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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 Feb 20 2026
Journal Name
Journal Of Baghdad College Of Dentistry
An evaluation of an Iraqi phosphate-bonded investment and a commercial type on the marginal fit of ceramometalcopings using three different investing and burnout techniques
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Background: The accuracy of fitness of any dental casting is imperative for the success of any prosthodontic treatment. From the time that dental casting was first introduced, efforts have been made to produce more accurate and better fitted castings with minimal marginal discrepancy. The aim of this in vitro study was to evaluate the effects of three different investing and burnout techniques on the vertical marginal discrepancies ofceramometalcopings invested with two types of phosphate- bonded investments. Materials and methods: Sixty wax patterns were fabricated on a standardized prepared brass die representing an upper central incisor by the aid of a custom-made split mold. Three different investing and burnout techniques were applied

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Publication Date
Wed Sep 15 2021
Journal Name
Al-academy
Processes directing the scenographic space in the Iraqi theatrical show Shakespeare texts as a model: فرحان عمران موسى - سماء محي عطية محمد
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The operative system of theatrical performance depends on the construction of the scenographic space, as it constitutes the most aesthetic effect of the recipient, and the body of the theatrical discourse that contains the signs of the show, and it comes as an embodiment of the directing vision of the show director, so most of the world directors resorted to attention to the output treatment to establish the scenographic space, and thus it possesses a contrast in The embodiment of the directing vision according to the stylistic and hermeneutical dimension of the director, so the two researchers found the importance of studying the topic, and the study came under the title (Directing Treatments of the Scenographic Space in the Iraqi Theat

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Publication Date
Mon Dec 31 2018
Journal Name
Journal Of The Faculty Of Medicine Baghdad
Dyslipidemia and CA15-3 serum level in Iraqi Women with Breast Tumor: A Comparative Study
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Publication Date
Wed Jun 14 2023
Journal Name
Al-academy
Expressive Topics in Plastic Art Achievement A comparative study between Gustav Klimt and Star Kauusch
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 Schools and artistic trends derive their themes from artistic styles and styles as methods followed by the artist to express his themes embodied in the values of artistic and plastic elements as symbols and signs that can be described according to the type of art school and the extent to which the artist is influenced in employing them as a goal to achieve the plastic achievement in the painting, and from those vocabulary (human beings nature Life) as encoded messages that have an appearance and an interior, the appearance of which are forms, colors, formats and distributions of space and their interior meanings and semantics embody attitudes, events and circumstances that stem from the social depth and daily life and derive their comp

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Publication Date
Tue Dec 06 2022
Journal Name
International Journal Of Professional Business Review
A Comparative Study to Reveal Earnings Management in Emerging Markets: Evidence from Tunisia and Iraq
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Purpose: The purpose of the study is to compare and evaluate Earnings Management in Tunisia and Iraq.   Theoretical framework: Earnings Management is an important topic that has been studied by a significant number of researchers, as well as those who are interested in the accounting profession. Earnings Management has gotten a lot of attention from academics, professionals, and other interested parties in recent years (e.g. Kliestik et al., 2020; Rahman et al., 2021; Gamra &Ellouze, 2021)   Design/methodology/approach: The sample includes ten banks listed on the Bourse of Tunisia and Iraq Stock Exchanges for the year 2017. We have used a model of Kothari et al., (2005) as a tool to measure Earnings Management in both mark

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Publication Date
Thu Jun 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Methods of Forecasting Credit Losses in A Sample of Iraqi Banks - A Comparative Analysis
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  The general trend in Iraqi banks is focused towards the application of international financial reporting standards, especially the international financial reporting standard IFRS 9 “Financial Instruments”, in addition to the directives issued on the Central Bank of Iraq’s instructions for the year 2018 regarding the development of expected credit losses models, and not to adhere to a specific method for calculating these losses and authorizing the banks’ departments to adopt the method of calculating losses that suits the nature of the bank’s activity and to be consistent in its use from time to time. The research problem revolves around the different methodologies for calculatin

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Publication Date
Wed Sep 15 2021
Journal Name
Al-academy
The plastic structure in the lyrical introduction to pre-Islamic poetry " The hanging Tarfa bin Al-Abd as a model": زينب خليل حسين
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The research deals with the lyrical introduction in the commentary of Tarfa bin al-Abd as a formative system characterized by flexibility and richness of imagination, which achieved a formative treatment and a unique construction within the structures of the structural and semantic language. I dealt with the poetic verses represented by the lyrical introduction as a formative hypothesis, basing its goal on a methodological framework distributed on the problem that was summarized by the following question: Is it possible to look at the poetic pattern within the pre-Islamic poem / hanging blinking as a model, in its plastic dimensions and to identify the stylistic treatment that achieves the formation space within the poetic text. The rese

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Publication Date
Tue Feb 05 2019
Journal Name
Journal Of The College Of Education For Women
A comparative study in disruptive behavior at the Deprived and non-Deprived students from their parents at the Secondary stage
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The current research aims to :
•know the level of the chaotic behavior of the sample as a whole .
•Know the differences with statistical significance in disorderly behavior between the
disadvantaged and non-disadvantaged peers .
To achieve these objectives, the selected sample of Talbhalmrahlh medium and specifically
students of the second grade average, were chosen randomly stratified's (360) students
included sex (male, female) and (deprived of the Father and the non-deprived) for the
academic year (2013-2014) to the province Baghdad on both sides (Rusafa-Karkh (
As applied to them measurements of disorderly behavior, which is prepared by the researcher,
having achieved _khasaúsma of psychometric (valid

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for three mB2

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for thr

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