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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
Wed Nov 21 2018
Journal Name
International Journal Of Control, Automation And Systems
Design and Stability Analysis of a Fractional Order State Feedback Controller for Trajectory Tracking of a Differential Drive Robot
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Publication Date
Wed Nov 05 2025
Journal Name
Journal Of Oral Biology And Craniofacial Research
The effect of thermocycling on fracture resistance of zirconia crowns cemented with polylysine modified resin cements (Comparative in vitro study)
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ABSTRACT Background: resin cement type and intraoral temperature fluctuations may affect the fracture performance of successful zirconia restorations. To fill this gap, the purpose of this study is to evaluate and compare the influence of thermocycling on fracture resistance and mode of failure of monolithic zirconia crowns luted with Rely X™ U200 and BreezeTMself-adhesive resin cements as well as imply the effect of adding 2 % of polylysine (PLS) to these cements. Materials: 64 maxillary premolars were milled out of zirconia blocks using CAD/CAM milling system. They were divided into four groups (n = 16) according to the cement type. Four different resin cements were used (RelyXTMU200, Breeze™, RelyX™ U200 with 2 % PLS

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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
Study of the Spectral Energy Distribution Model of the Protoplanetary Disk Geometric around the Brown Dwarf CFHT-BD-Tau 4
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The accretion circumstellar disk of young stars and the Brown dwarf plays an essential role in the formation and evaluation of the planet. Our main work in this paper is to investigate the geometrical shape model for the protoplanetary disk around one of the Brown Dwarfs. The photometric measurements for the brown dwarf CFHT-BD-Tau 4 were extracted from the Vizier archive. We used a numerical simulation to build a model of the spectral energy distribution of our target CFHT-BD-Tau 4. The spectral energy distribution model was fitted with observational data for the brown dwarf CFHT-BD-Tau 4. A transitional disk has been assumed around CFHT-BD-Tau 4. We obtained physical properties of the two disks and the size of the gap between them

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Publication Date
Sun Jun 01 2025
Journal Name
Results In Materials
Adsorption, thermodynamic and corrosion study of enalapril malate pharmaceutical drug as corrosion inhibitor for carbon steel in saline solution
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Unused and expired pharmaceutical drugs are a novel type of organic corrosion inhibitor. They are less expensive, more effective, and less harmful than conventional organic corrosion inhibitors. This study investigated the effects of concentration, adsorption mechanism and thermodynamic parameters of enalapril malate (ENAP) as a corrosion inhibitor for carbon steel in a saline solution (3.5 % NaCl). The polarization method was used to determine the corrosion rate and inhibition efficiency. Field emission scanning electron microscopy (FE-SEM) and atomic force spectroscopy (AFM) were used to investigate the surface morphology and topography of carbon steel after immersion in both uninhibited and inhibited media for 24 h. Fourier transform inf

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Publication Date
Sun Mar 25 2018
Journal Name
Biomedical And Pharmacology Journal
Comparing the Impact Strength and Transverse Flexure Strength of Three Different Dentures Base Materials
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Publication Date
Sun May 01 2016
Journal Name
Journal Of Engineering
Three-Dimensional Finite Element Simulation of the Buried Pipe Problem in Geogrid Reinforced Soil
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Buried pipeline systems are commonly used to transport water, sewage, natural oil/gas and other materials. The beneficial of using geogrid reinforcement is to increase the bearing capacity of the soil and decrease the load transfer to the underground structures.

This paper deals with simulation of the buried pipe problem numerically by finite elements method using the newest version of PLAXIS-3D software. Rajkumar and Ilamaruthi's study, 2008 has been selected to be reanalyzed as 3D problem because it is containing all the properties needed by the program such as the modulus of elasticity, Poisson's ratio, angle of internal friction. It was found that the results

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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
A study to determine the most important factors affecting student performance In the secondary school in Diwaniya
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Student performance may influence by several factors in all his study levels such as primary school, intermediate school and even in his college; some of these factors are psychological factors, social factors, and the factors which correlate with student environment.

In this paper we study some of these factors to discover their influence by using canonical correlation analysis to analyze the data. Many conclusions are discovered to help who focuses student performance or to make it pest in future.

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Publication Date
Sun Nov 27 2022
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Extent of auditors' commitment to the quality control system according to the Iraqi Audit guide / 7 : A field study of a sample of auditors of the second district audit office In the The Federal Financial Supervision Board
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The research aims to achieve a set of objectives, the most important of which is determining the extent to which the auditors of the research sample in the Federal Bureau of Financial Supervision adhere to the requirements of the quality control system according to the Iraqi Audit Manual No. The federal financial / research sample with the quality control system according to the Iraqi audit guide No. 7), and the researcher seeks to test the main research hypothesis and sub-hypotheses, and to achieve this, a questionnaire was designed by (Google Form) and distributed electronically to the elements of the research sample, Through the statistical package program (SPSS), the results of the questionnaire were analysed. In light of the applied

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Publication Date
Sun Jun 01 2025
Journal Name
Journal Of The College Of Languages (jcl)
Rebellious Self - A Reading in Madame Bovary's Character of Flubert and Hanna Konin by Amos Oz - Comparative study: האני המורדת - קריאה בדמותה של מאדאם בובארי של פלובר וחנה גונן של עמוס עוז – מחקר השוואתי
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The problem of rebellion is considered one of the features of rapid changes that a society undergoes in all spheres and directions of life, especially in the realm of social relations, customs, traditions, values, and principles. Rebellion may manifest itself in rebellion against oneself, against values or traditions, or against social or governmental authority. One may find that submission plays a vital role in all of these interactions. This study deals with the problem of rebellion in the works of two renowned authors: The French Gustave Flaubert and the Israeli Amos Oz, through two main characters who share similar qualities and traits. Emma Bovary and Henna Konin demonstrate this through their rebellion against themselves, their relati

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Publication Date
Thu May 31 2012
Journal Name
Al-khwarizmi Engineering Journal
An Experimental Study on the Effect of Shape and Location of Vortex Generators Ahead of a Heat Exchanger
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An experimental study is carried out on the effect of vortex generators (Circular and square) on the flow and heat transfer at variable locations at (X = 0.5, 1.5, 2.5 cm) ahead of a heat exchanger with Reynolds number ranging from 62000< Re < 125000 and heat flux from 3000 ≤ q ≤ 8000 W/m2 .

In the experimental investigation, an apparatus is set up to measure the velocity and temperatures around the heat exchanger.                     

The results show that there is an effect for using vortex generators on heat transfer. Also, heat transfer depends on the shape and location. The circular is found t

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