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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 Dec 01 2020
Journal Name
Minar International Journal Of Applied Sciences And Technology
INNOVATE GESTATIONAL AGE ESTIMATION MODEL FOR IRAQI FETUSES BASED ON ULTRASOUND IMAGES MEASUREMENTS
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Imaging by Ultrasound (US) is an accurate and useful modality for the assessment of gestational age (GA), estimation fetal weight, and monitoring the fetal growth during pregnancy, is a routine part of prenatal care, and that can greatly impact obstetric management. Estimation of GA is important in obstetric care, making appropriate management decisions requires accurate appraisal of GA. Accurate GA estimation may assist obstetricians in appropriately counseling women who are at risk of a preterm delivery about likely neonatal outcomes, and it is essential in the evaluation of the fetal growth and detection of intrauterine growth restriction. There are many formulas are used to estimate fetal GA in the world, but it's not specify fo

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Publication Date
Sun Feb 03 2019
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Effect of The Mental image Building Dimensions for The Company to Aattract Attention of Iraqi Consumers for local Products: Exploratory Study
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The survey showed sample opinions of officials in the general company for vegetable oils industry, and the statement of the order of the effect of these dimensions depending on the degree of importance, the questionnaire was used as a key tool in collecting data and information of the sample consisted of 30 officials, arithmetic mean, standard deviation, percentages, Spearman correlation coefficient and the global statistical analysis as a statistical methods that based on statistical program (SPSS), The researcher came to several conclusions, most important that there is high agreement by the respondents of the importance of the dimensions of building a mental picture of the company and to attract the consumer's attention, Also research

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Publication Date
Wed Dec 27 2023
Journal Name
Journal Of Planner And Development
Priorities for the reconstruction of religious buildings in the old city of Mosul using Expert Choice program
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This paper attempts to shed light on the most influential factors in the importance of religious buildings were destroyed because of the recent war due to the control of terrorist gangs of ISIS over the city of Mosul, and to prioritize their reconstruction and their role in reviving the historical center of Mosul.

The research’s problem emerged in the lack of knowledge about the identifying the most influential factors in the importance of religious buildings and utilizing them to prioritize their reconstruction. This study aims to analyze the factors influencing the importance of religious buildings using the Expert Choice software through the Analytic Hierarchy Process (AHP) to reach an analysis of their weights and propose p

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Publication Date
Sat Feb 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
Applying some hybrid models for modeling bivariate time series assuming different distributions for random error with a practical application
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Abstract

  Bivariate time series modeling and forecasting have become a promising field of applied studies in recent times. For this purpose, the Linear Autoregressive Moving Average with exogenous variable ARMAX model is the most widely used technique over the past few years in modeling and forecasting this type of data. The most important assumptions of this model are linearity and homogenous for random error variance of the appropriate model. In practice, these two assumptions are often violated, so the Generalized Autoregressive Conditional Heteroscedasticity (ARCH) and (GARCH) with exogenous varia

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Publication Date
Fri Aug 24 2018
Journal Name
Indian Journal Of Physics
Study of the nuclear deformation of some even–even isotopes using Hartree–Fock–Bogoliubov method (effect of the collective motion)
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In the present research, the nuclear deformation of the Ne, Mg, Si, S, Ar, and Kr even–even isotopes has been investigated within the framework of Hartree–Fock–Bogoliubov method and SLy4 Skyrme parameterization. In particular, the deform shapes of the effect of nucleons collective motion by coupling between the single-particle motion and the potential surface have been studied. Furthermore, binding energy, the single-particle nuclear density distributions, the corresponding nuclear radii, and quadrupole deformation parameter have been also calculated and compared with the available experimental data. From the outcome of our investigation, it is possible to conclude that the deforming effects cannot be neglected in a characterization o

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Publication Date
Sun Jan 01 2023
Journal Name
Desalination And Water Treatment
Optimization of chemical oxygen demand removal from petroleum refinery wastewater by electrocoagulation using tubular electrochemical reactor with a novel design
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Publication Date
Tue Jun 07 2022
Journal Name
Journal Of Nuclear Engineering And Radiation Science
Radon and Exhalation Rate Measurement of Soil Samples in Al-Amiriya Area in Baghdad Governorate Using a Nuclear Track Detector
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Abstract<p>Radon is the most dangerous natural radioactive component affecting the human population, since it is a radioactive gas that results from the decomposition process of uranium deposits in soil, rocks, and water, and it is damaging both humans and the ecosystem. The radon concentrations and exhalation rate in soil samples from various locations were determined using a passive approach with a CR-39 (CR-39 is Columbia Resin #39; it is allyl diglycol carbonate C12H18O7) detector in Amiriya region in Baghdad Governorate. The average values of radon concentrations are ranged from 47.3 to 54.2 Bq·m−3. From the obtained results, we can conclude that the values of all studied locations are</p> ... Show More
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Publication Date
Thu Jan 01 2015
Journal Name
International Journal Of Optics And Applications
Modeling and Analysis of a Miniaturized Ring Modulator Using Silicon-Polymer-Metal Hybrid Plasmonic Phase Shifter. Part I: Theoretical Framework
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This paper presents comprehensive analysis and investigation for 1550nm and 1310nm ring optical modulators employing an electro-optic polymer infiltrated silicon-plasmonic hybrid phase shifter. The paper falls into two parts which introduce a theoretical modeling framework and performance assessment of these advanced modulators, respectively. In this part, analytical expressions are derived to characterize the coupling effect in the hybrid phase shifter, transmission function of the modulator, and modulator performance parameters. The results can be used as a guideline to design compact and wideband optical modulators using plasmonic technology

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Publication Date
Thu Jan 01 2015
Journal Name
International Journal Of Optics And Applications
Modeling and Analysis of a Miniaturized Ring Modulator Using Silicon-Polymer-Metal Hybrid Plasmonic Phase Shifter. Part II: Performance Predictions
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The ring modulator described in part I of this paper is designed here for two operating wavelengths 1550nm and 1310nm. For each wavelength, three structures are designed corresponding to three values of polymer slot widths (40, 50 and 60nm). The performance of these modulators are simulated using COMSOL software (version 4.3b) and the results are discussed and compared with theoretical predictions. The performance of intensity modulation/direct detection short range and long rang optical communication systems incorporating the designed modulators is simulated for 40 and 100Gb/s data rates using Optisystem software (version 12). The results reveal that an average energy per bit as low as 0.05fJ can be obtained when the 1550nm modulator is d

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Publication Date
Tue Nov 24 2020
Journal Name
Experimental Heat Transfer
Thermal performance of a flat-plate solar collector using aqueous colloidal dispersions of multi-walled carbon nanotubes with different outside diameters
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The thermal performance of a flat-plate solar collector (FPSC) using novel heat transfer fluids of aqueous colloidal dispersions of covalently functionalized multi-walled carbon nanotubes with β-Alanine (Ala-MWCNTs) has been studied. Multi-walled carbon nanotubes (MWCNTs) with outside diameters of (< 8 nm) and (20–30 nm) having specific surface areas (SSAs) of (500 m2/g) and (110 m2/g), respectively, were utilized. For each Ala-MWCNTs, waterbased nanofluids were synthesized using weight concentrations of 0.025%, 0.05%, 0.075%, and 0.1%. A MATLAB code was built and a test rig was designed and developed. Heat flux intensities of 600, 800, and 1000 W/m2; mass flow rates of 0.6, 1.0, and 1.4 kg/min; and inlet fluid temperatures of 30, 40, an

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