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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 Jun 30 2020
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
EVALUATION OF SPORTS AWARENESS AMONG WOMEN AT THE UNIVERSITY OF BAGHDAD FOR THE PERIOD 2011-2016 AND STUDY THE FACTORS AFFECTING THEIR PARTICIPATION IN SPORTS ACTIVITIES: EVALUATION OF SPORTS AWARENESS AMONG WOMEN AT THE UNIVERSITY OF BAGHDAD FOR THE PERIOD 2011-2016 AND STUDY THE FACTORS AFFECTING THEIR PARTICIPATION IN SPORTS ACTIVITIES
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The exercise of activities and sports are of great importance to public health and to maintain the ideal health weight as well as the psychological and mental comfort of humans. The aim of this study is to determine the contribution and participation of educated females in physical activities at the University of Baghdad hall for the years 2011-2016, and to show the factors that influence women's contribution to physical activities at the university by selecting 100 students of males and 100 females' students randomly. During the questioning questions and statistical analysis of the questioning to find out the reasons for the discouraging contribution of the women to the various physical activities and try to find solutions and r

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Publication Date
Mon Feb 04 2019
Journal Name
Iraqi Journal Of Physics
Evaluated the level density for proton induced nuclear resonances in (P+48Ti) reaction using different models
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The experimental proton resonance data for the reaction P+48Ti have been used to calculate and evaluate the level density by employed the Gaussian Orthogonal Ensemble, GOE version of RMT, Constant Temperature, CT and Back Shifted Fermi Gas, BSFG models at certain spin-parity and at different proton energies. The results of GOE model are found in agreement with other, while the level density calculated using the BSFG Model showed less values with spin dependence more than parity, due the limitation in the parameters (level density parameter, a, Energy shift parameter, E1and spin cut off parameter, σc). Also, in the CT Model the level density results depend mainly on two parameters (T and ground state back shift energy, E0), which are app

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
Experimental study of nonlinear characterization of hybrid SWCNTs/Ag-NPs fluids, using nonlinear diffraction technique
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Based on nonlinear self- diffraction technique, the nonlinear optical properties of thin slice of matter can be obtained. Here, nonlinear characterization of nano-fluids consist of hybrid Single Wall Carbon Nanotubes and Silver Nanoparticles (SWCNTs/Ag-NPs) dispersed in acetone at volume fraction of 6x10-6, 9x10-6, 18x10-6 have been investigated experimentally. Therefore, CW DPSS laser at 473 nm focused into a quartz cuvette contains the previous nano-fluid was utilized. The number of diffraction ring patterns (N) has been counted using Charge - Coupled- Device (CCD) camera and Pc with a certain software, in order to find the maximum change of refractive index ( of fluids. Our result show that the fraction volume of 18x10-6 is more nonli

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Publication Date
Tue May 26 2026
Journal Name
Al–bahith Al–a'alami
ELEMENTS OF BUILDING CONTENT FOR GOVERNMENT WEBSITES: : (An Experimental Study)
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The study dealt with measuring the impact of the availability of each of the content elements of the interaction, electronic services, and information on the evaluation of the users of the government website for its effectiveness in terms of the site’s functions and for measuring the site’s ability to present the organization’s tasks to customer groups.

Authority is concerned with measuring the confidence of customers in the content of the site, and in the organization as a whole. Validity is related to measuring the effectiveness of employing the site’s content to achieve the goal of its creation and in communicating with customers. Availability It is for measuring the ease of use of the site. The relevance, which means

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Publication Date
Wed May 01 2019
Journal Name
Iraqi Journal Of Science
Fabrication and Study of Nano catalysis for Alkaline Fuel Cell
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Publication Date
Tue May 26 2026
Journal Name
Al–bahith Al–a'alami
IRAQ YOUTH TRENDS TOWARDS CELEBRITY ADVERTISEMENTS ON SOCIAL MEDIA : (A research taken from a Master Degree thesis)
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In the light of what is witnessing in the advertising arena of new ways and methods in delivering advertising message to consumers by finding new outlets to communicate with them especially through social networking sites, which became the first choice of advertising companies in order to spread its goods and services. These companies now are relying gradually on celebrities to appear with their products and goods to drive the audience's  attention towards them. The thesis aims to find out the attitudes of young people towards the the advertisements that show famous celebrities on social networking sites. The researcher used survey method which aims to record, analyze and interpret the phenomenon after collecting the necessa

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Publication Date
Sun Jun 01 2025
Journal Name
Chemical Engineering And Processing - Process Intensification
Wastewater treatment through a hybrid electrocoagulation and electro-Fenton process with a porous graphite air-diffusion cathode
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Publication Date
Sun Jun 01 2025
Journal Name
Chemical Engineering And Processing - Process Intensification
Wastewater treatment through a hybrid electrocoagulation and electro-Fenton process with a porous graphite air-diffusion cathode
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Publication Date
Sun Jun 01 2025
Journal Name
Chemical Engineering And Processing - Process Intensification
Wastewater treatment through a hybrid electrocoagulation and electro-Fenton process with a porous graphite air-diffusion cathode
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Publication Date
Sun Mar 01 2020
Journal Name
Astrophysics And Space Science
The compound stream event of March 20-25, 2011 as measured by the STEREO B spacecraft
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Abstract<p>The interaction of interplanetary coronal mass ejections (ICME) with each other and with co-rotating interaction regions (CIR) changes their configuration, dynamics, magnetic field and plasma characteristics and can make space weather forecasting difficult. During the period of March 20–25, 2011, the Solar Terrestrial Relation Observatory (<italic>STEREO</italic> B) encountered a compound stream containing several interacting structures. Our analysis suggests that the stream consists of two ICMEs followed by an embedded ICME/CIR. The sudden appearance of the third ICME within the fast wind side of the CIR causes the proton temperature(<inline-formula><alternatives><tex-math></tex-math></alternatives></inline-formula></p> ... Show More
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