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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 Oct 01 2011
Journal Name
Journal Of Engineering
REMOVAL OF CHROMIUM(VI) FROM AQUEOUS SOLUTIONS USING SAWDUST AS ADSORBENT
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In the present study, a low cost adsorbent is developed from the naturally available sawdust
which is biodegradable. The removal capacity of chromium(VI) from the synthetically prepared
industrial effluent of electroplating and tannery industrial is obtained.
Two modes of operation are used, batch mode and fixed bed mode. In batch experiment the
effect of Sawdust dose (4- 24g/L) with constant initial chromium(VI) concentration of 50 mg/L and
constant particle size less than1.8 mm were studied.
Batch kinetics experiments showed that the adsorption rate of chromium(VI) ion by Sawdust
was rapid and reached equilibrium within 120 min. The three models (Freundlich, Langmuir and
Freundlich-Langmuir) were fitted to exper

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Publication Date
Mon Oct 01 2018
Journal Name
Iraqi Journal Of Physics
Preparation single layer of (MgO) as antireflection coating using PLD technique
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In this work preparation of antireflection coating with single layer of MgO using pulsed laser deposition (PLD) method which deposit on glass substrate with different thicknesses (90 and 100) nm annealed at temperature 500 K was done.
The optical and structural properties (X-ray diffraction) have been determined. The optical reflectance was computed with the aid of MATLAB over the visible and near infrared region. Results shows that the best result obtained for optical performance of AR'Cs at 700 shots with thickness 90 nm nanostructure single layer AR'Cs and low reflection at wavelength 550 nm.

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Publication Date
Thu Sep 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Determination of Surface Roughness and Accuracy of Alginate Impression Material Disinfected by Immersion
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Background: This study was conducted to evaluate the surface roughness and dimensional accuracy of commercially obtainable alginate impression material in terms of imbibition after immersion in two different media. Materials and method: Two disinfecting agents, ethanol 70% and povidone-iodine 4%, were used to access the dimensional accuracy and surface roughness of alginate impression material. Weights of specimen discs of alginate impressions were measured before and immediately after immersion to gain a measure of imbibition. For surface roughness, disinfected specimens rectangle was examined before and after disinfection. Results: Minimal changes in weight were observed after disinfection, but a statistically non-significant differenc

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Publication Date
Thu Dec 01 2022
Journal Name
Al-khwarizmi Engineering Journal
Comparative Transfer Learning Models for End-to-End Self-Driving Car
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Self-driving automobiles are prominent in science and technology, which affect social and economic development. Deep learning (DL) is the most common area of study in artificial intelligence (AI). In recent years, deep learning-based solutions have been presented in the field of self-driving cars and have achieved outstanding results. Different studies investigated a variety of significant technologies for autonomous vehicles, including car navigation systems, path planning, environmental perception, as well as car control. End-to-end learning control directly converts sensory data into control commands in autonomous driving. This research aims to identify the most accurate pre-trained Deep Neural Network (DNN) for predicting the steerin

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Publication Date
Sun Nov 23 2025
Journal Name
Revista Iberoamericana De Psicología Del Ejercicio Y El Deporte, Issn 1886-8576, Vol. 18, Nº. 4, 2023, Págs. 361-363
The Effect of a Training Curriculum in Developing the Speed Endurance and Strength Characterized By Speed for the Muscles of the Legs for Female Basketball Students
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Autorías: Mariam Liwa Abdel Fattah, Liqaa Abdullah Ali. Localización: Revista iberoamericana de psicología del ejercicio y el deporte. Nº. 4, 2023. Artículo de Revista en Dialnet.

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Publication Date
Thu Oct 31 2019
Journal Name
Asian Journal Of Pharmaceutical And Clinical Research
DESIGN, SYNTHESIS, DOCKING, ANTITUMOR SCREENING, AND ABSORPTION, DISTRIBUTION, METABOLISM, AND EXCRETION PREDICTION OF NEW HESPERDIN DERIVATIVE
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Objective: Hesperidin (HSP) is a pharmacologically active organic compound found in citrus fruits and peppermint. We synthesized a new HSP derivative by reacting it with 5-Amino-1,3,4-thiadiazole-2-thiol in acetic acid. Methods: This compound was characterized by Fourier-transform infrared, proton nuclear magnetic resonance, and electron impact mass spectra. A molecular docking study explores the predicted binding of the compound and its possible mode of action. Bioavailability, site of absorption, drug mimic, and topological polar surface was predicted using absorption, distribution, metabolism, and excretion (ADME) studies. Results: The docking study predicts that the new compound binds to the active sites of Aurora-B

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Publication Date
Wed Jan 29 2025
Journal Name
Jornal Brasileiro De Patologia E Medicina Laboratorial
First Report of Three Root-Maggot Fly Genera (Diptera: Anthomyiidae) in the Fauna of Iraq
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Publication Date
Tue Feb 01 2022
Journal Name
Journal Of Engineering
Numerical analysis of a concrete foundation under a combination of a dynamic and a seismic load
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Improving in assembling technology has provided machines of higher evaluation with better resistances and managed behavior. This machinery led to remarkably higher dynamic forces and therefore higher stresses. In this paper, a dynamic investigation of rectangular machine diesel and gas engines foundation at the top surface of one-layer dry sand with various states (i.e., loose, medium and dense) was carried out. The dynamic investigation is performed numerically by utilizing limited component programming, PLAXIS 3D. The soil is accepted as flexible totally plastic material submits to Mohr-Coulomb yield basis. A harmonic load is applied at the foundation with amplitude of 10 kPa at a frequency of (10, 15 and 20) HZ and se

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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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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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