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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
Thu Feb 28 2019
Journal Name
Journal Of Engineering
Hydraulic Analysis and Performance Evaluation of Combined Trunk Sewers: A Case Study of Baghdad City.
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Sewer system plays an indispensable task in urban cities by protecting public health and the environment. The operation, maintenance, and rehabilitation of this network have to be in a sustainable and scientific manner. For this purpose, it is important to support operators, decision makers and municipalities with performance evaluation procedure that is based on operational factors. In this paper, serviceability and performance indicator (PI) principles are employed to propose methodology comprising two enhanced PI curves that can be used to evaluate the individual sewers depending on operational factors such as flowing velocity and wastewater level in the sewers. In order to test this methodology; a case study of al-Ru

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Publication Date
Fri Oct 02 2026
Journal Name
Advances In Environmental Biology
A study effect of thyme on biochemical and histological changes in liver of male rats
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Publication Date
Sun Sep 01 2019
Journal Name
Baghdad Science Journal
The Effect of MHD on a Longitudinal Flow of a Fractional Maxwell Fluid between Two Coaxial Cylinders
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      In this paper fractional Maxwell fluid equation has been solved. The solution is in the Mettag-Leffler form. For  the corresponding solutions for ordinary Maxwell fluid are obtained as limiting case of general solutions. Finally, the effects of different parameters on the velocity and shear stress profile are analyzed through plotting the velocity and shear stress profile.

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Publication Date
Thu Nov 30 2023
Journal Name
Research Journal Of Pharmacy And Technology
Preparation and Evaluation of Aceclofenac Solid Dispersion by Fusion Technique and Effervescent Assisted Fusion Technique: Comparative Study
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Solid dispersion (SD) is one of the most widely used methods to resolve issues accompanied by poorly soluble drugs. The present study was carried out to enhance the solubility and dissolution rate of Aceclofenac (ACE), a BCS class II drug with pH-dependent solubility, by the SD method. Effervescent assisted fusion technique (EFSD) using different hydrophilic carriers (mannitol, urea, Soluplus®, poloxamer 188, and poloxamer 407) in the presence of an effervescent base (sodium bicarbonate and citric acid) in different drug: carrier: effervescent base ratio and the conventional fusion technique (FSD) were used to prepare ACE SD. Solubility, dissolution rate, Fourier transformation infrared spectroscopy (FTIR), PowderX-ray diffraction

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Publication Date
Mon Dec 21 2020
Journal Name
International Journal Of Environmental Analytical Chemistry
Comparative study of embedded functionalised MWCNTs and GO in Ultrafiltration (UF) PVC membrane: interaction mechanisms and performance
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Publication Date
Thu Nov 03 2022
Journal Name
Frontiers In Applied Mathematics And Statistics
Prey fear of a specialist predator in a tri-trophic food web can eliminate the superpredator
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We propose an intraguild predation ecological system consisting of a tri-trophic food web with a fear response for the basal prey and a Lotka–Volterra functional response for predation by both a specialist predator (intraguild prey) and a generalist predator (intraguild predator), which we call the superpredator. We prove the positivity, existence, uniqueness, and boundedness of solutions, determine all equilibrium points, prove global stability, determine local bifurcations, and illustrate our results with numerical simulations. An unexpected outcome of the prey's fear of its specialist predator is the potential eradication of the superpredator.

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Publication Date
Sat Mar 01 2008
Journal Name
Al-khwarizmi Engineering Journal
Effect Of Polar Component(1-Propanol) On The Relative Volatility Of The Binary System N-Hexane - Benzene
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Vapor-liquid equilibrium data are presented for the binary systems n-hexane - 1-propanol, benzene - 1-propanol and n-hexane – benzene at 760 mm of mercury pressure. In addition ternary data are presented at selected compositions with respect to the 1-propanol in the 1-propanol, benzene, n-hexane system at 760 mmHg. The results indicate the relative volatility of n-hexane relative to benzene increases appreciably with addition of 1-propanol.

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Publication Date
Thu Jun 02 2011
Journal Name
Ibn Al-haithem Journal For Pure And Applied Sciences
On modified pr-test double stage shrinkage estimators for estimate the parameters of simple linear regression model
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Publication Date
Sat Apr 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
Application the generalized estimating equation Method (GEE) to estimate of conditional logistic regression model for repeated measurements
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Conditional logistic regression is often used to study the relationship between event outcomes and specific prognostic factors in order to application of logistic regression and utilizing its predictive capabilities into environmental studies. This research seeks to demonstrate a novel approach of implementing conditional logistic regression in environmental research through inference methods predicated on longitudinal data. Thus, statistical analysis of longitudinal data requires methods that can properly take into account the interdependence within-subjects for the response measurements. If this correlation ignored then inferences such as statistical tests and confidence intervals can be invalid largely.

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Engineering
Calibration and Verification of the Hydraulic Model for Blue Nile River from Roseires Dam to Khartoum City
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This research represents a practical attempt applied to calibrate and verify a hydraulic model for the Blue Nile River. The calibration procedures are performed using the observed data for a previous period and comparing them with the calibration results while verification requirements are achieved with the application of the observed data for another future period and comparing them with the verification results. The study objective covered a relationship of the river terrain with the distance between the assumed points of the dam failures along the river length. The computed model values and the observed data should conform to the theoretical analysis and the overall verification performance of the model by comparing i

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