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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 Sep 13 2022
Journal Name
وقائع المؤتمر العلمي الدولي التاسع / المجلة الامريكية الدولية للعلوم الانسانية والاجتماعية
The Relationship between Job Satisfaction and Organizational Loyalty among Baghdad University Employees in light of Covid- 19 A Descriptive Analytical Study (University of Baghdad as a model)
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The educational service industry is one of the most negatively affected industries by the spread of the COVID-19 pandemic. Government agencies have taken many measures to slow its spread, and then restrict movement and gatherings and stop recreational activities. Furthermore, the repercussions of the curfew had a significant impact due to the interruption in actual attendance for students and employees, and the severity of the Covid-19 crisis and its (economic, social, security, humanitarian and behavioral) effects on all societies and work sectors is no secret to anyone. Iraq, like other countries, was also affected by the negative impact of Covid-19 pandemic in all fields of institutional work, especially public fields, and specifically t

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
The Word " בַּיִת " (House) in the Book of Joshua A Comparative Semitic Linguistic Study
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In this paper we have dealt with the word "  בַּיִת" in the Book of Joshua because it makes one of those that highly employed the  word    בַּיִת"  " in the Old Testament. The Book of Joshua comes  sixth   in the order of tanakh wich was written by Joshua son of  Noon in Palestine during the fifteenth century  B.C. and it covers a three-decade era extending from the death  of Moses til the death of Joshua son of Noon.

      The word " בַּיִת " in this paper refers to the place, where expressions are made by a noun modified by a noun . The modifier is"" בַּיִת , and the modified is another noun. Herein, we

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Publication Date
Fri Jan 01 2021
Journal Name
Annals Of Maxillofacial Surgery
The use of screw retained hybrid arch bar for maxillomandibular fixation in the treatment of mandibular fractures: A comparative study
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Introduction: The use of screw-retained hybrid arch bars (HABs) is a relatively recent development in the treatment of mandibular fractures. The purpose of this study is to compare the clinical outcome between HAB and the conventional Erich arch bar (EAB) in the closed treatment of mandibular fractures. Materials and methods: This study included 18 patients who were treated for mandibular fractures with maxillomandibular fixation (MMF), patients were randomly assigned into a control group (n = 10) in which EAB was used and study group (n = 8) in which HAB was used. The outcome variables were time required for application and removal, gingival inflammation scores, postoperative complications, and incidence of wire-stick injury or gloves perf

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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Development of an ANN Model for RGB Color Classification using the Dataset Extracted from a Fabricated Colorimeter
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Codes of red, green, and blue data (RGB) extracted from a lab-fabricated colorimeter device were used to build a proposed classifier with the objective of classifying colors of objects based on defined categories of fundamental colors. Primary, secondary, and tertiary colors namely red, green, orange, yellow, pink, purple, blue, brown, grey, white, and black, were employed in machine learning (ML) by applying an artificial neural network (ANN) algorithm using Python. The classifier, which was based on the ANN algorithm, required a definition of the mentioned eleven colors in the form of RGB codes in order to acquire the capability of classification. The software's capacity to forecast the color of the code that belongs to an ob

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Publication Date
Fri Dec 01 2023
Journal Name
Al-khwarizmi Engineering Journal
Development of an ANN Model for RGB Color Classification using the Dataset Extracted from a Fabricated Colorimeter
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Codes of red, green, and blue data (RGB) extracted from a lab-fabricated colorimeter device were used to build a proposed classifier with the objective of classifying colors of objects based on defined categories of fundamental colors. Primary, secondary, and tertiary colors namely red, green, orange, yellow, pink, purple, blue, brown, grey, white, and black, were employed in machine learning (ML) by applying an artificial neural network (ANN) algorithm using Python. The classifier, which was based on the ANN algorithm, required a definition of the mentioned eleven colors in the form of RGB codes in order to acquire the capability of classification. The software's capacity to forecast the color of the code that belongs to an object under de

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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
1-DOF Model for Fluid-Structure-Interaction Vibration Analysis
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In this paper an attempt to provide a single degree of freedom lumped model for fluid structure interaction (FSI) dynamical analysis will be presented. The model can be used to clarify some important concept in the FSI dynamics such as the added mass, added stiffness, added damping, wave coupling ,influence mass coefficient and critical fluid depth . The numerical results of the model show that the natural frequency decrease with the increasing of many parameters related to the structure and the fluid .It is found that the interaction phenomena can become weak or strong depending on the depth of the containing fluid .The damped and un damped free response are plotted in time domain and phase plane for different model parameters It is fou

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
ETHICAL JOURNALISM IN IRAQ AFTER 2003: Baghdad edition as a model
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The fact of having Journalism being open to people from different orientations professions, working as journalists requiring protection just to spread corruption, is one of the biggest threats faced by journalism.

Journalists noticed the spread of unprincipled journalists with no journalistic ethics amongst them, they tried to protect their profession from these corrupt outsiders who might annihilate the mighty of journalism. The principles of the journalism profession known as journalistic ethics, are one the most important formulations of the law concluded by the journalists and those concerned by the the profession, they were then published in public in order to prove their professionalism, especially for those who don’t und

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Publication Date
Fri Dec 15 2023
Journal Name
Al-academy
Design contexts in interior space design (sewing workshops as a model)
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The topic of context is one of the important topics, which was mentioned as a concept in several fields and different fields, and there were many points of view that defined that concept.
He specified the title of the research (design contexts in the design of the interior space), as the research sought to identify the concept of context in the interior design of the spaces of sewing workshops. The research was divided into four chapters:
The first chapter, which consists of the methodological framework, the problem of research and the need for it, the importance of research, the goal and limits of research for sewing workshops for vocational schools from (2020-2021).
The second chapter: consists of previous studies and the theo

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Publication Date
Sun Jun 15 2025
Journal Name
Iraqi Journal Of Science
Synthesis, Characterization and Quantum Mechanical Study of Some New 2-benzylidenehydrazinecarbothioamide Derivatives as Corrosion Inhibitors for Carbon/mild Steel in Acidic Medium.
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In this work, some of new 2-benzylidenehydrazinecarbothioamide derivatives have been prepared by condensation of thiosemicarbazide and different substituted aromatic benzaldehydes in presence of glacial acetic acid to give compounds (1-6), these compounds have characterized by its physical properties and spectroscopic methods. This work also included theoretical study to prove the ability of these compounds as corrosion inhibitors; The program package of Gaussian 09W with its graphical user interface GaussView 5.0 had used for this purpose; the methods of Density Functional Theory (DFT) with basis set of 6-311G (d,p) / hybrid function of B3LYP and semiempirical method of PM3 have been used, the study included theoretical simulation

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Publication Date
Wed May 10 2023
Journal Name
Journal Of Planner And Development
The impact of population density in sustainable housing - An applied study in the city of Baghdad (Mahalla 817), Al-Bayaa as a model
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Population density represents an important indicator for determining the growth of the size of urban areas. Population density has a direct impact on the quality of life, and its excessive rise may lead to the deterioration of basic service facilities. The problem of the research is that the increase in the total population densities of the residential neighborhood may reflect negatively on the nature of the services provided to the residents in these shops, and thus the failure to achieve sustainability in the residential locality. The research assumes that the increase in population densities negatively affects the achievement of sustainability in the residential neighborhood.

 

      

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