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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 Sep 30 2020
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The Impact of Earnings Quality using the Sustainability model (Persistence) and predictability in the Continuity of the Banks: بحث تطبيقي في عينة من المصارف التجارية المدرجة في سوق العراق للاوراق المالية
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The research aims to measure the extent of the impact of Earnings quality in the continuity of the company for a sample of private commercial banks listed on the Iraq Stock Exchange. The research sample included (15) of the listed commercial banks that continue to issue their financial statements for the period from (2009-2018).The research relied on three main models of measurement and on four steps. The first step is to measure the Persistence (Earnings Quality) by Depending the sustainability model. While the second step included measuring the Predictability of accounting profits by deriving the square root of the disparity of the estimation error from the first model Persistence (Earnings Quality), and the third step included

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Publication Date
Sat Feb 02 2019
Journal Name
Journal Of The College Of Education For Women
The Babylonian Woman As Heroine In Dekker’s Drama: The Babylonian Woman As Heroine In Dekker’s Drama
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Abstract
The present research paper provides an analysis of Thomas Dekker’s
exaltation of the figure of the Babylonian woman as a tragic heroine in his dramatic
art. The paper falls into two sections. The first section outlines the deliberate
mispresentation of the figure of the Babylonian woman in the Bible and the
misreading of that figure. The second section reveals Dekker’s rectification of the
distorted image of the Babylonian woman, whom he defends and glorifies as a
heroine and a victim of misinterpretation and conspiracy.

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Evaluation of Integrated Information Technology System in Organizations “Exploratory Comparative Search for opinions of sample of Workers in the Faculties of Science & Education AL- Asma'I at the University of Diyala
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       The subject of the information technology system ( ITS ) of the important issues And contemporary thought in management, and various types of organizations seeking to apply and try to

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Publication Date
Wed Nov 26 2025
Journal Name
Al-fatih Journal
The impact of the use of some herbal sedative level of achievement in the development of air pistolEmpirical researchOn a sample of players Faculty of Physical Education for Girls
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تعد الرماية واحدة من الألعاب التي يقاس مستوى الانجاز فيها بالأرقام إذ ارتفعت الأرقام المسجلة بالنسبة لسلاح المسدس الهوائي حتى وصلت عند بعض الأبطال العالميين إلى الانجاز النهائي ، وقد لجأ المدربون إلى مختلف الطرق التدريبية, وان ضعف الثبات والتركيز هما اللذان يقودان إلى هبوط مستوى الانجاز في الرماية ، ولتحقيق التركيز والثبات المطلوبين أثناء الرمي يجب التدريب على مطاولة حمل السلاح التي تعد من أصعب تدريبات الر

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Publication Date
Mon Dec 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Biodiesel production from used vegetable oil (sunflower cooking oil) using eggshell as bio catalyst
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Bio-diesel is an attractive fuel fordiesel engines. The feedstock for bio-diesel production is usually vegetable oil, waste cooking oil, or animal fats. This work provides an overview concerning bio-diesel production. Also, this work focuses on the commercial production of biodiesel. The objective is to study the influence of these parameters on the yield of produced. The biodiesel production affecting by many parameters such s alcohol ratio (5%, 10%,15 %, 20%,25%,30%35% vol.), catalyst loading (5,10,15,20,25) g,temperature (45,50,55,60,65,70,75)°C,reaction time (0-6) h, mixing rate (400-1000) rpm. the maximum bio-diesel production yield (95%) was obtained using 20% methanol ratio and 15g biocatalyst at 60°C.

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Publication Date
Thu Mar 17 2016
Journal Name
International Journal Of Computer Applications
Analysis of Wind Speed Data and Annual Energy Potential at Three locations in Iraq
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Publication Date
Sat Jan 01 2022
Journal Name
Journal Of Applied Biology & Biotechnology
Field treatment of three wheat varieties with Trichoderma harzianum bioagent to control Anguina tritici
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Publication Date
Tue Dec 20 2022
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
FIRST RECORD OF TWO DIPLECTANID MONOGENOIDS FROM THREE SPARID FISHES IN IRAQI MARINE WATERS
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Parasitological examination of gills of three species of sparid fishes in the territorial waters of Iraq was performed, two diplectanid monogenoids were isolated and described; Lamellodiscus indicus Tripathi, 1959 from both Haffara seabream Rhabdosargus haffara (Forsskål, 1775) and Goldline seabream R. sarba (Forsskål, 1775) and Protolamellodiscus senilobatus Kritsky, Jiménez-Ruiz and Sey, 2000 from King soldierbream Argyrops spinifer (Forsskål, 1775). The record of the parasites is considered new to the parasite fauna of Iraq. The redescription of L. indicus for the first time which is collected from a new distribution area (Arabian Gulf). R. haffara is considered a new host record .

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Publication Date
Thu Sep 01 2011
Journal Name
Journal Of Economics And Administrative Sciences
Comparison of BASE methods with other methods for estimating the measurement parameter for WEBB distribution using simulations
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  Weibull distribution is considered as one of the most widely  distribution applied in real life, Its similar to normal distribution in the way of applications, it's also considered as one of the distributions that can applied in many fields such as industrial engineering to represent replaced and manufacturing time ,weather forecasting, and other scientific uses in reliability studies and survival function in medical and communication engineering fields.

   In this paper, The scale parameter has been estimated for weibull distribution using Bayesian method based on Jeffery prior information as a first method , then enhanced by improving Jeffery prior information and then used as a se

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Publication Date
Mon Jan 01 2024
Journal Name
Journal Of Stomatology
The effect of Winter’s red line, angle of impaction, and radio-morphometric indices on surgical difficulty of impacted mandibular third molar: a prospective observational study
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