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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 May 11 2021
Journal Name
Photonics And Nanostructures - Fundamentals And Applications
The spontaneous emission performance of a quantum emitter coupled to a hybrid plasmonic waveguide with specified output polarization for on-chip plasmonic single-photon source
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Nowadays, most of the on-chip plasmonic single-photon sources emit an unpolarized stream of single photons that demand a subsequent polarizer stage in a practical quantum cryptography system. In this paper, we numerically demonstrated the coupling of the light emitted from a quantum emitter (QE) at 700 nm wavelength to the propagation mode supported by an on-chip hybrid plasmonic waveguide (HPW) polarization rotator. Our results proved that the light emitted is linearly polarized at 0º, 45º/−45º, and 90º with propagation lengths of 5 μm, 3.3 μm, and 3.9 μm, respectively. Moreover, high power-conversion efficiency was obtained from an applied transverse magnetic (TM) mode (0º-polarization) to a transverse electric (TE) (90º-polari

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Publication Date
Thu Jul 01 2021
The spontaneous emission performance of a quantum emitter coupled to a hybrid plasmonic waveguide with specified output polarization for on-chip plasmonic single-photon source
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Publication Date
Mon Apr 03 2023
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
A General Overview on the Categories of Image Features Extraction Techniques: A Survey
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In the image processing’s field and computer vision it’s important to represent the image by its information. Image information comes from the image’s features that extracted from it using feature detection/extraction techniques and features description. Features in computer vision define informative data. For human eye its perfect to extract information from raw image, but computer cannot recognize image information. This is why various feature extraction techniques have been presented and progressed rapidly. This paper presents a general overview of the feature extraction categories for image.

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Publication Date
Sun Jul 01 1990
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
KEY TO THE SPECIES OF THE GENUS STACHYS L. (LABIATAE) IN IRAQ WITH THREE NEW RECORDS
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A simplified parallel key was presented in this work for the Taxa of Stackys L. wildly grown in Iraq. Three records within this genus were newly recorded to our country in the present work and they are S. kermanshahansis Rech S. setifera C.A. Mey. subsp setifera, S. setifera ssp iranica (Reck.) The characteristics of these new records were also given with some representative specimens.

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Publication Date
Sun Dec 02 2018
Journal Name
Journal Of The College Of Education For Women
The Role of Local Satellite Channels in the formation of knowledge and trends of the Iraqi Public Towards Terrorism: A Field Study
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Terrorism is a global phenomenon that engulfs most regions of the world to varying degrees. Media outlets are aware of the many incidents of violence and terrorism that have increased in recent times. The differences between the size of the phenomenon in different societies are the causes and severity of the phenomenon. On the role of local satellite channels in shaping the knowledge and trends of the Iraqi public towards the events of terrorism, in light of the assumptions of reliance on the media. The importance of this study is that it assesses the role of local satellite channels in the formation of knowledge and trends The study seeks to know the extent of exposure of the Iraqi public to local satellite channels, and to reveal the e

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Publication Date
Sat Sep 01 2018
Journal Name
International Journal Of Renewable Energy Research
Performance of Wind Turbines at Three Sites in Iraq
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Matching between wind site characteristics and wind turbine characteristics for three selected sites in Iraq was carried out. Site-turbine matching for potential wind power application in Iraq has not yet been well reported on. Thus, in this study, five years’ wind speed data for sites located in Baghdad (33.34N, 44.40E), Nasiriyah (31.05N, 46.25E), and Basrah (30.50N, 47.78E) were collected. A full wind energy analysis based on the measured data, Weibull distribution function, and wind turbine characteristics was made. A code developed using MATLAB software was used to analyse the wind energy and wind turbines models. The primary objective was to achieve a standard wind turbine-site matching based on the capacity factor. Another matching

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Publication Date
Tue Aug 01 2017
Journal Name
International Journal Of Scientific & Engineering Research
Integrated System of Information hiding by Applying Three levels
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MB Mahmood, BN Dhannoon

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Publication Date
Tue May 23 2023
Journal Name
Journal Of Engineering
Competitive Adsorption of Three Reactive Dyes by Activated Carbon
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In this study three reactive dyes (blue B, red R and yellow Y) in single , binary and ternary solution were adsorbed by activated carbon AC in equilibrium and kinetic experiments. Surface area, Bulk and real density, and porosity were carried out for the activated carbon.
Batch Experiments of pH (2.5-8.5) and initial concentration (5-100) mg/l were carried out for single solution for each dye. Experiments of adsorbent dosage effect (0.1-1)g per 100 ml were studied as a variable to evaluate uptake% and adsorption capacity for single dyes(5, 10) ppm, binary and ternary (10) ppm of mixture solutions solution of dyes. Langmuir, and Freundlich, models were used as Equilibrium isotherm models for single solution. Extended Langmuir and Freun

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Publication Date
Fri Feb 08 2013
Journal Name
Advances In Life Science And Technology
An Analytical and Clinical Study for Measure the Bioavailabilityof Zinc in Serum Using Flame Atomic Absorption Technique
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An analytical and clinical study has been applied for measure the bioavailability of Zinc in serum of twenty adults healthy volunteers, using flame atomic absorption spectrophotometer (FAAS) at 213.9 nm. The calibration graph is linear in the ranges of 0.25-1.5 μg.mL-1 with correlation coefficient (R) 0.09996)μg.mL1-and molar absorpitivites 22957.76(L.mol1-cm-1.The concentration of Zinc determined in serum of all volunteers before and after administered orally a tablet of 50 mg zinc sulphate, produced by Samara drugs company (SDI). All data were subjected to statistical analysis by calculating accuracy, precision in addition to other parameters. The results indicate that the average maximum concentration (C-max ± SD) of blood zinc was 0.

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Publication Date
Mon Mar 09 2015
Journal Name
Monthly Notices Of The Royal Astronomical Society
A reliable iterative method for solving Volterra integro-differential equations and some applications for the Lane–Emden equations of the first kind
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