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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
Thu Oct 31 2013
Journal Name
Al-khwarizmi Engineering Journal
Enhancement of a Power System Transient Stability Using Static Synchronous Series Compensator SSSC
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Static Synchronous Series Compensator (SSSC) is a well known device for effectively regulating the active power flow in a power system. In this paper, the SSSC linearized power flow equations are incorporated into Newton-Raphson algorithm in a MATLAB written program to investigate the control of active poweer flow and the transient stability of a five bus and a thirty bus IEEE test systems, during abnormal conduction (three phase fault near buses). A comparison of the results obtained for the base case without SSSC and with it to investigate the effectiveness of the device on both of the active power flow and the transient stability.

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Publication Date
Sat Feb 05 2011
Journal Name
International Journal Of Chemical Reactor Engineering
Mass Transport Properties of a Flow-Through Electrolytic Reactor Using Zinc Reduction System
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An electrolytic process for the removal of Zn(II) from aqueous solution using a parallel amalgamated copper screens cathode operated in the flow through mode is proposed. The current-potential curves recorded at a rotating amalgamated copper disc electrode were used to determine diffusion coefficient of Zn(II). The performance of electrolytic reactor was investigated by using different flow rates at initial zinc ion concentration(48 mg/L). Taking into account the residential Zn(II) concentration, the best results were obtained for cathode potential of (-1.35 V vs. SCE) at flow rate (320 L/h). Zinc ion concentration was found to decrease from 48 mg/L to 1 mg/L during 120 min. of electrolysis. The experimental data are well correlate

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Publication Date
Sat Dec 30 2017
Journal Name
International Journal Of Heat And Technology
Optimization of a rectangular pin fin using rectangular perforations with different inclination angles
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Publication Date
Fri Jul 01 2022
Journal Name
International Journal Of Nonlinear Analysis And Applications
Survey on distributed denial of service attack detection using deep learning: A review
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Distributed Denial of Service (DDoS) attacks on Web-based services have grown in both number and sophistication with the rise of advanced wireless technology and modern computing paradigms. Detecting these attacks in the sea of communication packets is very important. There were a lot of DDoS attacks that were directed at the network and transport layers at first. During the past few years, attackers have changed their strategies to try to get into the application layer. The application layer attacks could be more harmful and stealthier because the attack traffic and the normal traffic flows cannot be told apart. Distributed attacks are hard to fight because they can affect real computing resources as well as network bandwidth. DDoS attacks

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Publication Date
Sat Oct 29 2022
Journal Name
Current Trends In Geotechnical Engineering And Construction
Simulation Design and Performance of a Residential Complex Using Liquefied Petroleum Gas Network
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The population has been trying to use clean energy instead of combustion. The choice was to use liquefied petroleum gas (LPG) for domestic use, especially for cooking due to its advantages as a light gas, a lower cost, and clean energy. Residential complexes are supplied with liquefied petroleum gas for each housing unit, transported by pipes from LPG tanks to the equipment. This research aims to simulate the design and performance design of the LPG system in the building that is applied to a residential complex in Baghdad taken as a study case with eight buildings. The building has 11 floors, and each floor has four apartments. The design in this study has been done in two parts, part one is the design of an LPG system for one building, an

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Publication Date
Fri Mar 01 2019
Journal Name
Al-khwarizmi Engineering Journal
A Digital-Based Optimal AVR Design of Synchronous Generator Exciter Using LQR Technique
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In this paper a new structure for the AVR of the power system exciter is proposed and designed using digital-based LQR. With two weighting matrices R and Q,  this method produces an optimal regulator that is used to generate the feedback control law. These matrices are called state and control weighting matrices and are used to balance between the relative importance of the input and the states in the cost function that is being optimized. A sample power system composed of single machine connected to an infinite- bus bar (SMIB) with both a conventional and a proposed Digital AVR (DAVR) is simulated. Evaluation results show that the DAVR damps well the oscillations of the terminal voltage and presents a faster respo

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Engineering
Removal of Cadmium from Simulated Wastewaters Using a Fixed Bed Bio-electrochemical Reactor
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In this research, the removal of cadmium (Cd) from simulated wastewater was investigated by using a fixed bed bio-electrochemical reactor. The effects of the main controlling factors on the performance of the removal process such as applied cell voltage, initial Cd concentration, pH of the catholyte, and the mesh number of the cathode were investigated. The results showed that the applied cell voltage had the main impact on the removal efficiency of cadmium where increasing the applied voltage led to higher removal efficiency. Meanwhile increasing the applied voltage was found to be given lower current efficiency and higher energy consumption.  No significant effect of initial Cd concentration on the removal efficie

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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
Sun Oct 01 2017
Journal Name
Journal Of Mechanical Science And Technology
Optimization of a rectangular pin fin using elliptical perforations with different inclination angles
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Publication Date
Mon Jun 05 2023
Journal Name
Journal Of Engineering
Effect of Velocity on Dissolved Oxygen Cathodic Polarization using a Rotating Cylinder Electrode
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The aim of the present work to study the effect of changing velocity (Reynold's number) on oxygen cathodic polarization using brass rotating cylinder electrode in 0.1, 0.3 and 0.5N NaCl solutions (PH = 7) at temperatures 40, 50 and 600 C. Cathodic polarization experiments were conducted as a function of electrode rotational speed and concentration.

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