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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
Mon May 31 2021
Journal Name
Journal Of Research In Medical And Dental Science
A Stereomicroscopic Evaluation of Four Endodontic Sealers Penetration into Artificial Lateral Canals Using Gutta-Percha Single Cone Obturation Technique
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A Stereomicroscopic Evaluation of Four Endodontic Sealers Penetration into Artificial Lateral Canals Using Gutta-Percha Single Cone Obturation Technique, Omar Jihad Banawi*, Raghad

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Publication Date
Sun Apr 30 2023
Journal Name
Iraqi Journal Of Science
Numerical and Analytical Solutions of Space-Time Fractional Partial Differential Equations by Using a New Double Integral Transform Method
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  This work discusses the beginning of fractional calculus and how the Sumudu and Elzaki transforms are applied to fractional derivatives. This approach combines a double Sumudu-Elzaki transform strategy to discover analytic solutions to space-time fractional partial differential equations in Mittag-Leffler functions subject to initial and boundary conditions. Where this method gets closer and closer to the correct answer, and the technique's efficacy is demonstrated using numerical examples performed with Matlab R2015a.

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Publication Date
Mon May 13 2024
Journal Name
Journal Of Engineering And Applied Science
Assessment of using different ozone-friendly R22 alternative refrigerants in residential air conditioners in a high-ambient temperature country
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Abstract<p>The performance of a vapor compression refrigeration system (VCRS)-based residential air conditioner operating in a high-ambient temperature (HAT) country was investigated using six zero-ODP (ozone depletion potential) refrigerants as replacements to R22. The non-flammable alternative refrigerants considered in the present research were R134a, R404A, R407C, R410A, R448A, and R507A. Using the basic conservation laws, the VCRS was modeled during steady-state operation and solved using engineering equation solver (EES) software. Coefficient of performance (COP), pressures and temperatures at compressor suction and discharge, Global Warming Potential (GWP), critical pressure and temperature, compressor </p> ... Show More
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Publication Date
Sat Jan 13 2018
Journal Name
Journal Of Engineering
Zn(II) Removal from Wastewater by Electrocoagulation/Flotation Method using New Configuration of a Split-Plate Airlift Electrochemical Reactor
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In this paper, split-plate airlift electrochemical reactor as an apparatus with new configuration for wastewater treatment was provided. Two aluminum plates were fixed inside the reactor and present two functions; first it works as split plates for internal loop generation of the airlift system (the zone between the two plates acts as riser while the other two zones act as downcomer) and second it works as two electrodes for electrocoagulation process. Simulated wastewater contaminated with zinc ions was used to test the performance of this apparatus for zinc removal by studying the effect of different experimental variables such as initial concentration of zinc (50-800 ppm), electrical current density (2.67-21.4 mA/cm2), init

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of the method of partial least squares and the algorithm of singular values decomposion to estimate the parameters of the logistic regression model in the case of the problem of linear multiplicity by using the simulation
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The logistic regression model is an important statistical model showing the relationship between the binary variable and the explanatory variables.                                                        The large number of explanations that are usually used to illustrate the response led to the emergence of the problem of linear multiplicity between the explanatory variables that make estimating the parameters of the model not accurate.    

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Publication Date
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Marketing decisions as an intermediary variable of the nature of the relationship between Environmental Turbulence and marketing effectiveness exploratory study of Carrefour branches in Erbil Governorate
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The organizations, represented by its Management, are working hard in various ways to identify the environmental disturbances that occur in their environment and to investigate and follow up the movement of these disturbances and to respond to them through the decisions they make in an attempt to keep pace with the work and sustainability of their activities, including those decisions, marketing decisions taken by the environmental disturbulence in the market of the organization, the inability of these organizations to read the indicators of these disturbulence correctly displays their marketing effectiveness to vibration and decline in the negative.The current research is based on a fundamental problem that envi

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Publication Date
Tue Sep 01 2020
Journal Name
Ain Shams Engineering Journal
Estimating server utilization rate in single server queuing models using an approximate solution of stiff fluid flow model
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Publication Date
Tue May 01 2018
Journal Name
Journal Of Engineering
Performance enhancement of Echo Cancellation Using a Combination of Partial Update ( PU) Methods and New Variable Length LMS (NVLLMS) Algorithm
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In this paper, several combination algorithms between Partial Update LMS (PU LMS) methods and previously proposed algorithm (New Variable Length LMS (NVLLMS)) have been developed. Then, the new sets of proposed algorithms were applied to an Acoustic Echo Cancellation system (AEC) in order to decrease the filter coefficients, decrease the convergence time, and enhance its performance in terms of Mean Square Error (MSE) and Echo Return Loss Enhancement (ERLE). These proposed algorithms will use the Echo Return Loss Enhancement (ERLE) to control the operation of filter's coefficient length variation. In addition, the time-varying step size is used.The total number of coefficients required was reduced by about 18% , 10% , 6%

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Publication Date
Fri May 01 2020
Journal Name
Applied Thermal Engineering
Thermal performance of a flat-plate solar collector using aqueous colloidal dispersions of graphene nanoplatelets with different specific surface areas
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The effects of using aqueous nanofluids containing covalently functionalized graphene nanoplatelets with triethanolamine (TEA-GNPs) as novel working fluids on the thermal performance of a flat-plate solar collector (FPSC) have been investigated. Water-based nanofluids with weight concentrations of 0.025%, 0.05%, 0.075%, and 0.1% of TEA-GNPs with specific surface areas of 300, 500, and 750 m2/g were prepared. An experimental setup was designed and built and a simulation program using MATLAB was developed. Experimental tests were performed using inlet fluid temperatures of 30, 40, and 50 °C; flow rates of 0.6, 1.0, and 1.4 kg/min; and heat flux intensities of 600, 800, and 1000 W/m2. The FPSC’s efficiency increased as the flow rate and hea

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Publication Date
Mon Apr 15 2002
Journal Name
Alustath Journal For Human And Social Sciences
The Intersectionality in I've Been Meaning to Tell You: A Letter to My Daughter: A Post-Colonial Perspective
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Intersectionality is a concept that focuses on social inequality towards black people and provides an analytical instruments for creating social justice issues in such a way in order to depict how social marginalization, or privilege occurs differently in various social positions. It does this by focusing on the interaction of multiple systems of oppression. Intersectionality is used to examines how the social factors; race, gender, and class can affect the people’s life especially the immigrants, black people, and refuges. This article will depicts how blacks in Canada are segregated and distinguished from white race. David Chariandy’s I’ve Been Meaning To Tell You: A Letter to My Daughter 2018 is analyzed through Kimberle Crenshaw

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