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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 Apr 24 2020
Journal Name
Opción
Hyperbole in poetry: A case study of exaggeration
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The present study identifies the linguistic means used to realize hyperbole in poetry as a rhetorical device that makes readers experience the beauty of poetic language. To achieve the aim of the study, a model of analysis in accordance with Spitzbardt (1963), Norrick (1982), and McCarthy & Carter (2004) is used. The analysis of data under investigation reveals that hyperbole is a crucial aid used by poets to portrait the real world as imaginative. In conclusion, poets prefer using lexico-grammatical repertoires than lexico-grammatical configurations. Keywords

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Publication Date
Mon Jan 02 2023
Journal Name
Welcome To International Journal Of Research In Social Sciences & Humanities
A Pragmatic Study of Hedging in Academic Discourse
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Welcome to International Journal of Research in Social Sciences & Humanities (IJRSSH). It is an international refereed journal of Social Sciences, Humanities & Linguistics in English published quarterly, both print and online.

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Publication Date
Fri Sep 30 2016
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Morphological Study of Alumina Hollow Fiber Membrane
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Morphologies of ceramic hollow fiber membranes prepared by a combined phase-inversion and sintering method were studied. The organic binder spinning solution containing suspended Al₂O₃ powders was spun to a hollow fiber precursor, which was then sintered at elevated temperatures( 300 ˚C, 1400 ˚C, 25 ˚C) in order to obtain the Al₂O₃ hollow fiber membranes. The spinning solution consisted of polyether sulfone (PES), N-methyl-2-pyrrolidone (NMP), which were used as polymer binder, solvent, respectively. The prepared Al₂O₃ hollow fiber membranes were characterized by a scanning electron microscope (SEM). It is believed that finger-like void formation in asymmetric ceramic membranes is initiated by hydrodynamically unstable vis

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Publication Date
Tue Aug 16 2016
Journal Name
Case Studies In Surgery
Ameloblastoma: A clinical study of 25 Iraqi patients
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Objective: Geographic differences in clinical and pathological aspects of ameloblastoma have been suggested, therefore the purpose of this study was to analyze cases of ameloblastoma in terms of clinical and radiographic manifestations, histopathological types, treatment modalities and recurrence rate and compare them with reports from other parts of the world. Methods: The medical reports of patients diagnosed with ameloblastoma were reviewed and the data concerning the age, gender, chief complaint, the anatomical site of the lesion, radiographic appearance, histopathological diagnosis, treatment approach and recurrence were retrieved. Surgical treatment consisted of either enucleation with curettage and peripheral ostectomy or resection;

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Application of Finite Element Technique: A Review Study
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The finite element approach is used to solve a variety of difficulties, including well bore stability, fluid flow production and injection wells, mechanical issues and others. Geomechanics is a term that includes a number of important aspects in the petroleum industry, such as studying the changes that can be occur in oil reservoirs and geological structures, and providing a picture of oil well stability during drilling. The current review study concerned about the advancements in the application of the finite element method (FEM) in the geomechanical field over a course of century.

Firstly, the study presented the early advancements of this method by development the structural framework of stress, make numerical computer solution

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Publication Date
Wed May 29 2019
Journal Name
Iraqi Journal Of Physics
A Spectroscopic and structural study of FeCoSb alloy
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Fe, Co and Sb nanopowders were fruitfully prepared by electrical wire explosion method in Double distilled and de-ionized water (DDDW) media. The formation of iron, cobalt and antimony (FeCoSb) alloy nanopowder was monitored by X-ray diffraction. The x-ray diffraction pattern indicates that there are iron, cobalt and antimony peaks. Optical properties of this alloy nanoparticles were characterized by UV-Visible absorption spectra. The absorption peak position is shifted to the lower wavelengths when the current increases. That means the mean size of the nanoparticles controlled by changing the magnitude of the current. The surface morphological analysis is carried out by employing Scanning Electron Microscope (SEM). Particles with varies

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Publication Date
Wed May 17 2023
Journal Name
Journal Of Engineering
A Simulation of Core Displacement Experiments for the Determination of the Relative Permeability
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Computations of the relative permeability curves were made through their representation by two functions for wetting and nonwetting phases. Each function contains one parameter that controls the shape of the relative permeability curves. The values of these parameters are chosen to minimize an objective function, that is represented as a weighted sum of the squared differences between experimentally measured data and the corresponding data calculated by a mathematical model simulating the experiment. These data comprise the pressure drop across core samples and the recovery response of the displacing phase. Two mathematical models are constructed in this study to simulate incompressible, one-dimensional, two-phase flow. The first model d

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Publication Date
Thu Jun 06 2013
Journal Name
Advances In Physics Theories And Applications
Adsorption study of Symmetrical schiff base ligand 4,4 -[hydrazine -1,2- diylidenebis ( methan-1-yl-1-ylidene) bis ( 2-methoxyphenol)] on Granulated Initiated calcined Iraqi …
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Publication Date
Fri Jan 01 2016
Journal Name
European Journal Of Biology And Medical Science Research
Impact of an educational intervention of training of breast feeding promoting on the knowledge and attitude of a sample of mothers: a study of a pre and post evaluation.
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Background: Health professionals have a crucial role in promotion, support and management of breastfeeding. To be effective in this effort, the clinician should focus on the issue from the preconception stage through pregnancy and delivery, and continue in subsequent infant care. Aim of the study: to assess the effectiveness of the UNICEF/WHO 40-hour of breast feeding training through the assess breastfeeding knowledge and attitudes of the health profession staff before and after training course.

Publication Date
Wed Jun 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
The role of the cognitive peak and its implications for achieving outstanding performanceAnalytical study of the views of a sample of the staff of the University of Baghdad
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        Knowledge represents the foundation stone for the work of all organizations, are working who leads the thinking of individuals is the ability that leads to behavior based on rationality, it is the work that creates value to the organization and thus gain access to performance winning where that knowledge is a new type of capital based on the thought and experience and is the so-called intellectual capital, which is renewable and is constantly evolving. The study sought to explain the role of the climax  knowledge in achieving the highest levels of performance Organizational and then access to the performance winning in educational organizations the study sample, was found to be a co

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