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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 Sep 20 1930
Journal Name
College Of Islamic Sciences
The causes of defeat and weakness and humiliation as described by Al - Imran: Objective study
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Praise be to Allah. Praise be to Him. We seek refuge in Him. We seek forgiveness from him. We seek forgiveness from him.
And the disadvantages of our actions, of his hands
e
It is important, if not all, to pay tribute to God
Muhammad Abdo and Rasoulou, there is no way to deprive the nation of the weakness of God alone and not to share it
 Which suffer from the Quran, and the loss of its borders, bad
The work did not work and did not improve
Do what they offer and delay the others, except by reference to this Koran and the extraction of treasures and secrets
 And news.
The Great Quran Study

Lu Imito ordered each poisoned, and achieved several targets of
YEMYA: Knowing the secrets of the Grea

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Publication Date
Wed Feb 10 2016
Journal Name
ألمؤتمر الدولي العلمي الخامس للاحصائيين العرب/ القاهرة
Proposition of Modified Genetic Algorithm to Estimate Additive Model by using Simulation
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Often phenomena suffer from disturbances in their data as well as the difficulty of formulation, especially with a lack of clarity in the response, or the large number of essential differences plaguing the experimental units that have been taking this data from them. Thus emerged the need to include an estimation method implicit rating of these experimental units using the method of discrimination or create blocks for each item of these experimental units in the hope of controlling their responses and make it more homogeneous. Because of the development in the field of computers and taking the principle of the integration of sciences it has been found that modern algorithms used in the field of Computer Science genetic algorithm or ant colo

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Comparison of HF and HCl Chemical Laser Parameters by using Mathematical Model
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A simplified theoretical comparison of the hydrogen chloride (HCl) and hydrogen fluoride (HF) chemical lasers is presented by using computer program. The program is able to predict quantitative variations of the laser characteristics as a function of rotational and vibrational quantum number. Lasing is assumed to occur in a Fabry-Perot cavity on vibration-rotation transitions between two vibrational levels of hypothetical diatomic molecule. This study include a comprehensive parametric analysis that indicates that the large rotational constant of HF laser in comparison with HCl laser makes it relatively easy to satisfy the partial inversion criterion. The results of this computer program proved their credibility when compared with th

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Publication Date
Wed Sep 11 2019
Journal Name
Aip Conference Proceedings
Estimation of shock wave position in plasma plume using Sedov-Taylor model
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In this work, radius of shock wave of plasma plume (R) and speed of plasma (U) have been calculated theoretically using Matlab program.

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
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
Tue Dec 07 2021
Journal Name
Tencon 2021 - 2021 Ieee Region 10 Conference (tencon)
Robust State Feedback Control of Electric Heating Furnace Using a New Disturbance Observer
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As one type of heating furnaces, the electric heating furnace (EHF) typically suffers from time delay, non-linearity, time-varying parameters, system uncertainties, and harsh en-vironment of the furnace, which significantly deteriorate the temperature control process of the EHF system. In order to achieve accurate and robust temperature tracking performance, an integration of robust state feedback control (RSFC) and a novel sliding mode-based disturbance observer (SMDO) is proposed in this paper, where modeling errors and external disturbances are lumped as a lumped disturbance. To describe the characteristics of the EHF, by using convection laws, an integrated dynamic model is established and identified as an uncertain nonlinear second ord

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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
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
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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