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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
Sun Dec 01 2013
Journal Name
Baghdad Science Journal
Food dyes as an alternative tracking dye for DNA gel electrophoresis
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The chemical, physical and toxicological effects on health of synthetic dyes that used as tracking dye in the electrophoresis requires seriously search about alternative tracking dye. The present study is aimed to find an alternative dye from safe food dyes which commonly used in food coloring. Five dyes were selected depending on their chemical properties and the availability in local market: Brilliant Blue FCF, Tartrazine, Sunset Yellow FCF, Carmoisine, and green traditional, three dyes were chosen to be mixed as loading buffer: Brilliant Blue FCF, Sunset Yellow FCF as a basic because it give the whole range size of most traditional loading buffers that available in market, and adding the Carmoisine as a new indicator for the bands less t

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Publication Date
Mon Sep 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Synthesized 2nd Generation Zeolite as an Acid-Catalyst for Esterification Reaction
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MCM-48 zeolites have unique properties from the surfaces and structure point of view as it’s shown in the results ,and unique and very sensitive to be prepared, have been experimentally prepared and utilized as a second-generation/ acid - catalyst for esterification reactions of oleic acid as a model oil for a free fatty acid source with Ethanol. The characterization of the catalyst used in the reaction has been identified by various methods indicating the prepared MCM-48 is highly matching the profile of common commercial MCM-48 zeolite. The XRF results show domination of SiO2 on the chemical structure with 99.1% and  agreeable with the expected from MCM-48 for it's of silica-based, and the SEM results show the cubic c

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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Role of E-Learning in enhancing Total Quality Management in Educational Institutions: an exploratory study of the opinions of a sample of the staff of the Directorate of Education in the province of Nineveh
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Purpose: The research aims to determine the relationship between E-Learning and Total Quality Management (TQM) in Educational institutions in Nineveh Governorates.

Methodology / Design: The researchers distributed (30) questionnaires to employees (teachers and administrators) of Nineveh Governorate education who represent the community of the research sample, as they were analyzed using the SPSS V.20

The importance of research: The importance of the research in the fact that it focuses on one of the educational methods represented in integrating the traditional method and relying on modern technologies using computers and the Internet in the field of education to improve the reali

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Publication Date
Sat Jun 30 2012
Journal Name
Al-kindy College Medical Journal
The Detection of Silent Celiac Disease In patients With Type 1 Diabetes Mellitus by the use of Anti Tissue Transglutaminase Antibodies
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Objective: Detection the presumptive prevalence of
silent celiac disease in patients with type 1 diabetes
mellitus with determination of which gender more
likely to be affected.
Methods: One hundred twenty asymptomatic patients
[75 male , 45 female] with type 1 diabetes mellitus
with mean age ± SD of 11.25 ± 2.85 year where
included in the study . All subjects were serologically
screened for the presence of anti-tissue transglutaminase
IgA antibodies (anti-tTG antibodies) by Enzyme-
Linked Immunosorbent Assay (ELISA) & total IgA
was also measured for all using radial
immunodiffusion plate . Anti-tissue transglutaminase
IgG was selectively done for patients who were
expressing negative anti-

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Publication Date
Sun Dec 30 2012
Journal Name
Al-kindy College Medical Journal
The Detection of Silent Celiac Disease In patients With Type 1 Diabetes Mellitus by the use of Anti Tissue Transglutaminase Antibodies
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Objective: Detection the presumptive prevalence of silent celiac disease in patients with type 1 diabetes mellitus with determination of which gender more likely to be affected.
Methods: One hundred twenty asymptomatic patients [75 male , 45 female] with type 1 diabetes mellitus with mean age ± SD of 11.25 ± 2.85 year where included in the study . All subjects were serologically screened for the presence of anti-tissue transglutaminase IgA antibodies (anti-tTG antibodies) by Enzyme-Linked Immunosorbent Assay (ELISA) & total IgA was also measured for all using radial immunodiffusion plate . Anti-tissue transglutaminase IgG was selectively done for patients who were expressing negative anti-tissue transglutaminase IgA with low tot

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Publication Date
Sat Jan 02 2021
Journal Name
Journal Of The College Of Languages (jcl)
Determining situational dimensions as a method of Equivalence in the source and target language in the translation of Russian and Arab: ( Понимание реальности ) средство полной эквивалентности текста оргинала и текста перевода на русском и арабском языках
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The present paper stresses the direct effect of the situational dimension termed as “reality” on the authors’ thoughts and attitudes. Every text is placed within a particular situation which has to be correctly identified by the translator as the first and the most important step for a good translation. Hence, the content of any word production reflects some part of reality. Comprehending any text includes comprehending the reality’s different dimensions as reflected in the text and, thus illuminating the connection of reality features.

Аннотация 

Исследование под названием  ((«Понимание реальности» средство полно

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Publication Date
Tue Oct 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Comparison Robust M Estimate With Cubic Smoothing Splines For Time-Varying Coefficient Model For Balance Longitudinal Data
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In this research، a comparison has been made between the robust estimators of (M) for the Cubic Smoothing Splines technique، to avoid the problem of abnormality in data or contamination of error، and the traditional estimation method of Cubic Smoothing Splines technique by using two criteria of differentiation which are (MADE، WASE) for different sample sizes and disparity levels to estimate the chronologically different coefficients functions for the balanced longitudinal data which are characterized by observations obtained through (n) from the independent subjects، each one of them is measured repeatedly by group of  specific time points (m)،since the frequent measurements within the subjects are almost connected an

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Scenarios for investment of proposed marshes and requirements for success:a case study in the Marshlands of maysan
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  The research aims to presenting a number of scenarios for the investment of the marshes. The problem of research problem was that there is no in-depth analysis of the marshes  environment. The traditional methods of  the environmental analysis are insufficient. The research community is represented by the decision makers in Maysan Governorate. The research led to proposing of three scenarios with statement  the requirements for the success of each one. The most important conclusions are that the three proposed scenarios for marshes investment depend on the availability of the required volunteers for each scenario. The higher the availability of the requirements, the more optimistic the scenario becomes. If t

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Publication Date
Sat Mar 31 2018
Journal Name
Journal Of Engineering
Effect of Using Extra Fins on the Pin Fin Classic Geometry for Enhancement Heat Sink Performance using EGM Method
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In the present study, the effect of new cross-section fin geometries on overall thermal/fluid performance had been investigated. The cross-section included the base original geometry of (triangular, square, circular, and elliptical pin fins) by adding exterior extra fins along the sides of the origin fins. The present extra fins include rectangular extra fin of 2 mm (height) and 4 mm (width) and triangular extra fin of 2 mm (base) 4 mm (height). The use of entropy generation minimization method (EGM) allows the combined effect of thermal resistance and pressure drop to be assessed through the simultaneous interaction with the heat sink. A general dimensionless expression for the entropy generation rate is obtained by con

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Publication Date
Wed Nov 23 2022
Journal Name
Dental Hypotheses
Remineralization of Dentine Caries Using Moringa Oleifera Based Nano-Silver Fluoride: A Single-Blinded, Randomized, Active-Controlled Clinical Trial
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