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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
Fri Mar 01 2024
Journal Name
Journal Of Applied Spectroscopy
Spectrophotometric Method for Determination of Cu(II) Using a New Schiff Base Ligand
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The Cu(II) was found using a quick and uncomplicated procedure that involved reacting it with a freshly synthesized ligand to create an orange complex that had an absorbance peak of 481.5 nm in an acidic solution. The best conditions for the formation of the complex were studied from the concentration of the ligand, medium, the eff ect of the addition sequence, the eff ect of temperature, and the time of complex formation. The results obtained are scatter plot extending from 0.1–9 ppm and a linear range from 0.1–7 ppm. Relative standard deviation (RSD%) for n = 8 is less than 0.5, recovery % (R%) within acceptable values, correlation coeffi cient (r) equal 0.9986, coeffi cient of determination (r2) equal to 0.9973, and percentage capita

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Publication Date
Mon Nov 01 2021
Journal Name
Journal Of Engineering
Study of Using of Recycled Brick Waste (RBW) to produce Environmental Friendly Concrete: A Review
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Several million tons of solid waste are produced each year as a result of construction and demolition activities around the world, and brick waste is one of the most widely wastes. Recently, there has been growing number in studies that conducted on using of recycling brick waste (RBW) to produce environmentally friendly concrete. The use of brick waste (BW) as potential partial cement or aggregate replacement materials is summarized in this review where the performance is discussed in the form of the mechanical strength and properties that related to durability of  concrete. It was found that, because the pozzolanic activity of clay brick powder, it can be utilized as substitute for cement in replacement level up to 10%. Whereas,

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Publication Date
Mon Nov 01 2021
Journal Name
Journal Of Engineering
Study of Using of Recycled Brick Waste (RBW) to produce Environmental Friendly Concrete: A Review
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Several million tons of solid waste are produced each year as a result of construction and demolition activities around the world, and brick waste is one of the most widely wastes. Recently, there has been growing number in studies that conducted on using of recycling brick waste (RBW) to produce environmentally friendly concrete. The use of brick waste (BW) as potential partial cement or aggregate replacement materials is summarized in this review where the performance is discussed in the form of the mechanical strength and properties that related to durability of  concrete. It was found that, because the pozzolanic activity of clay brick powder, it can be utilized as substitute for cement in replacement level up t

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Publication Date
Sat Jul 22 2023
Journal Name
Journal Of Engineering
The Influence of Politics on Architectural Thought A Descriptive and Analytical Study of the Effect of Political Ideology on the Achieved Architecture (Berlin City as an Example)
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The research investigates the political effect and its directions on the architectural thoughts and its achievements and how can this political system affect all fields of life in communities including architectural urban design. The problem of the research lies in the ambiguity effects of the ideological national directions of the Nazi Party on the architecture and urban design of the city of Berlin, then determining the aims of the research to discuss the concepts of politics and architecture and their relation to the way of thinking that plays a role in the process of design that works on property and achieving the suitable urban environments for those communities. After that, the Nazi's party's thought would be studied and analyzed,

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Publication Date
Thu Feb 29 2024
Journal Name
Sabrao Journal Of Breeding And Genetics
LOW-‎COST SOIL ‎MOISTURE SENSORS’ ASSESSMENT FOR THEIR ACCURACY AFTER CALIBRATION THROUGH THE ‎GRAVIMETRIC METHOD
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The existing study aimed to assess four soil moisture sensors’ capacitive (WH51 and SKU: S EN0193) and resistive (Yl69 and IC Station) abilities, which are affordable and medium-priced for their accuracy in six common soil types in the central region of Iraq. The readings’ calibration for the soil moisture sensor devices continued through two gravimetric methods. The first depended on the protocols’ database, while the second was the traditional calibration method. The second method recorded the lowest analysis error compared with the first. The moderate-cost sensor WH51 showed the lowest standard error (SE), MAD , and RMSE and the highest R² in both methods. The performance accuracy of WH51 was close to readings shown by the manufac

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Publication Date
Fri Jan 30 2026
Journal Name
Journal Of Baghdad College Of Dentistry
A study to compare the efficiency of different instrumentation systems for cleaning oval-shaped root canals (An in vitro study)
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Background: Proper cleaning and shaping of the whole root canal space have been recognized as a real challenge, particularly in oval-shaped canals.This in vitro study was conducted to evaluate and compare the efficiency of different instrumentation systems in removing of dentin debris at three thirds of oval-shaped root canals and to compare the percentage of remaining dentin debris among the three thirds for each instrumentation system. Materials and methods: Fifty freshly extracted human mandibular molars with single straight oval-shaped distal root canals were randomly divided into five groups of ten teeth each. Group One: instrumentation with ProTaper Universal hand instruments, Group Two: instrumentation with ProTaper Universal rotary

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Publication Date
Sat Apr 09 2022
Journal Name
Engineering, Technology & Applied Science Research
A Semi-Empirical Equation based on the Strut-and-Tie Model for the Shear Strength Prediction of Deep Beams with Multiple Large Web Openings
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The behavior and shear strength of full-scale (T-section) reinforced concrete deep beams, designed according to the strut-and-tie approach of ACI Code-19 specifications, with various large web openings were investigated in this paper. A total of 7 deep beam specimens with identical shear span-to-depth ratios have been tested under mid-span concentrated load applied monotonically until beam failure. The main variables studied were the effects of width and depth of the web openings on deep beam performance. Experimental data results were calibrated with the strut-and-tie approach, adopted by ACI 318-19 code for the design of deep beams. The provided strut-and-tie design model in ACI 318-19 code provision was assessed and found to be u

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Publication Date
Fri Jan 30 2026
Journal Name
Journal Mustansiriyah Of Sports Science
The Effect of Ocular Reflex Exercises Using a Proposed Device on Eyes - Hands Coordination for Junior Boxers
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Publication Date
Fri Feb 08 2019
Journal Name
Journal Of The College Of Education For Women
The House of Illusions A Study in Genet's The Balcony
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The definition of "prostitute" and prostitution is a difficult one and a
question over which the legislators of many lands and nations differed. A
notable feature of prostitution is its epidemic increase at times of war,
revolution and armed commotion, on account of economic, social and
psychological factors generated by such conditions of mortal conflicts. Wars
invariably deprive young wives and lovers of their men folk, resulting in
financial , sexual and emotional frustrations . At no time is the natural
balance between the sexes more seriously disturbed than during wars, when
thousands of men are thrown into one sector of the country and hundreds of
towns and villages are left to women and children only. Lo

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Publication Date
Sun Feb 28 2021
Journal Name
Journal Of Economics And Administrative Sciences
Determine The Factors Affecting Product Quality Using FMEA Analysis: A Case Study in Al Zawraa State Company
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The research aims to identify the factors that affect the quality of the product by using the Failure Mode and Effect Analysis (FMEA) tool and to suggest measures to reduce the deviations or defects in the production process. I used the case study approach to reach its goals, and the air filter product line was chosen in the air filters factory of Al-Zawraa General Company. The research sample was due to the emergence of many defects of different impact and the continuing demand for the product. I collected data and information from the factory records for two years (2018-2019) and used a scheme Pareto Fishbone Diagram as well as an FMEA tool to analyze data and generate results.

Par

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