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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 Jan 01 2024
Journal Name
Lecture Notes In Electrical Engineering
A Method Combining Compressive Sensing-Based Method of Moment and LU Decomposition for Solving Monostatic RCS
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Publication Date
Mon Dec 31 2012
Journal Name
Al-khwarizmi Engineering Journal
Genetic Algorithm Based PID Controller Design for a Precise Tracking of Two-Axis Piezoelectric Micropositioning Stage
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 In this paper, an intelligent tracking control system of both single- and double-axis Piezoelectric Micropositioner stage is designed using Genetic Algorithms (GAs) method for the optimal Proportional-Integral-Derivative (PID) controller tuning parameters. The (GA)-based PID control design approach is a methodology to tune a (PID) controller in an optimal control sense with respect to specified objective function. By using the (GA)-based PID control approach, the high-performance trajectory tracking responses of the Piezoelectric Micropositioner stage can be obtained. The (GA) code was built and the simulation results were obtained using MATLAB environment. The Piezoelectric Micropositioner simulation model with th

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of Applied Engineering Science
Design and implementation of a smart home automation system based on global system for mobile communications
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Recently, there has been an increasing advancement in the communications technology, and due to the increment in using the cellphone applications in the diverse aspects of life, it became possible to automate home appliances, which is the desired goal from residences worldwide, since that provides lots of comfort by knowing that their appliances are working in their highest effi ciency whenever it is required without their knowledge, and it also allows them to control the devices when they are away from home, including turning them on or off whenever required. The design and implementation of this system is carried out by using the Global System of Mobile communications (GSM) technique to control the home appliances – In this work, an ele

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Publication Date
Thu Dec 13 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
A New Measurement Scale for Evaluating Health-Related Quality of Life in Men with Prostate Cancer
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Objectives: This study aimed to identify and study most properties of the specific and general health-related
quality-of-life (HRQoL) in prostate cancer patients, as well as creating a new measurement scale for assessing QoL
among prostate cancer patients.
Methodology: A cross sectional (descriptive) study was conducted to evaluate General Quality of life in patients
with prostate cancer. A sample of 100 prostate cancer patients from Al-Amal National hospital for cancer
management and Oncology Center in Baghdad Medical City. This study applied format of General World Health
Organization Quality of Life-BERF questionnaire. The methods used descriptive statistics to evaluate the General
QoL-Improvements, as well as inf

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Publication Date
Mon Apr 27 2020
Journal Name
Journal Of Mechanics Of Continua And Mathematical Sciences
A COMPARISON OF TOPOLOGICAL KRIGING AND AREA TO POINT KRIGING FOR IRREGULAR DISTRICT AREA IN IRAQ
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Publication Date
Wed Mar 03 2021
Journal Name
Innovative Infrastructure Solutions
Experimental investigation of a new sustainable approach for recycling waste styrofoam food containers in lightweight concrete
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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Engineering
Efficient Energy Management for a Proposed Integrated Internet of Things-Electric Smart Meter (2IOT-ESM) System
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In this work, an efficient energy management (EEM) approach is proposed to merge IoT technology to enhance electric smart meters by working together to satisfy the best result of the electricity customer's consumption. This proposed system is called an integrated Internet of things for electrical smart meter (2IOT-ESM) architecture. The electric smart meter (ESM) is the first and most important technique used to measure the active power, current, and energy consumption for the house’s loads. At the same time, the effectiveness of this work includes equipping ESM with an additional storage capacity that ensures that the measurements are not lost in the event of a failure or sudden outage in WiFi network. Then then these

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Publication Date
Fri May 03 2024
Journal Name
Optical And Quantum Electronics
Design and analysis of a dual-core PCF biosensor based on SPR for cancerous cells detection
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Publication Date
Thu Dec 15 2022
Journal Name
Journal Of Inorganic And Organometallic Polymers And Materials
Ultrasound-Assisted and One-Pot Synthesis of New Fe3O4/Mo-MOF Magnetic Nano Polymer as a Strong Antimicrobial Agent and Efficient Nanocatalyst in the Multicomponent Synthesis of Novel Pyrano[2,3-d]pyrimidines Derivatives
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Publication Date
Wed Jun 01 2005
Journal Name
Journal Of The College Of Languages (jcl)
The Picture of the romantic hero in: A Bridge Towards the Basific and The Lover
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This research deals with number of novels for Marguerit Doras , specially A Bridge Towards Basfic and The Lover . we specialize the first chapter for discussing a very important issue , which is the Maraguerit Doras novelist world in another word the most important themes . that we discuss and through that we tried to clerify the privacy the characters of Marguerit Doras in comparative with her own generation and in the second chapter we discussed the most important characteristics of the romantic hero spedially the characteristics of women in her novels.

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