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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
Mon Mar 18 2019
Journal Name
Al-khwarizmi Engineering Journal
Best Level of Parameters for a Critical Buckling Load for Circular Thin- Walled Structure Subjected to Bending
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Circular thin walled structures have wide range of applications. This type of structure is generally exposed to different types of loads, but one of the most important types is a buckling. In this work, the phenomena of buckling was studied by using finite element analysis. The circular thin walled structure in this study is constructed from; cylindrical thin shell strengthen by longitudinal stringers, subjected to pure bending in one plane. In addition, Taguchi method was used to identify the optimum combination set of parameters for enhancement of the critical buckling load value, as well as to investigate the most effective parameter. The parameters that have been analyzed were; cylinder shell thickness, shape of stiffeners section an

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Publication Date
Mon Sep 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
The New Synthesis of Potassium-Exchange Zeolite A
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Publication Date
Wed May 12 2021
Journal Name
Journal Of Biotechnology Research Center
A review of the Common Food-borne Viruses
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Publication Date
Wed Jan 01 2020
Journal Name
Italian Journal Of Pure And Applied Mathematics
The non-zero divisor graph of a ring
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Publication Date
Sun Mar 06 2016
Journal Name
Baghdad Science Journal
A Note on the Perturbation of arithmetic expressions
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In this paper we present the theoretical foundation of forward error analysis of numerical algorithms under;• Approximations in "built-in" functions.• Rounding errors in arithmetic floating-point operations.• Perturbations of data.The error analysis is based on linearization method. The fundamental tools of the forward error analysis are system of linear absolute and relative a prior and a posteriori error equations and associated condition numbers constituting optimal of possible cumulative round – off errors. The condition numbers enable simple general, quantitative bounds definitions of numerical stability. The theoretical results have been applied a Gaussian elimination, and have proved to be very effective means of both a prior

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Publication Date
Sun Mar 01 2020
Journal Name
Al-mustansiriyah Journal Of Science
Evaluation the activity of Petroselinum crispum aqueous extract as promoter rooting for stem cuttings of some plants
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This study was conducted in the botanical garden, Department of biology, College of Science/ Mustansiriyah University in from (15 February to 15 March, 2019) under the natural environmental conditions in the greenhouse in order to evaluate the effectiveness of parsley aqueous extract as a promoter for rooting. The study included the use of aqueous extract of a plant Parsley (Petroselinum crispum) extract was used in concentrations (1.25, 2.5 g / l), compare with IBA in concentration (100 mg / L) with dipping time 24 hour for all treatments. The cutting stems were included Rosmarinus officinalis, Nerium oleander, Olea europaea, Plumeria alba, Hibiscus rosa, Pelargonium graveolens, and Myrtus communis. The following measurements were

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Publication Date
Sat May 01 2021
Journal Name
Journal Of Physics: Conference Series
Evaluate the performance of horizontal flow wetlands as an option for tertiary treatment of secondary sedimentation basins
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Abstract<p>Constructed wetlands (CWs) are simple low-cost wastewater treatment units that use natural process to improve the effluent water quality and make it possible for its reuse.in this study used the horizontal flow system for the tertiary treatment of wastewater effluent from secondary basins at Al-Rustamiya wastewater treatment plant / old project / Baghdad / Iraq. the Phragmites Australis plant was used for wastewater treatment and the horizontal subsurface flow system was applied. the experimental study was carried out in February 2020 to October 2020. the parameters were monitored for a period of five weeks, Concentration-based average removal efficiencies for HSSF-CW were COD,53% [NO</p> ... Show More
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Publication Date
Fri May 19 2023
Journal Name
Revista Iberoamericana De PsicologÍa Del Ejercicio Y El Deporte
THE EFFECT OF SPECIAL EXERCISES ACCORDING TO A DESIGNED DEVICE IN DEVELOPING THE PERFORMANCE OF A KINETIC CHAIN ON THE BALANCE BEAM DEVICE
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Publication Date
Tue Dec 13 2022
Journal Name
Dental Hypotheses
Comparative Evaluation of Marginal Microleakage Between Bulk-Fill, Preheated Bulk-Fill, and Bulk-Fill Flowable Composite Resins Above and Below Cemento-Enamel Junction Using Micro-Computed Tomography: An In Vitro Study
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Objective: The aim of this study was to compare the marginal microleakage between bulk-fill, preheated bulk-fill, and bulk-fill flowable composite resins above and below cemento-enamel junction (CEJ) using micro-computed tomography. Methods: Sixty freshly extracted premolar teeth were prepared with a slot shaped cavities of a total of 120 Class II: 3mm (bucco-lingual), 2mm (mesio-distal) with mesial-gingival margin located 1mm coronal to CEJ, and distal gingival margin located 1mm apical to the CEJ. The samples were randomly divided into two main groups according to the restorative material (Tetric EvoCeram and 3M Filtek), and each group was further sub-divided into three subgroups according to the consistency (bulk fill, preheated bulk fil

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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of The College Of Languages (jcl)
Interlanguage Pragmatics of Non-Institutional Criticism: A Study of Native and Non-Native Speakers of English
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Criticism is inherently impolite and a face-threatening act generally leading to conflicts among interlocutors. It is equally challenging for both native and non-native speakers, and needs pre-planning before performing it. The current research examines the production of non-institutional criticism by Iraqi EFL university learners and American native speakers. More specifically, it explores to what extent Iraqi EFL learners and American native speakers vary in (i) performing criticism, (ii) mitigating criticism, and (iii) their pragmatic choices according to the contextual variables of power and distance. To collect data, a discourse-completion task was used to elicit written data from 20 Iraqi EFL learners and 20 American native speaker

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