning (stonex X-300) de

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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
Wed Mar 01 2023
Journal Name
Journal Of Engineering
Effect of a Parked Car Orientation on a Temperature Distribution and Cooling Load Calculation: Experimental Study
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When a vehicle is left parked in the sun for an extended period, the gathered heat causes damage to several interiors within the cabin and causes discomfort for people and animals left inside the car. In the present work, the effect of the orientation of a parked white minibus on temperature distribution and cooling load calculation is studied experimentally in an open environment. Two different cases were studied facing south and facing east. For several hours, the temperature inside the car cabin had been monitored and measured at five separate locations. The cooling load calculations are carried out based on the experimental measurements. The results show that the overheating of parked cars always happens as a result

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Publication Date
Mon Feb 01 2016
Journal Name
International Journal Of Transportation Engineering And Traffic System, Ijtets
Comparative Modeling of Pavement Surface Texture Variables Using ANN and SPSS Software
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The health of Roadway pavement surface is considered as one of the major issues for safe driving. Pavement surface condition is usually referred to micro and macro textures which enhances the friction between the pavement surface and vehicular tires, while it provides a proper drainage for heavy rainfall water. Measurement of the surface texture is not yet standardized, and many different techniques are implemented by various road agencies around the world based on the availability of equipment’s, skilled technicians’ and funds. An attempt has been made in this investigation to model the surface macro texture measured from sand patch method (SPM), and the surface micro texture measured from out flow time (OFT) and British pendul

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Publication Date
Wed Dec 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment of Composite Nanoleakage Using Various Dentine Surface Treatments
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Background: The treatment of dental tissues proceeding to adhesive procedures is a crucial step in the bonding protocol and decides the clinical success ofrestorations. This study was conducted in vitro, with the aim of evaluating thenanoleakage on the interface between the adhesive system and the dentine treated by five surface modalities using scanning electron microscopy and energydispersiveX-ray spectrometry. Materials and methods: Twenty five extracted premolars teeth were selected in the study. Standardized class V cavities were prepared on the buccal and lingual surfaces then the teeth divided into five main groups of (5 teeth in each group n=10) according to the type of dentine surface treatment that was used: Group (A): dentine was

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Publication Date
Thu Dec 01 2016
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment of Composite Nanoleakage Using Various Dentine Surface Treatments
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Background: The treatment of dental tissues proceeding to adhesive procedures is a crucial step in the bonding protocol and decides the clinical success ofrestorations. This study was conducted in vitro, with the aim of evaluating thenanoleakage on the interface between the adhesive system and the dentine treated by five surface modalities using scanning electron microscopy and energydispersiveX-ray spectrometry. Materials and methods: Twenty five extracted premolars teeth were selected in the study. Standardized class V cavities were prepared on the buccal and lingual surfaces then the teeth divided into five main groups of (5 teeth in each group n=10) according to the type of dentine surface treatment that was used: Group (A): dentine was

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Publication Date
Tue Jun 01 2021
Journal Name
Baghdad Science Journal
Three-Dimensional Nonlinear Integral Operator with the Modelling of Majorant Function
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In this paper, the process for finding an approximate solution of nonlinear three-dimensional (3D) Volterra type integral operator equation (N3D-VIOE) in R3 is introduced. The modelling of the majorant function (MF) with the modified Newton method (MNM) is employed to convert N3D-VIOE to the linear 3D Volterra type integral operator equation (L3D-VIOE). The method of trapezoidal rule (TR) and collocation points are utilized to determine the approximate solution of L3D-VIOE by dealing with the linear form of the algebraic system. The existence of the approximate solution and its uniqueness are proved, and illustrative examples are provided to show the accuracy and efficiency of the model.

Mathematical Subject Classificat

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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
Thu Jun 15 2017
Journal Name
International Journal Of Computer Applications
Assessment of Annual Wind Energy Potential at Three Sites in Iraq for Wind Energy Applications
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Assessment of annual wind energy potential for three selected sites in Iraq has been analyzed in the present work. The wind velocities data from August 2014 to July 2015 were collected from the website of Weather Underground Organization (WUO) at stations elevation (35m, 32m, and 17m) for Baghdad, Najaf, and Kut Al-Hai respectively. Extrapolation of stations elevation and wind velocities was used to estimate wind velocities at (60m, 90m, and 120m). The objectives are to analyze the wind speed data and assess the wind energy potential for wind energy applications. Computer code for MATLAB software has been developed to solve the mathematical model. The results are presented as a monthly and annual average for wind velocities, standard deviat

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