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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 Feb 21 2017
Journal Name
Biomechanics And Modeling In Mechanobiology
A novel method for non-invasively detecting the severity and location of aortic aneurysms
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The influence of an aortic aneurysm on blood flow waveforms is well established, but how to exploit this link for diagnostic purposes still remains challenging. This work uses a combination of experimental and computational modelling to study how aneurysms of various size affect the waveforms. Experimental studies are carried out on fusiform-type aneurysm models, and a comparison of results with those from a one-dimensional fluid–structure interaction model shows close agreement. Further mathematical analysis of these results allows the definition of several indicators that characterize the impact of an aneurysm on waveforms. These indicators are then further studied in a computational model of a systemic blood flow network. This demonstr

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
Use The Wallpaper Three-Dimensional in Living Room in the House of Iraq (Future spaces)
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يرغب المرء أن يعيش في منزل يعبر عن اصالة تصميمه ذا اهداف جمالية كحاجته الى تحقيق الأهداف العملية. وعليه فمن الأهمية بمكان ان يشارك أصحابه مع المعنيين[1] بشؤون التصميم... وهنا ارتأت الباحثة ان تقوم بدراسة علمية حديثة حول ورق الجدران ثلاثي الابعاد وتوظيفة في غرفة المعيشة, وباسلوب عصري حديث يجمع بين جمالية التصميم والحداثة , إضافة الى تناول الإضاءة لما لها من دور في ابراز معالم وتفاصيل الأثاث

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Publication Date
Thu Mar 01 2012
Journal Name
Journal Of Economics And Administrative Sciences
The importance of drafting Arab accounting standards Comparative study in light of international accounting compliance and different environmental factors
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Importance of accounting standards belong to be the instructor and the advisor for accountant in performing his work . For each invironment a group of political, social, economical  and cultural factors which distinguish it about other environments . In  order to perform its aim in produsing accouting information helps in making decisions on different levels, accounting standards should established in a form that harmonized with the environment that apply in it . Establishing international accounting standards comes with the same direction and then it has put influential with standards some states that have influence on international accounting standards committee. So because of the big changes that happened in the inte

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Publication Date
Tue Feb 14 2023
Journal Name
Journal Of Educational And Psychological Researches
Comparative Study in Attitudes towards the Covid-19 Vaccine According to Locus of Control (Internal - External) of University Students
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Abstract

The current research aims to identify the attitudes towards the Covid-19 vaccine and the Locus of Control (internal, external) among university students, to identify the significance of the difference in attitudes towards the Covid-19 vaccine, the significance of the difference in the Locus of Control (internal, external) according to the gender variable (male, female), and to identify the significance of the difference in students’ attitudes towards Covid-19 vaccine according to the Locus of Control (internal, external). To achieve the objective of the research, the researcher developed two scales, a scale of (20) items to identify the attitudes toward a covid-19 vaccine, and a scale of the locus of c

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Publication Date
Sun Jun 30 2019
Journal Name
International Journal Of Research In Social Sciences And Humanities
CHARACTERISTICS OF THE POWER CHAIN FUNCTION CURVE AND ITS RELATION TO THE ACCURACY OF THE HIGH-JUMP JUMP IN THE HANDBALL
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The skill high-jump scoring is based on mechanical and physical abilities. The most important of all is the strength used by the player from the moment of preparation to the moment of scoring, which led the researchers to study the characteristics of the series of power chain functions of this skill according to (Biosyn System) The players of the national team's back line have a handball to find out the relationship between the properties of the power chain curve and the accuracy of the high jump to the upper and lower target angles. The aim of the research was to identify the values of the Force Series variables for the skill of the high-jump curve of the handball as well as the relationship between the properties of the power chain functi

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Publication Date
Thu Dec 01 2022
Journal Name
Baghdad Science Journal
Enhancement Ear-based Biometric System Using a Modified AdaBoost Method
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          The primary objective of this paper is to improve a biometric authentication and classification model using the ear as a distinct part of the face since it is unchanged with time and unaffected by facial expressions. The proposed model is a new scenario for enhancing ear recognition accuracy via modifying the AdaBoost algorithm to optimize adaptive learning. To overcome the limitation of image illumination, occlusion, and problems of image registration, the Scale-invariant feature transform technique was used to extract features. Various consecutive phases were used to improve classification accuracy. These phases are image acquisition, preprocessing, filtering, smoothing, and feature extraction. To assess the proposed

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Publication Date
Tue Feb 20 2024
Journal Name
Baghdad Science Journal
A New Strategy to Modify Hopfield by Using XOR Operation
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The Hopfield network is one of the easiest types, and its architecture is such that each neuron in the network connects to the other, thus called a fully connected neural network. In addition, this type is considered auto-associative memory, because the network returns the pattern immediately upon recognition, this network has many limitations, including memory capacity, discrepancy, orthogonally between patterns, weight symmetry, and local minimum. This paper proposes a new strategy for designing Hopfield based on XOR operation; A new strategy is proposed to solve these limitations by suggesting a new algorithm in the Hopfield network design, this strategy will increase the performance of Hopfield by modifying the architecture of t

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Publication Date
Mon Jan 01 2024
Journal Name
Lecture Notes In Networks And Systems
Using Machine Learning to Control Congestion in SDN: A Review
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Publication Date
Wed Jun 11 2003
Journal Name
Iraqi Journal Of Laser
Microdrop Size Measurement in a Mixing Unit Using Laser Technique
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One of the troublesome duties in chemical industrial units is determining the instantaneous drop size distribution, which is created between two immiscible liquids within such units. In this work a complete system for measuring instantaneous droplet size is constructed. It consists of laser detection system (1mW He-Ne laser), drop generation system (turbine mixer unit), and microphotography system. Two immiscible liquids, water and kerosene were mixed together with different low volume fractions (0.0025, 0.02) of kerosene (as a dispersed phase) in water (as a continuous phase). The experiments were carried out at different rotational speed (1180- 2090 r.p.m) of the turbine mixer. The Sauter mean diameter of the drops was determined by la

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Publication Date
Wed Jun 29 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Measuring Dyes Concentration Using a Low-Cost Visible-Light Spectrophotometer
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   A low-cost, RGB LED-based visible-light spectrophotometer was designed to measure dyes concentration. Dyes are widely used as indicators or coloring agents in different applications and knowing their concentration is an essential part for many studies. The proposed spectrophotometer provides many functionalities that clones the traditional expensive spectrophotometers for a budged price under $50. It was aimed to provide a versatile tool for instructors and educators to teach their students the fundamental concepts behind spectrophotometry. Malachite green, methyl red, and methyl orange dyes were chosen to be good samples to show the integrity of the proposed spectrophotometer in terms of accuracy, repeatability, and sensitivity as

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