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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 Aug 01 2016
Journal Name
Indonesian Journal Of Electrical Engineering And Computer Science
Wireless Indoor Localization Systems and Techniques: Survey and Comparative Study
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<p>The popularity, great influence and huge importance made wireless indoor localization has a unique touch, as well its wide successful on positioning and tracking systems for both human and assists also contributing to take the lead from outdoor systems in the scope of the recent research works. In this work, we will attempt to provide a survey of the existing indoor positioning solutions and attempt to classify different its techniques and systems. Five typical location predication approaches (triangulation, fingerprinting, proximity, vision analysis and trilateration) are considered here in order to analysis and provide the reader a review of the recent advances in wireless indoor localization techniques and systems to hav

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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Professional awareness among Riyadh teachers government and private (Comparative Study)
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Take the teacher's key position in the educational system as a foundation stone and primarily responsible for achieving the goals of Education , and efficient teacher conscious is the teacher who prepared educationally and specialized training well add to the enjoyment of a range of features that enable them to adjust and compatibility with educational developments
Hence the problem of the study questioning the Kindergarten Does teacher professional awareness that enable it to perform its work learned from experienceThe research sought to measure
1-Professional awareness among teacher Kindergarten
2-Professional awareness of Kindergarten parameters depending on the type of kindergarten.
Limited search parameters Riyadh govern

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn: 1683 - 3597 , E-issn : 2521 - 3512)
Single Dose Antibiotic Prophylaxis in Outpatient Oral Surgery Comparative Study
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         It is clear that correct application of antibiotic prophylaxis can reduce the incidence of infection  resulting from the bacterial  inoculation in a variety of clinical situations; it cannot   prevent  all  infections  any  more  than it  can   eliminate  all  established infections. Optimum  antibiotic   prophylaxis  depends on:  rational  selection  of the drug(s),  adequate  concentrations  of the  drug  in  the  tissues that  are at risk, and attention to  timing  of  administration.  Moreover,  the  risk  of  infection  in  some situations  does not outweigh  the risks which  attend the administration of even the safest antibiotic drug. The aim of this study was to comp

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Publication Date
Wed Aug 19 2020
Journal Name
Applied Water Science
Spiral path three phase fluidized bed reactor for treating wastewater contaminated with engine oil
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Abstract<p>In this study, a new type of circulating three-phase fluidized bed reactor was conducted by adding a spiral path and was named as spiral three-phase fluidized bed reactor (TPFB-S) to investigate the possibility for removing engine oil (virgin and waste form) from synthetic wastewater by using Ricinus communis (RC) leaves natural and activated by KOH. The biosorption process was conducted by changing particle diameter in the range 150–300 and 300–600 µm, liquid flow rate in the range 2.5–4.5 L/min and gas flow rate in range of 0–1 L/min, while other parameters initial oil emulsion concentration, pH, adsorbent concentration, agitation speed and contact time were kept constant at 2000 mg/L, 2,</p> ... Show More
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Publication Date
Wed Aug 20 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of antibacterial action of photosensitizer solution activated by diode lamp and three intracanal medicaments (in vitro study)
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Background: The elimination of the microorganisms from the root canal systems, an important step for the successful root canal treatment. This study was conducted to evaluate the antibacterial effectiveness of the photoactivated disinfection by using the toluidine blue O and a low- energy light emitting diode (LED) lamp . Materials and method: Sixty single rooted extracted teeth were decoronated, instrumented, irrigated, sealed at the apex and contaminated with endodontic anaerobic bacteria for 7 days to form biofilms in prepared root canals. Group I. Twelve teeth were medicated by photosensitizer (toluidine blue O) solution activated by diode lamp (FotoSan; CMS Dental, Copenhagen, Denmark).Group II. Twelve teeth were medicated by the tricr

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Publication Date
Mon Jan 01 2018
Journal Name
The Journal Of Contemporary Dental Practice
Assessment of Ions released from Three Types of Orthodontic Brackets immersed in Different Mouthwashes: An in vitro Study
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Publication Date
Tue Jan 01 2019
Journal Name
Journal Of Global Pharma Technology
Study of the genetic diversity in three species belonging to family: Daphniidae (Crustaceae, Cladocera) collected from different regions in Baghdad Province/Iraq
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Publication Date
Thu Oct 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
Choose the best model for building life tables in Iraq
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Demography or population studies or demography is the science that is based on the different characteristics of the population scientific study, and represent a population studies principled way to understand the population of society, in addition to verification of the population in a given area determine the reason for the increase or decrease this number from the previous statistical As these studies estimate future trends for the occurrence of demographic change in terms of birth, death and migration That the registration of deaths of paramount importance narrated that way can the demographic reality of the population analysis, and coverage of the health authorities' needs and enable government institutions of decision-making

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Publication Date
Tue May 16 2023
Journal Name
Journal Of Engineering
Statistical Model for Predicting the Optimum Gypsum Content in Concrete
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The problem of internal sulfate attack in concrete is widespread in Iraq and neighboring countries.This is because of the high sulfate content usually present in sand and gravel used in it. In the present study the total effective sulfate in concrete was used to calculate the optimum SO3 content. Regression models were developed based on linear regression analysis to predict the optimum SO3 content usually referred as (O.G.C) in concrete. The data is separated to 155 for the development of the models and 37 for checking the models. Eight models were built for 28-days age. Then a late age (greater than 28-days) model was developed based on the predicted optimum SO3 content of 28-days and late age. Eight developed models were built for all

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Publication Date
Thu Apr 08 1999
Journal Name
Abhath Al- Yarmouk [basic Sciences And Engineering]
Model for Predicting the Cracking Moment in Structural Concrete Members
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