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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
Sun Apr 03 2022
Journal Name
Iraqi Journal Of Laser
On the use of Aluminium as a plasmonic material in polarization rotators based on a hybrid plasmonic waveguide
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: The Aluminium (Al) material emerged as a plasmonic material in the wavelength ranges from the ultraviolet to the visible bands in different on-chip plasmonic applications. In this paper, we demonstrate the effect of using Al on the electromagnetic (EM) field distribution of a compact hybrid plasmonic waveguide (HPW) acting as a polarization rotator. We compare the performance of Al with other familiar metals that are widely used as plasmonic materials, which are Silver (Ag) and Gold (Au). Furthermore, we study the effect of reducing the geometrical dimensions of the used materials on the EM field distributions inside the HPW and, consequently, on the efficiency of the polarization rotation. We perform the study based o

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Publication Date
Sun Aug 05 2018
Journal Name
Journal Of Entomology And Zoology Studies
Some biochemical traits in broiler chicken as affected by insulin-like growth factor-1 (IGF-1) gene polymorphisms
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This study was conducted during the period 1/9/2014 – 1/2/2015 and aimed to identify the polymorphisms of IGF-1 gene in broiler chickens and their effects on some biochemical traits. A total of 300 one-day-old broiler chicks (Cobb500, n=150; Hubbard F-15, n=150) were evaluated in this study. Blood samples were individually collected from all birds for DNA extraction. PCR-RFLP method being used for determination the genotypes of IGF-1 gene which then correlated with biochemical traits studied. Cobb500 broilers with TT genotype had significantly (p˂0.05) higher serum triglycerides values than those of TC and CC genotypes. Low density lipoprotein (LDL) were significantly (p˂0.05) higher in Hubbard F-15 broilers with TT genotype than those

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Publication Date
Sun Jan 01 2023
Journal Name
Journal Of Population Therapeutics And Clinical Pharmacology
Evaluation of the Expression of RCC and KIM-1 Biomarkers in Nephrotoxicity of Rabbits Treated with Ochratoxins A
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Publication Date
Tue Feb 26 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Return Variation on Investment as a Function for the Difference of Market Share: An Applied Research on a Sample of Private Banks listed in Iraq Stock Exchange (ISX)
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    The research specified with study the relation  between the market share for the sample research banks and the amount of the achieved revenues from the investment, where the  dominated belief  that there potentiality enhancing the revenue on investment with the increase of the banks shares in their markets after their success in achieving rates of successive growth in their sales of sales and to a suitable achieve  market coverage for their products and they have dissemination and suitable  promotion activity, the  market share represented the competition  for the banks, and the markets pay attention to the  market share as a strategic objective and to maintain them also increasi

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Publication Date
Tue Oct 02 2018
Journal Name
Iraqi Journal Of Physics
Informative accuracy investigation and updating map using remote sensing technique and GIS
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In this work, using GPS which has best accuracy that can be established set of GCPs, also two satellite images can be used, first with high resolution QuickBird, and second has low resolution Landsat image and topographic maps with 1:100,000 and 1:250,000 scales. The implementing of these factors (GPS, two satellite images, different scales for topographic maps, and set of GCPs) can be applying. In this study, must be divided this work into two parts geometric accuracy and informative accuracy investigation. The first part is showing geometric correction for two satellite images and maps.
The second part of the results is to demonstrate the features (how the features appearance) of topographic map or pictorial map (image map), Where i

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Publication Date
Sun May 15 2022
Journal Name
Bionatura
Comparative anatomical study to skeleton for same species of Turtles in Iraq
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Bones were recorded in the skeleton of some species of Iraqi turtle Mauremys rivulata; the objectives of this study came in light of current conditions, environmental developments, talents and techniques of biological studies taking place in the country, need for an anatomy guide in river turtles of Iraqi species, to identify all kinds of similarities and differences with their preaching, this work or study has become written in response to those modern needs. It is designed to be one of the resources for those interested in biological studies, beginners or professionals, and veterinarians, distinguishing them from marine and global species. Turtles were dissected in the laboratories of the Research Center and Museum of Natural Hist

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Publication Date
Tue May 16 2023
Journal Name
International Journal Of Online And Biomedical Engineering (ijoe)
Comparative Study of Anemia Classification Algorithms for International and Newly CBC Datasets
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Data generated from modern applications and the internet in healthcare is extensive and rapidly expanding. Therefore, one of the significant success factors for any application is understanding and extracting meaningful information using digital analytics tools. These tools will positively impact the application's performance and handle the challenges that can be faced to create highly consistent, logical, and information-rich summaries. This paper contains three main objectives: First, it provides several analytics methodologies that help to analyze datasets and extract useful information from them as preprocessing steps in any classification model to determine the dataset characteristics. Also, this paper provides a comparative st

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Publication Date
Fri Dec 15 2023
Journal Name
Iraqi Journal Of Laser
D-shape Optical Fiber Development and Enhancement as a Refractive Indices Sensor Using Surface Plasmon Resonance
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This article showcases the development and utilization of a side-polished fiber optic sensor that can identify altered refractive index levels within a glucose solution through the investigation of the surface Plasmon resonance (SPR) effect. The aim was to enhance efficiency by means of the placement of a 50 nm-thick layer of gold at the D-shape fiber sensing area. The detector was fabricated by utilizing a silica optical fiber (SOF), which underwent a cladding stripping process that resulted in three distinct lengths, followed by a polishing method to remove a portion of the fiber diameter and produce a cross-sectional D-shape. During experimentation with glucose solution, the side-polished fiber optic sensor revealed an adept detection

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
A study for Bacterial Infection in Acute Diarrhea Patients
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500 samples of diarrhea stool were collected from different ages(less than 1year –upto30years) and for both genders from some patients in (Alwiya hospital for children, Al-kendi, central health public laboratory and some gavernarated labs) period(1/11/2009—1/10/2010). Kinds of bacteria and parasites agents were isolated and identified from patients with diarrhea. Nine species of gram negative bacteria from enterobacteriaceae were isolated, E. coli isolated are the higher ratio 4.8% of all, then Salmonella typhi4.6% while the lowest ratios is Citrobacterfreundii 0.4%, while the other identified species were be among the previous rotios. also Plesomonasshigelloides was isolated which concedride one of the bacterial local studies.many met

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Publication Date
Wed Feb 01 2023
Journal Name
Journal Of Engineering
Checking the Accuracy of Selected Formulae for both Clear Water and Live Bed Bridge Scour
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Due to severe scouring, many bridges failed worldwide. Therefore, the safety of the existing bridge (after contrition) mainly depends on the continuous monitoring of local scour at the substructure. However, the bridge's safety before construction mainly depends on the consideration of local scour estimation at the bridge substructure. Estimating the local scour at the bridge piers is usually done using the available formulae. Almost all the formulae used in estimating local scour at the bridge piers were derived from laboratory data. It is essential to test the performance of proposed local scour formulae using field data. In this study, the performance of selected bridge scours estimation formulae was validated and sta

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