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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
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
Thu Dec 21 2023
Journal Name
Mathematical Modelling Of Engineering Problems
Enhancing Spatial Accuracy of OpenStreetMap Data: A Geometric Approach
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OpenStreetMap (OSM), recognised for its current and readily accessible spatial database, frequently serves regions lacking precise data at the necessary granularity. Global collaboration among OSM contributors presents challenges to data quality and uniformity, exacerbated by the sheer volume of input and indistinct data annotation protocols. This study presents a methodological improvement in the spatial accuracy of OSM datasets centred over Baghdad, Iraq, utilising data derived from OSM services and satellite imagery. An analytical focus was placed on two geometric correction methods: a two-dimensional polynomial affine transformation and a two-dimensional polynomial conformal transformation. The former involves twelve coefficients for ad

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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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Publication Date
Sun Dec 28 2025
Journal Name
Al–bahith Al–a'alami
Evaluation of the Iraqi Community for Election Campaigns for Candidates of the House of Representatives and Media Coverage in March 2010: (Cairo as a Model)
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The elections of the Council of Representatives in Iraq are one of the manifestations of political participation, which makes it attracts the attention of researchers. Where Iraq witnessed in 2005 important political events in the Iraqi arena, a pluralist parliamentary elections or elections in Iraq by direct free election on January 30, the first almost half a century ago. On November 15 of the same year, Iraq adopted a permanent constitution for the country through a popular referendum.

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Publication Date
Thu Oct 15 2020
Journal Name
International Journal Of Energy Research
Mixed-ligand complexes of ampicillin derived Schiffbase ligand and Nicotinamide: Synthesis, physico-chemical studies, DFT calculation, antibacterial study and molecular docking analysis
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A novel series of mixed-ligand complexes of the type, [ML 1 (L 2 ) 3 ]Cl x [M = Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiffbase (HL 1 ) as main ligand, nicotinamide (L 2 ) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL 1 was prepared by the interaction of ampicillin drug and 4-chlorobenzophenone. The synthesized mixed ligand complexes were characterized by elemental analysis, UV-Vis, FT-IR, 1 H-NMR, 13 C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiffbase ligand, HL 1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxy- gen atom

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Publication Date
Sat Dec 24 2022
Journal Name
Research Journal Of Pharmacy And Technology
Biological Study of protease produced by clinical isolates of Staphylococcus aureus
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The bacterial isolates were obtained from Al-Kindi Hospital were diagnosed by the Vitek-2 system and re confirm by 16srRNA gene as S. aurous, the results were shown 20 isolates (66.7%) out of 30 isolates were positive to protease production. All bacterial isolates (100%) were sensitive to Gentamicin and Levofloxacin. but resistant (100%) to aztreonam. The best temperature for enzyme production from bacteria was 37 °C, and the best pH for enzyme production was 7. Partial purification of the bacterial enzyme (protease) was carried out using short steps included ammonium sulfate 65% saturation, ion exchange using DEAE- cellulose column and then applied on gel filtration chromatography using Sephadex G-200 column. The enzymatic activit

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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Legal Sciences
Judicial Tools in Developing Civil Law Rules – France as a Model
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Despite the principle of separation of powers brought by the French Revolution, which entrusted the task of drafting legislation and its amendment to the legislative authority and the task of settling disputes and settling them in the judiciary. However, since that date, the French judiciary has played a major role in the development of French civil law (In spite of all the economic and social developments that have taken place in French society throughout these years) since its promulgation until February of 2016, the date of the Legislative Decree No. 131 of the year 2016 A modification is the largest in the history of the French Civil Code (which was the judicial precedents in which a significant impact), was assisted by the French judic

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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
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
Mon Sep 12 2016
Journal Name
Revista Pesquisa Em Fisioterapia
YOGA AS A TREATMENT FOR MUSCULOSKELETAL DISCOMFORTS: A HYPOTHESIS
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Introduction: Nowadays, the prevalence of Musculoskeletal Discomforts (MSD) is increasing in the world. As treatment, usually surgery or physiotherapyare recommended, but they are expensive and may cause side effects. Apracticalcourse of treatment without negative side effects and with permanent positive effects is lacking. Objective: To suggest a practical course of treatment, introduced by a licensed Yoga coach who is experienced in this field, and through thatto shed a light on yoga as treatment for MSD. The hypothesis is that yoga may decrease the pain among individuals with MSD. Methods: This hypothesis is presented based on the practical techniques used in Yoga including body relaxation and breathing awareness (2 minutes & 3 minutes r

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