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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
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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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
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
Sun May 01 2022
Journal Name
Journal Of Engineering
Attitude and Altitude Control of Quadrotor Carrying a Suspended Payload using Genetic Algorithm
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The need for quick airborne transportation is critical, especially in emergencies. Drones with suspended payloads might be used to accomplish quick airborne transportation. Due to the environment or the drone's motion, the slung load may oscillate and lead the drone to fall. The altitude and attitude controls are the backbones of the drone's stability, and they must be adequately designed. Because of their symmetrical and simple structure, quadrotor helicopters are one of the most popular drone classes. In this work, a genetic algorithm with two weighted terms fitness function is used to adjust a Proportional-Integral-Derivative (PID) controller to compensate for the altitude and attitude controllers in a quadrotor drone

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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
Thu Sep 06 2018
Journal Name
Al-khwarizmi Engineering Journal
Performance Augmenting of a Vertical Axis Wind Turbine using Adaptable Convergent Ducting System
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Developments are carried out to enhance the performance of vertical axis wind turbines (VAWT). This paper studies the performance of the ducted wind turbine with convergent duct (DAWT). Basically, the duct technique is utilized to provide the desired wind velocity facing the turbine. Methodology was developed to estimate the decisive performance parameter and to present the effect of the convergent duct with different inlet angles. The ducted wind turbine was analyzed and simulated using MATLAB software and numerically using ANSYS-Fluent 17.2. Result of both approaches were presented and showed good closeness for the two cases of covering angles 12  and 20 respectively. Results also showed that the convergent duct with an inlet angl

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Publication Date
Thu Mar 12 2020
Journal Name
Al-khwarizmi Engineering Journal
Inverse Kinematics Analysis and Simulation of a 5 DOF Robotic Arm using MATLAB
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Kinematics is the mechanics branch which dealswith the movement of the bodies without taking the force into account. In robots, the forward kinematics and inverse kinematics are important in determining the position and orientation of the end-effector to perform multi-tasks. This paper presented the inverse kinematics analysis for a 5 DOF robotic arm using the robotics toolbox of MATLAB and the Denavit-Hartenberg (D-H) parameters were used to represent the links and joints of the robotic arm. A geometric approach was used in the inverse kinematics solution to determine the joints angles of the robotic arm and the path of the robotic arm was divided into successive lines to accomplish the required tasks of the robotic arm.Therefore, this

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Publication Date
Sun Jan 01 2023
Journal Name
E3s Web Of Conferences
Comparing the Design Alternatives Using Building Information Model (BIM) and Constructability in Iraqi Construction Projects
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The Iraqi construction industry suffers from many issues that lead to many design errors, clashes, delays and cost overruns. Therefore, applying constructability will prevent these issues from happening, as it has proven its positive effect in different projects around the world. The goal of this paper is to use building information modelling (BIM) to assess the constructability, provide the opportunities for the project stakeholders to choose the best constructable design alternative and find the affection of applying constructability on project cost. The practical side of this research consists of two parts: in the first part, 37 factors are collected from the literature review as factors that effect on constructability. After tha

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Publication Date
Sun Sep 07 2025
Journal Name
Wasit Journal Of Sports Sciences
The impact of the Needham model on learning the skills of dribbling and handling in football for students
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Publication Date
Wed Jun 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
The role of strategic memory in the successful use of the COSO model for auditing human resource management
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The main purpose of the research is to diagnose the importance of the role that strategic memory plays with its three variables (content, structure, and processes) in helping the human resource department to use the COSO model with its five components (culture and governance, strategy and objectives, performance, communications and information, and feedback) in auditing activities and tasks Her own. As the research problem emphasized the existence of a lack of cognitive perception, of the importance of strategic memory, and the investment of its components in the rationalization of the application of the COSO model. and therefore it can be emphasized that the importance of the research is to provide treatments for problems relate

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