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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
Tue Sep 09 2025
Journal Name
Journal Of Engineering
Drag Reduction Using Passive Methods on KIA PRIDE Car Model
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An experimental study on a KIA pride (SAIPA 131) car model with scale of 1:14 in the wind tunnel was made beside the real car tests. Some of the modifications to passive flow control which are (vortex generator, spoiler and slice diffuser) were added to the car to reduce the drag force which its undesirable characteristic that increase fuel consumption and exhaust toxic gases. Two types of calculations were used to determine the drag force acting on the car body. Firstly, is by the integrating the values of pressure recorded along the pressure taps (for the wind tunnel and the real car testing), secondly, is by using one component balance device (wind tunnel testing) to measure the force. The results show that, the average drag estimated on

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Improving the efficiency and security of passport control processes at airports by using the R-CNN object detection model
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The use of real-time machine learning to optimize passport control procedures at airports can greatly improve both the efficiency and security of the processes. To automate and optimize these procedures, AI algorithms such as character recognition, facial recognition, predictive algorithms and automatic data processing can be implemented. The proposed method is to use the R-CNN object detection model to detect passport objects in real-time images collected by passport control cameras. This paper describes the step-by-step process of the proposed approach, which includes pre-processing, training and testing the R-CNN model, integrating it into the passport control system, and evaluating its accuracy and speed for efficient passenger flow

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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
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
Fri Apr 21 2023
Journal Name
Aip Conference Proceedings
Study the contrast of thermal expansion behavior for PMMA denture base, single and hybrid reinforced using the thermomechanical analysis technique (TMA)
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This research investigated the effect of adding two groups of reinforcement materials, including bioactive materials Hydroxyapatite (HA) and halloysite nanoclay and bioinert materials Alumina (AL2O3) and Zirconia (ZrO2), each of them with various weight ratios (1,2,3,4 &5)% to the polymer matrix PMMA. The best ratios were selected, and then a hybrid was preparing Composite red from the best ratios from each group. Thermal properties, including thermal conductivity and Thermomechanical Analysis (TMA) technology, have been studied. The results showed that adding 3% Hydroxyapatite (HA) and 5% halloysite nanoclay to the polymethacrylate (PMMA) mer leads to an increase in thermal conductivity. It was also found from the Thermomechanical Analysis

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Publication Date
Sun Jan 01 2023
Journal Name
Technologies And Materials For Renewable Energy, Environment And Sustainability: Tmrees22fr
Study the contrast of thermal expansion behavior for PMMA denture base, single and hybrid reinforced using the thermomechanical analysis technique (TMA)
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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
Thu Mar 01 2012
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of Cost awareness of activation of strategic cost management techniques of industrial units: A prospective study at the General Company for the manufacture of medicines and medical supplies in the province of Mosul
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The last ten years observed a shift enormous scientific in the method and way that it deals professional with the cost accounting and reflected the result those shift enormous scientific of increase the competitive environmental that accompanied the emergence of a modern manufacturing environmental on surface the long roductive life and emergence advanced information technology that give a central focus of his important on client with growing global markets growth on a large scale.

        The research aim to define the concept of cost awareness, the concept and methods of  strategic cost management and the role of cost awareness for managers of industrial units in strategic of cost managem

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Publication Date
Tue May 11 2021
Journal Name
Photonics And Nanostructures - Fundamentals And Applications
The spontaneous emission performance of a quantum emitter coupled to a hybrid plasmonic waveguide with specified output polarization for on-chip plasmonic single-photon source
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Nowadays, most of the on-chip plasmonic single-photon sources emit an unpolarized stream of single photons that demand a subsequent polarizer stage in a practical quantum cryptography system. In this paper, we numerically demonstrated the coupling of the light emitted from a quantum emitter (QE) at 700 nm wavelength to the propagation mode supported by an on-chip hybrid plasmonic waveguide (HPW) polarization rotator. Our results proved that the light emitted is linearly polarized at 0º, 45º/−45º, and 90º with propagation lengths of 5 μm, 3.3 μm, and 3.9 μm, respectively. Moreover, high power-conversion efficiency was obtained from an applied transverse magnetic (TM) mode (0º-polarization) to a transverse electric (TE) (90º-polari

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Publication Date
Thu Jul 01 2021
The spontaneous emission performance of a quantum emitter coupled to a hybrid plasmonic waveguide with specified output polarization for on-chip plasmonic single-photon source
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