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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
Wed Mar 01 2023
Journal Name
Al-khwarizmi Engineering Journal
A Methodology for Evaluating and Scheduling Preventive Maintenance for a Thermo-Electric Unit Using Artificial Intelligence
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Flow-production systems whose pieces are connected in a row may not have maintenance scheduling procedures fixed because problems occur at different times (electricity plants, cement plants, water desalination plants). Contemporary software and artificial intelligence (AI) technologies are used to fulfill the research objectives by developing a predictive maintenance program. The data of the fifth thermal unit of the power station for the electricity of Al Dora/Baghdad are used in this study. Three stages of research were conducted. First, missing data without temporal sequences were processed. The data were filled using time series hour after hour and the times were filled as system working hours, making the volume of the data relativel

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Publication Date
Wed Sep 05 2007
Journal Name
Neural Network World
A canonical generic algorithm for likelihood estimator of first order moving average model parameter
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The increasing availability of computing power in the past two decades has been use to develop new techniques for optimizing solution of estimation problem. Today's computational capacity and the widespread availability of computers have enabled development of new generation of intelligent computing techniques, such as our interest algorithm, this paper presents one of new class of stochastic search algorithm (known as Canonical Genetic' Algorithm ‘CGA’) for optimizing the maximum likelihood function strategy is composed of three main steps: recombination, mutation, and selection. The experimental design is based on simulating the CGA with different values of are compared with those of moment method. Based on MSE value obtained from bot

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Publication Date
Mon Mar 15 2021
Journal Name
Al-academy
Anthropology and Representations of Magic in Arab Theatrical Text Harut and Marut's Play as a Model: وصال خلفة كاظم البكري
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The research (Anthropology and Representations of magic in Arab Theatrical Text, Harut and Marut's play as a Model) is concerned with studying magic and the forms of its presence in the theatrical text in different human cultures where it belongs. The research consists of four chapters.
The first chapter includes the research problem that revolves around the following questions: (what is the mechanism of employing magic anthropology and its representations in the Arab theatrical text Harut and Marut's play as a model?), and the research importance which is attributed to the necessity of studying (magic) in the Arab theatrical text as it is considered the inauguration of one of the social phenomena that many researchers in the field o

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Publication Date
Fri Feb 10 2023
Journal Name
Journal Of Applied Mathematics
The Dynamics of a Delayed Ecoepidemiological Model with Nonlinear Incidence Rate
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In this paper, the general framework for calculating the stability of equilibria, Hopf bifurcation of a delayed prey-predator system with an SI type of disease in the prey population, is investigated. The impact of the incubation period delay on disease transmission utilizing a nonlinear incidence rate was taken into account. For the purpose of explaining the predation process, a modified Holling type II functional response was used. First, the existence, uniform boundedness, and positivity of the solutions of the considered model system, along with the behavior of equilibria and the existence of Hopf bifurcation, are studied. The critical values of the delay parameter for which stability switches and the nature of the Hopf bifurcat

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Publication Date
Wed Dec 15 2021
Journal Name
Al-academy
The communicative education of fine arts in the COVID-19 crisis and its manifestations in the modernization of the works of the Iraqi painter "Nabil Ali as a model"
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 This study attempts to address the importance of communicative digitization in the field of various arts for the sake of continuity of shopping and aesthetic, artistic and intellectual appreciation of artistic achievements by the recipient on various places of their residence in light of the COVID 19 crisis, and to highlight the importance of the plastic arts of the Iraqi painter exclusively and how it expresses in a contemporary way the environment or life reality in Iraq in light of this crisis. With all its implications affecting the life reality from various aspects and methods of its negative and positive employment. As for the research procedures, the researcher reviewed the research methodology represented by the descriptive ana

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Publication Date
Tue Feb 01 2022
Journal Name
Baghdad Science Journal
An Epidemiological and Multidrug Resistance Study for E. coli Isolated from Urinary Tract Infection (Three Years of Study)
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Uropathogenic E. coli (UPEC) is problematic and still the leading cause of urinary tract infections worldwide. It is developed resistance against most antibiotics. The investigation, surveillance system, and efficient strategy will facilitate selecting an appropriate treatment that could control the bacterial distribution. The present study aims to investigate the epidemiology and associated risk factors of uropathogenic E. coli and to study their antibiotic resistance patterns. 1585 midstream urine specimens were collected from symptomatic urinary tract infections (UTI) patients (225 males and 1360 females) admitted to Zakho emergency hospital, Zakho, Kurdistan Region, Iraq from January 2016 until the end of December 2

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Publication Date
Wed May 19 2010
Journal Name
Journal Of College Of Science, University Of Babylon
H-Point Standard Addition Method for Simultaneous Determination of Cimetidine and Erythromycin Ethylsuccinate Drugs Using Bromothymol Blue as a Chromogenic Complexing Agent
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The H-Point Standard Addition Method (H-PSAM) has been applied for spectrophotometric simultaneous determination of Cimetidine and Erythromycin ethylsuccinate using Bromothymol Blue (BTB) as a chromogenic complexing agent in a buffer solution at pH 5.5.

Publication Date
Tue Dec 01 2020
Journal Name
Baghdad Science Journal
Determination of Phosphodiesterase Type 5 Enzyme (PDE-5) Inhibitors and Analogues as Adulterants in Selected Herbal Products using Gas Chromatography–Electron Impact-Mass Spectrometer (GC-EI-MS)
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       Sildenafil, tadalafil, and vardenafil are phosphodiesterase type 5 enzyme (PDE-5) inhibitors used for the treatment of male erectile dysfunction. This present study aims to investigate 55 herbal products indicated for men’s sexual health from the Malaysian market for adulteration of PDE-5 inhibitors and analogues. The screening and identification of 20 PDE-5 inhibitors and analogues in herbal products of various forms (powder, capsules, tablets, and pastels) were conducted using gas chromatography–electron impact-mass spectrometer (GC-EI-MS). The analysis has shown that 19 herbal products were adulterated with PDE-5 inhibitors and analogues. Unique ion fragmentations and the presence of molecular

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Publication Date
Thu Jun 15 2017
Journal Name
International Journal Of Computer Applications
Analytical and Numerical Study of the Temperature Distribution for a Solid Sphere subjected to a Uniform Heat Generation
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Publication Date
Wed Jan 01 2020
Journal Name
Journal Of Southwest Jiaotong University
A Recognition System for Subjects' Signature Using the Spatial Distribution of Signature Body
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This investigation proposed an identification system of offline signature by utilizing rotation compensation depending on the features that were saved in the database. The proposed system contains five principle stages, they are: (1) data acquisition, (2) signature data file loading, (3) signature preprocessing, (4) feature extraction, and (5) feature matching. The feature extraction includes determination of the center point coordinates, and the angle for rotation compensation (θ), implementation of rotation compensation, determination of discriminating features and statistical condition. During this work seven essential collections of features are utilized to acquire the characteristics: (i) density (D), (ii) average (A), (iii) s

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