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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 Apr 24 2022
Journal Name
Egyptian Journal Of Chemistry
A novel Tubular Electrochemical Reactor with a Spiral Design of Anode for Treatment of Petroleum Refinery Wastewater
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Publication Date
Sun Dec 12 2010
Journal Name
Journal Of Planner And Development
A documentary study of natural resources and ways of protecting them
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The problem of research is that there are ways to protect and sustain environmentally important sites in Iraq. There are no documentary sources for these sites, such as the natural landscape of natural and important natural resources, which suffer from severe environmental neglect

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Publication Date
Mon Dec 03 2018
Journal Name
Journal Of Engineering
Comparative Analysis of Various Multicarrier Modulation Techniques for Different Multilevel Converters
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The applications of Multilevel Converter (MLC) are increased because of the huge demand for clean power; especially these types of converters are compatible with the renewable energy sources. In addition, these new types of converters have the capability of high voltage and high power operation. A Nine-level converter in three modes of implementation; Diode Clamped-MLC (DC-MLC), Capacitor Clamped-MLC (CC-MLC), and the Modular Structured-MLC (MS-MLC) are analyzed and simulated in this paper. Various types of Multicarrier Modulation Techniques (MMTs) (Level shifted (LS), and Phase shifted (PS)) are used for operating the proposed Nine level - MLCs. Matlab/Simulink environment is used for the simulation, extracting, and ana

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Publication Date
Thu Sep 15 2022
Journal Name
Journal Of Baghdad College Of Dentistry
Dental Aerosol Hazard Prevention with Pre-procedural Antiseptic Mouthwashes (Comparative Study)
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Background: One of the recommended methods for reducing aerosol contamination during the daily regular usage of high-speed turbine and ultrasonic scaling is the use of preprocedural mouth rinse. Several agents have been investigated as a preprocedural mouth rinse. Chlorhexidine significantly reduce the viable microbial content of aerosol when used as a preprocedural rinse. Studies have shown that cetylpridinum chloride (CPC) mouthwash is equally effective as chlorhexidine in reducing plaque and gingivitis. This study compared the effect of 0.07% CPC to 0.2% chlorhexidine gluconate (CHX) as preprocedural mouth rinses in reducing the aerosol contamination by high-speed turbine. Materials and Methods: 36 patients were divided into three gro

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Publication Date
Sat Oct 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Entry cost based on activity-based cost specifications and comparative study
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Several recent approaches focused on the developing of traditional systems to measure the costs to meet the new environmental requirements, including Attributes Based Costing (ABCII). It is method of accounting is based on measuring the costs according to the Attributes that the product is designed on this basis and according to achievement levels of all the Attribute of the product attributes. This research provides the knowledge foundations of this approach and its role in the market-oriented compared to the Activity based costing as shown in steps to be followed to apply for this Approach. The research problem in the attempt to reach the most accurate Approach in the measurement of the cost of products from th

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
A Study of the Structural and Optical Properties of SnS:F prepared by chemical spray pyrolysis technique
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Thin films of pure tin mono-sulfide SnS and tin mono-sulfide for (1,2,3,4)% fluorine SnS:F with Thicknesses of (0.85 ±0.05) ?m and (0.45±0.05) ?m respectively were prepared by chemical spray pyrolysis technique. the effect of doping of F on structural and optical properties has been studied. X-Ray diffraction analysis showed that the prepared films were polycrystalline with orthorhombic structure. It was found that doping increased the intensity of diffraction peaks. Optical properties of all samples were studied by recording the absorption and transmission spectrum in range of wave lengths (300-900) nm. The optical energy gap for direct forbidden transi

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Publication Date
Wed Jan 03 2024
Journal Name
Revista Brasileira De Engenharia Agrícola E Ambiental
Effect of cold plasma technique on the quality of stored fruits - A case study on apples
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The consumption of fresh fruits has increased nowadays due to the lifestyle of the consumers. Maintaining the quality and nutritional value of cut fruits during storage is difficult compared to whole fruits. Deterioration of internal and external quality usually occurs in freshly harvested fruits. It is necessary to use different techniques to maintain the quality and increase the shelf life of the freshly cut product. This research studied the effect of treating apple slices with cold plasma once and with filtered water again on quality characteristics (hardness, moisture content, sugar content, carbohydrate content, and color) after being stored for five days. The best treatment was determined using two different pressures of the plasma j

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Publication Date
Mon Dec 18 2017
Journal Name
Agronomy
A Case Study of Potential Reasons of Increased Soil Phosphorus Levels in the Northeast United States
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Recent phosphorus (P) pollution in the United States, mainly in Maine, has raised some severe concerns over the use of P fertilizer application rates in agriculture. Phosphorus is the second most limiting nutrient after nitrogen and has damaging impacts on crop yield if found to be deficient. Therefore, farmers tend to apply more P than is required to satisfy any P loss after its application at planting. Several important questions were raised in this study to improve P efficiency and reduce its pollution. The objective of this study was to find potential reasons for P pollution in water bodies despite a decrease in potato acreage. Historically, the potato was found to be responsible for P water contamination due to its high P sensitivity a

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Publication Date
Fri Mar 15 2019
Journal Name
Al-khwarizmi Engineering Journal
Experimental and Theoretical Study of the Energy Flow of a Two Stages Four Generators Adsorption Chiller
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This work is concerned with a two stages four beds adsorption chiller utilizing activated carbon-methanol adsorption pair that operates on six separated processes. The four beds that act as thermal compressors are powered by a low grade thermal energy in the form of hot water at a temperature range of 65 to 83 °C.  As well as, the water pumps and control cycle consume insignificant electrical power. This adsorption chiller consists of three water cycles. The first water cycle is the driven hot water cycle. The second cycle is the cold water cycle to cool the carbon, which adsorbs the methanol. Finally, the chilled water cycle that is used to overcome the building load. The theoretical results showed that average cycle cooling power

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Publication Date
Sat Mar 30 2002
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Study of Absorption Column with Single Bubble Cap Tray in the Production of Sodium Bicarbonate
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