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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 May 01 2022
Journal Name
Journal Of Engineering
The Collapsible Soil, Types, Mechanism, and identification: A Review Study
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Collapsible soil has a metastable structure that experiences a large reduction in volume or collapse when wetting. The characteristics of collapsible soil contribute to different problems for infrastructures constructed on its such as cracks and excessive settlement found in buildings, railways channels, bridges, and roads. This paper aims to provide an art review on collapse soil behavior all over the world, type of collapse soil, identification of collapse potential, and factors that affect collapsibility soil. As urban grow in several parts of the world, the collapsible soil will have more get to the water. As a result, there will be an increase in the number of wetting collapse problems, so it's very important to com

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Publication Date
Wed Jun 01 2022
Journal Name
Political Sciences Journal
The Middle East and its Strategic Dimensions: a theoretical study
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Characterized the Middle East has geographic, economic, and geostrategic peculiarities, but it suffers from many problems, such as disagreement over what it means as a concept, or what it represents of a geographic extension. The question is related to the ambiguity surrounding the concept of the Middle East? The purpose of its launch? As it relates to its geostrategic, economic, and geo-cultural importance? And manifestations of this importance? And to what extent he retained his value in the strategies of the major powers? Research hypotheses:

-The multiplicity of concepts for the Middle East region, with international political and Geostrategic interests.- The geostrategic value of the Middle East has made it a focal point for

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Publication Date
Sat Jun 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
"Using Markov Switching Model to Investigate the Link between the Inflation and Uncertain Inflation in Iraq for the periods 1980-2010"
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In this paper we use the Markov Switching model to investigate the link between the level of Iraqi inflation and its uncertainty; forth period 1980-2010 we measure inflation uncertainty as the variance of unanticipated  inflation. The results ensure there are a negative effect of inflation level on inflation uncertainty and  all so there are a positive effect of inflation uncertainty on inflation level.                                                   &nbsp

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Publication Date
Wed Jun 28 2023
Journal Name
Al–bahith Al–a'alami
Public Attitudes Towards National Issues in Interactive Television Programs
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This research aims to investigate the extent to which the Iraqi audience relies on interactive television programs as a source of information regarding national issues and their resulting impacts. It seeks to identify the types and nature of attitudes developed among the public towards national issues through these programs and determine the prominent topics and issues highlighted to the audience. The researcher employed a field survey as the primary research method, employing a questionnaire for data collection along with scientific observation and the Likert three-point scale to measure attitudes. The study was guided by the media dependency theory. A sample of 520 questionnaires was distributed to residents in

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Publication Date
Tue Dec 01 2009
Journal Name
Al-khwarizmi Engineering Journal
Study the Axail Dispersion Model in Ion Exchange Column
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A mathematical model is developed which predicates the performance of cylindrical ion exchange bed involving comparing of axial dispersion model for cation exchange column with different assumption, this model permits the performance to predicate the residence time within the bed with the variance, axial dispersion and Pecklet No. to indicated deviation from plug flow model.

      Two type of systems are chosen for positive ions first with divalent ions (Ca+2) to exchange with resin of Na+1form used as application in  water softener units and second with monovalent ions (Na+1) to exchange with resin of H+1 form used as application in deionize water units &n

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Publication Date
Sat Dec 01 2012
Journal Name
Iraqi Journal Of Science
The Effect of Metallicity on the AGB Stars Evolution by Using Synthetic Model
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Abstract: Stars whose initial masses are between (0.89 - 8.0) M☉ go through an Asymptotic Giant Branch (AGB) phase at the end of their life. Which have been evolved from the main sequence phase through Asymptotic Giant Branch (AGB). The calculations were done by adopted Synthetic Model showed the following results: 1- Mass loss on the AGB phase consists of two phases for period (P <500) days and for (P>500) days; 2- the mass loss rate exponentially increases with the pulsation periods; 3- The expansion velocity VAGB for our stars are calculated according to the three assumptions; 4- the terminal velocity depends on several factors likes metallicity and luminosity. The calculations indicated that a super wind phase (S.W) developed on the A

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Publication Date
Thu Sep 01 2011
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The accountancy Using of Gaols programming model to determine the optimal production mix
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The research aims to determine the mix of production optimization in the case of several conflicting objectives to be achieved at the same time, therefore, discussions dealt with the concept of programming goals and entrances to be resolved and dealt with the general formula for the programming model the goals and finally determine the mix of production optimization using a programming model targets to the default case.

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Publication Date
Fri Jan 13 2023
Journal Name
World Academy Of Sciences Journal
Potential effects of miR‑146 expression in relation to malondialdehyde as a biomarker for oxidative damage in patients with breast cancer
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Publication Date
Sat Jun 15 2019
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the effectiveness of using platelet rich fibrin (PRF) as a sole grafting material and membrane in augmentation of dehiscence and fenestration defects encountered during dental implant surgery
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Background: Bone regeneration in dehiscence and fenestration defect can be improved with the use of platelet rich fibrin (PRF) that provides a scaffold for new bone regeneration. This study was conducted to assess the effectiveness of PRF as a graft material and membrane in dehiscence and fenestration defects. Materials and Methods: This prospective clinical study included patients who received dental implants that demonstrated peri-implant defects which were augmented using Leukocyte- PRF (L-PRF) or Advanced-PRF (A-PRF). Twenty four weeks postoperatively the defect resolution and the density of regenerated bone were assessed by CBCT and re-entry surgery. The assessment also included measurement of primary and secondary implant stability

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Publication Date
Mon Oct 01 2012
Journal Name
Al–bahith Al–a'alami
Dealing of the Providers of Sport Media Content with Crises : (The Department of Media of the Ministry of Youth and Sports a Model)
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In a report by Transparency Organization in 2010, Iraq has 200 newspapers, magazines, sixty-seven radio stations and 45 satellite TV channels. The increase in these figures is measured in days or weeks and not months and years. This fact confirms the importance of studying content providers, especially youth sports content, for two reasons: the first is that young people constitute the highest percentage in Iraqi society, with all the potential involved in shaping the future aspects; the second reason is that for years sport has become an important pillar in people's lives not only in the entertainment aspect as it was seen in the past; Rather, sport has an influential presence in politi

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