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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 02 2017
Journal Name
Journal Of Engineering
Estimation Curve Numbers using GIS and Hec-GeoHMS Model
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Recently, the development and application of the hydrological models based on Geographical Information System (GIS) has increased around the world. One of the most important applications of GIS is mapping the Curve Number (CN) of a catchment. In this research, three softwares, such as an ArcView GIS 9.3 with ArcInfo, Arc Hydro Tool and Geospatial Hydrologic Modeling Extension (Hec-GeoHMS) model for ArcView GIS 9.3, were used to calculate CN of (19210 ha) Salt Creek watershed (SC) which is located in Osage County, Oklahoma, USA. Multi layers were combined and examined using the Environmental Systems Research Institute (ESRI) ArcMap 2009. These layers are soil layer (Soil Survey Geographic SSURGO), 30 m x 30 m resolution of Digital Elevati

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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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Publication Date
Tue Sep 15 2020
Journal Name
Journal Of Baghdad College Of Dentistry
The impact of various staining substances and immersion time on the stainability of bonded sapphire brackets with three kinds of light cure orthodontic adhesives (An in-vitro study)
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Background: The need of the patient for a more reasonable esthetic orthodontic intervention has risen nowadays. Thus, orthodontists make use of esthetic orthodontic materials like brackets, ligature elastics, and arch wires. The esthetic brackets come as different forms of materials, such as ceramic brackets, which have their stainability remaining as the most important consideration for the patients and the orthodontists. This study aimed to compare the staining effects of various staining materials, including black tea, cigarette smoke and Pepsi, as well as the time effect on the color stability of sapphire ceramic brackets bonded with three kinds of light cure orthodontic adhesives: Transbond, Resilience and Enlight. Materials and Met

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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
Thu Jan 02 2020
Journal Name
Journal Of The College Of Languages (jcl)
The newspaper is a field for the use of phraseologism: Газета как сфера использованиея фразеологических единиц
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Idiomatic expressions in Russian journalism make one important borrowed means for making a dialogue with the receiver's intellect in so far as it has the distinct feature of  having clarity and exactness of meaning. The meaning is seen as a shortcut for covering a series of concepts and details so as to arrive at the intended meaning. This is done by stimulating the reader by the use of certain clear idioms. The use of such idioms in a journalistic text is not for a linguistic purpose only, but it is a cultural and social phenomenon reflecting the type of current changes in the society and it aims at discoursing with the reader's mind. This paper is a practi

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