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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
Sat Jul 30 2022
Journal Name
Global Academic Journal Of Linguistics And Literature
A Critical Stylistic Analysis of Transcultural Identity in Lyer’s The Global Soul (2001) Using the Tool of Negation
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This study is intended to examine the concept of transcultural identity in the travel book The Global Soul: Jet Lag, Shopping Malls, and the Search for Home by (Iyer, 2001). Jeffries’ model of critical stylistics (2010) (henceforth, CS) has been selected to analyze the book. To be more specific, Negation is selected to analyze the concept under study. As such, the study aims at finding out how Negation is used to portray ideological meanings representing the concept of transcultural identity in one non-fictional travel book; and finding out the ideologies related to the concept analyzed. The analysis of the data shows that Negation is a suitable analytical tool to reach the ideational meaning of the text towards the concept of tra

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Publication Date
Mon Mar 01 2010
Journal Name
Journal Of Economics And Administrative Sciences
Pais estimator for the reliability function of the Pareto model of Type I failure
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In this paper an estimator of reliability function for the pareto dist. Of the first kind has been derived and then a simulation approach by Monte-Calro method was made to compare the Bayers estimator of reliability function and the maximum likelihood estimator for this function. It has been found that the Bayes. estimator was better than maximum likelihood estimator for all sample sizes using Integral mean square error(IMSE).

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Publication Date
Sat Jul 01 2017
Journal Name
Journal Of Biological Chemistry
Functional and phylogenetic evidence of a bacterial origin for the first enzyme in sphingolipid biosynthesis in a phylum of eukaryotic protozoan parasites
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Publication Date
Sun Jan 01 2023
Journal Name
Chemical Engineering And Processing - Process Intensification
Optimization of a combined electrocoagulation-electro-oxidation process for the treatment of Al-Basra Majnoon Oil field wastewater: Adopting a new strategy
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Publication Date
Sun Jan 01 2023
Journal Name
Chemical Engineering And Processing - Process Intensification
Optimization of a combined electrocoagulation-electro-oxidation process for the treatment of Al-Basra Majnoon Oil field wastewater: Adopting a new strategy
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The performance of a synergistic combination of electrocoagulation (EC) and electro-oxidation (EO) for oilfield wastewater treatment has been studied. The effect of operative variables such as current density, pH, and electrolyte concentration on the reduction of chemical oxygen demand (COD) was studied and optimized based on Response Surface Methodology (RSM). The results showed that the current density had the highest impact on the COD removal with a contribution of 64.07% while pH, NaCl addition and other interactions affects account for only 34.67%. The optimized operating parameters were a current density of 26.77 mA/cm2 and a pH of 7.6 with no addition of NaCl which results in a COD removal efficiency of 93.43% and a specific energy c

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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

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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
Tue Aug 01 2023
Journal Name
Journal Of Engineering
Risk Response in Construction Project: A Review Study
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Construction projects are characterized as projects with multi phases and activities, complex, unique, and have many different parties and stakeholders. Risks could appear at one or more of the construction project stages and may affect the achievement of project objectives. Therefore, one of the key elements in the planning phase of any project is the risk management process (RMP). This study attempts to understand the terminology of risk in general, risk management, and response to risk in particular. This study is mainly a review of thirty-eight studies that have been published between 1997 and 2020 that demonstrate the importance of the crucial phase of risk response from the risk management process and its impact on

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