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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
Sat Jan 01 2011
Journal Name
Journal Of Engineering
TREATMENT OF A HIGH STRENGTH ACIDIC INDUSTRIAL CHEMICAL WASTEWATER USING EXPANDED BED ADSORBER
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Treatment of a high strength acidic industrial wastewater was attempted by activated carbon
adsorption to evaluate the feasibility of yielding effluents of reusable qualities. The experimental
methods which were employed in this investigation included batch and column studies. The
former was used to evaluate the rate and equilibrium of carbon adsorption, while the latter was
used to determine treatment efficiencies and performance characteristics. Fixed bed and expanded
bed adsorbers were constructed in the column studies. In this study, the adsorption behavior of acetic acid onto activated carbon was examined as a function of the concentration of the adsorbate, contact time and adsorbent dosage. The adsorption data was mo

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Publication Date
Wed Sep 01 2021
Journal Name
Journal Of Engineering
Thermal Buckling of Laminated Composite Plates Using a Simple Four Variable Plate Theory
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In this study, the thermal buckling behavior of composite laminate plates cross-ply and angle-ply all edged simply supported subjected to a uniform temperature field is investigated, using a simple trigonometric shear deformation theory. Four unknown variables are involved in the theory, and satisfied the zero traction boundary condition on the surface without using shear correction factors, Hamilton's principle is used to derive equations of  motion depending on a Simple Four Variable Plate Theory for cross-ply and angle-ply, and then solved through Navier's double trigonometric sequence, to obtain critical buckling temperature for laminated composite plates. Effect of changing some design parameters such as, ortho

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Engineering
Modeling and Simulation of Solar Module performance using Five Parameters Model by using Matlab in Baghdad City
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This work presents the modeling of the electrical response of monocrystalline photovoltaic module by using five parameters model based on manufacture data-sheet of a solar module that measured in stander test conditions (STC) at radiation 1000W/m² and cell temperature 25 . The model takes into account the series and parallel (shunt) resistance of the module. This paper considers the details of Matlab modeling of the solar module by a developed Simulink model using the basic equations, the first approach was to estimate the parameters: photocurrent Iph, saturation current Is, shunt resistance Rsh, series resistance Rs, ideality factor A at stander test condition (STC) by an ite

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Publication Date
Sat Jan 01 2022
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees21gr
Challenges facing the transition of traditional cities to smart: Studying the challenges faced by the transition of a traditional area such as Al-Kadhimiya city center to the smart style
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Challenges facing the transition of traditional cities to smart: Studying the challenges faced by the transition of a traditional area such as Al-Kadhimiya city center to the smart style

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Publication Date
Tue May 01 2018
Journal Name
Journal Of Global Pharma Technology
Equilibrium, thermodynamic and kinetic study of the adsorption of a new mono azo dye onto natural Iraq clay
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In the present work, bentonite clay was used as an adsorbent for the removal of a new prepared mono azo dye, 4-[6-bromo benzothiazolyl azo] thymol (BTAT) using batch adsorption method. The effect of many factors like adsorption time, adsorbent weight, initial BTAT concentration and temperature has been studied. The equilibrium adsorption data was described using Langmuir and frundlich adsorption isotherm. Based on kinetics study, it was found that the adsorption process follow pseudo second order kinetics. Thermodynamics data such as Gibbes Free energy ∆Gᵒ, entropy ∆Sᵒ and ∆Hᵒ were also determined using Vant Hoff plot.

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Publication Date
Fri Jun 01 2007
Journal Name
Journal Of The College Of Languages (jcl)
TECHNIQES OF SURREALISM: A STUDY IN TWO NOVELS BY THOMAS PYNCHON, V. AND THE CRYING OF LOT 49
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Surrealism is a twentieth-century literary and artistic movement oriented toward the liberation of the mind. Surrealism is a reaction to the philosophy of rationalism which was believed to be the cause of the disaster of World War I. It emphasizes the expression of the imagination as revealed in dreams and presented without conscious control, the unexpected juxtapositions of objects, the withdrawal of the self, and the exploitation of chance effects.
Surrealism began in Paris in the early 1920s, as Europe emerged from the devastation of World War I. A group of writers, artists, and filmmakers, led by the poet André Breton, adopted the word surréaliste (meaning, roughly, "super-real") as a label for their artistic activities. Influen

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Publication Date
Fri Dec 31 2021
Journal Name
Review Of International Geographical Education
Investing Organizational Identity in Improving Work Teams: An Exploratory Study of a Sample of The Capital's Traffic Directorates
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The research aims to identify the role of organizational identity in improving work teams, and to suggest ways to deal with the outputs of work teams in a way that achieves the goals of the Baghdad Traffic Directorate as it is the subject of the application of the research, while the research community was represented by its officers, while the research sample was embodied in (General Director, Associate The Director General, the directors of Rusafa and Karkh traffic and their assistants, as well as the heads of the divisions and the officials of the departments) in it. The sample was (200) observations. The descriptive exploratory approach was devoted to conducting the research, relying on the questionnaire in data collection, as well as e

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Publication Date
Fri Mar 31 2017
Journal Name
Al-khwarizmi Engineering Journal
Experimental Study to the Effect of Natural Particles Added to Unsaturated Polyester Resin of a Polymer Matrix Composite
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Experimental investigations had been done in this study to demonstrate the effect of natural particles used as a reinforcement material to unsaturated polyester resin. The tensile test and water absorption were investigated according to (ASTM D638) and (ASTM D570), respectively. The influence of sunflower husk and pomegranate husk particles, used as a reinforcement material, on the tensile strength, Young's modulus and water absorption with different weight fraction (3%, 7% and 10%) and particle grain size (50µm, 100 µm and 150 µm), has been investigated. The water absorption of polymer composites was studied by measuring the specimen weight before and after immersion in water for one hundred days. In the experiments of tensile test,

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Publication Date
Mon Sep 30 2019
Journal Name
College Of Islamic Sciences
Detailed interpretation of Sheikh Abdullah Knon A look at the curriculum and method of innovation Critical inductive study
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The problem lies in the main research Where the site of this interpretation of the books of interpretation and what is new and how?
The objectives of this research Vjat to give a quick overview of Sheikh Kenon and the qualifications that made him interpreter, as the goal of the research to reveal the method of Sheikh Kenon highlighting what he has and what is new and show.
The researcher used the inductive method to read the whole book and the comparative approach to compare it with others. He also used the critical method to distinguish between the positions of strength and weakness in the book. The most important results are as follows: :
1 - Sheikh Abdullah Kenon language writer familiar with many sciences, such as jurisprude

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Publication Date
Tue Apr 04 2023
Journal Name
International Journal Of Professional Business Review
Risk Premium, Interest Rate, Inflation and FDI in the Time of Coronavirus: a Case Study of Mena Countries
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Purpose:  the purpose of study is estimate the Risk premium, Interest rate, Inflation and FDI in the through of Coronavirus in the MENA countries.   Theoretical framework: The theoretical framework included the study of the main variables, which are risk premium, interest rate, inflation, and foreign direct investment during the Corona virus pandemic.   Design/methodology/approach:  Concentrating on “COVID-19”, as an effective factor on the Foreign direct investment (FDI), I employ data of “MENA (Middle East and Northern Africa)” countries from 2000 to 2021 to investigate the impact of COVID-19, financial and macroeconomic indicators on FDI relying on the analytic research approach of Static panel data regression, includ

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