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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
Thu Aug 31 2017
Journal Name
Journal Of Engineering
Urban agriculture as one of the ecological applications of the regenerative city
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Recently, several concepts and expressions have emerged that have often preoccupied the world . around the concept of environment and sustainability. This is due to the negative and irresponsible impact of man and his innovations in various industrial and technological fieldsthat have damaged the natural environment. Architecture and cities at the broader level are some of the man made components that caused these negative impacts and in the same time affected by them. What distinguishes architectural and urban projects is the consumption of large . quantities of natural resources and production larger amounts of waste and pollution, along the life of these projects. At the end of the twentieth century and the beginning of the twenty-fir

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Effect of Acidic and Energy Drinks on Surface Roughness of Three Types of Bulk Fill Composite Materials
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ABSTRACT Background: This study aimed to study the effect of some acidic drinks (Vinegars and fresh Orange juice) and energy drinks (Red bull) on surface roughness of three types of bulkfill composite materials: Filtek posterior bulkfill (3M), Sonicfill (Kerr) and Filtek p60 (3M). Materials and Methods: Total number of 120 samples are prepared by using a mold of (12mm diameter and 3mm height), which were divided into three groups forty samples for each group: Group A: Filtek bulkfill posterior composite (3M), Group B: Sonicfill composite (Kerr), Group C: Filtek P60 (3 M) which then divided into four sub- groups (n=10) (1) samples were kept in distilled water as a control group (2) samples were immersed in Redbull (3) samples were immersed

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Publication Date
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research & Development
A 4-Day Plaque-Regrowth Anti-Plaque Effect of a Combination of Green Tea and Salvadora Persica L.: A Randomized Controlled Crossover Clinical Trial
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Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Job involvement for workers and its influence in Crystallize organizational Identification (An analytical research of the opinions of a sample of workers in the Middle East, the Iraqi Investment Bank)
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Abstract:

     The current research is aimed at analyzing the impact of the dimensions of Job involvement of all of (the enthusiasm, the Devotion, Assimilation ) in the Crystallize organizational Identification across the dimensions of (organizational loyalty, membership, similarities) and was named the Middle East, the Iraqi Investment Bank room to look as the research community of staff adopted in the bank, to be applied to a Random sample of (100) employees working in the said bank, and developed for the purposes of data collection, a questionnaire form included three axes covered (32) paragraph of the measure, which is included adopted Liekrt Quintet for the

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Publication Date
Fri Jul 01 2022
Journal Name
Resmilitaris
The right to property is a constitutional restriction on the work of the tax legislator
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The study aims to reach a common point that achieves a balance between two interests, which are generally in conflict with the public interest and the interest of the individual owner of private property, by extrapolating the provisions of the constitutional judiciary that include the protection of private property, and this protection extends to every right of financial value and is not limited to a specific type, but It included everything that can be estimated with money, as ownership is no longer an advantage for the owner, but rather has become a right for him and a social function. The tax is imposed on what is derived from it, but if there is a need to prejudice it, the conditions, limits and restrictions expressly stipulated in the

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Publication Date
Mon Dec 01 2014
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Towards Perceptions building a descriptive and procedural for the knowledge assets at the center of learning and growth for the techniques of Balanced Score card in the light of the strategic map concepts to achieve the strategic and operational: requirements of the contemporary business
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Abstract:

   Witness the current business environment changes rapidly reflected on the performance of the facility wishing to stay , which is no longer style reaction enough to handle installations with their environment , and quickly began to lose its luster with the emergence of a message and the vision of contemporary business environment from a set of parts interacting with each other and the concept of behavioral includes all dimensions of performance, it is imperative to adopt a system installations influence variables and positive interaction through the development of strategic plans and the use of implementation and follow-up strategies to ensure the effectiveness of the method for meas

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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Expression of Syndecan 1 on Periodontium treated with Topical Application of Aloe-Vera
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Background: Periodontium mainly exposed to injury by trauma or pathologic diseases, Aloe vera is a plant has many basic ingredients in its extracted gel that acts as wound healing accelerator in addition to that it's safe, and economical and without recordable of side effect. This study aimed is to evaluate the effect of topical application of Aloe vera on expression of syndecan -1 by periodontium tissue. Materials and methods: Thirty six male Albino rats were subjected for periodontium defect by electric scaler on the distal sides of both lower anterior teeth. The animals divided into two groups; control group (without treatment) and the experimental group treated with 1µLAloe vera gel/normal saline. Periodontal healing was examined at

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Publication Date
Fri Nov 26 2021
Journal Name
Nanomaterials
Solidification Enhancement in a Multi-Tube Latent Heat Storage System for Efficient and Economical Production: Effect of Number, Position and Temperature of the Tubes
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Thermal energy storage is an important component in energy units to decrease the gap between energy supply and demand. Free convection and the locations of the tubes carrying the heat-transfer fluid (HTF) have a significant influence on both the energy discharging potential and the buoyancy effect during the solidification mode. In the present study, the impact of the tube position was examined during the discharging process. Liquid-fraction evolution and energy removal rate with thermo-fluid contour profiles were used to examine the performance of the unit. Heat exchanger tubes are proposed with different numbers and positions in the unit for various cases including uniform and non-uniform tubes distribution. The results show that

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Publication Date
Mon Sep 03 2018
Journal Name
Al-academy
The metaphoric problem of topography In the scenario of war films Model the film (fury)
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The study of topography most important studies and depth of any literary or artistic text and occupy the thinking of many who work in art at generally. There is hardly any film scenario from description in general of the indispensable elements of the composition and place one. So the place starts form since the scriptwriter begins to view the result of the description begins to feature the emergence of there are simple operations in the scenario soon to receive growth as a final achievement in the film. The description of the place begins to take on an allegorical character as a language version in the script, soon translated into another language, the language of the picture. Which in turn complement the creative ring of cinematic art a

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Publication Date
Fri Dec 31 2021
Journal Name
Iraqi Journal Of Laser
Experimental Study to The Effect of Applying Stressing Force on Etched Polarization Maintaining Fiber as Hybrid Fabry-Perot /Mach-Zehnder inline fiber interferometer
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Abstract: The increased interest in developing new photonic devices that can support high data rates, high sensitivity and fast processing capabilities for all optical communications, motivates a pre stage pulse compressor research. The pre-stage research was based on cascading single mode fiber and polarization maintaining fiber to get pulse compression with compression factor of 1.105. The demand for obtaining more précised photonic devices; this work experimentally studied the behavior of Polarization maintaining fiber PMF that is sandwiched between two cascaded singe mode fiber SMF and fiber Bragg gratings FBG. Therefore; the introduced interferometer performed hybrid interference of both Mach-Zehnder

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